Psyllid ID: psy12549

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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------
Protein Sequence
MYTAQTVQLSEEGIIIPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK
Secondary Structure (PSIPRED)
ccccccccccccccccccccEEEccccccccHHHHHHHHccccccEEEEEccccccccccccccEEEEcccccHHHHHHHHHHccccccccEEEEEEEcccccccccccccEEEEccccccccHHHHHHHHHccccEEEEEEEEccccccccEEEEEEccHHHHHHHHHHHcccccccEEEEEEcccccHHHHHHHHcccccccEEEEccccccccHHHHHHHHcccccEEEEEEEcccccccEEEEEEcccHHHHHHHHHHHcccccccEEEEEEcccccHHHHHHHHHHHHHHHHHHcccccccEEEEEcccccccHHHHHHHHcccccEEEEc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccEEEEccccccccccccccHHHHHHHHHHcccEEEEEEEEcccccEEEEEcccccHHHHHHHHHHHccccccccEEEEEcccccHHHHcccccEEEEEcccccccHHHHHHHHHHcccEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEEEcccHHHHHHHHHHHHHHcccEEEEcccccccHHHHHHHHHHcccEEEEEEEEccccccccEEEEcccHHHHHHHHHHHcccccccccEEEEEcccHHHHHHHHHHHHHHHHHHHHHHccccEEEEEcccccccHHHHHHHHcccccEcccc
Coil and Loop (DISEMBL)
mytaqtvqlseegiiipkhnvatRELSAKVVEGVSRSLsslidgntvkydwdsgytchqlgsgailvqlgqpymldTERALDTMnfdalkgrpirimwsqrdpslrksgvgnvFIKNLdksidnkamydtFSAFGSILSCKVaqdeqgnskgygfvhFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEmfepygtitsyrvmnndgksrgfgfvayespefAEKAVQAWngkevdgkiLYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVknlddsidderlrkeftpfgtitsak
Flexible Loop (DISEMBL)
mytaqtvqlseegiiipkhnvatrELSAKVVEGVsrslsslidgnTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNfdalkgrpirimwsqrdpslrksgvgNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVfvgkfiprkerekelgekaklftNVYIKNfgedfndekLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAwngkevdgkilyvgraqkkaertqelKRRFEMLkierlnryqgvnlyvknlddsidderlrkeftpfgtitsak
Low Complexity Region (SEG)
MYTAQTVQLSEEGIIIPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK
Disordered region (IsUnstruct)
************GIIIPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER*KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ********LKRRFEMLKIERLNRYQGVNLYVKNLDDSI*******************
Disordered Region (DISOPRED)
********************VATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRI****************VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV*********************NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG*****************************VNLYVKNLDDSIDDERLRKEFTPFGTITSAK
Disordered Region (DISEMBL)
MYTAQTVQLSEEGIIIPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR********QELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK
Disordered Region (DISPRO)
**************IIPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTIT***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MYTAQTVQLSEEGIIIPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRxxxxxxxxxxxxxxxxxxxxxRLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK
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	336	2.2.26 [Sep-21-2011]
P21187	634	Polyadenylate-binding pro	yes	N/A	0.809	0.429	0.760	1e-118
Q13310	644	Polyadenylate-binding pro	yes	N/A	0.806	0.420	0.723	1e-112
P20965	633	Polyadenylate-binding pro	N/A	N/A	0.806	0.428	0.72	1e-112
P29341	636	Polyadenylate-binding pro	yes	N/A	0.806	0.426	0.716	1e-112
Q9EPH8	636	Polyadenylate-binding pro	yes	N/A	0.806	0.426	0.716	1e-112
Q5R8F7	636	Polyadenylate-binding pro	yes	N/A	0.806	0.426	0.712	1e-111
P11940	636	Polyadenylate-binding pro	no	N/A	0.806	0.426	0.712	1e-111
P61286	636	Polyadenylate-binding pro	no	N/A	0.806	0.426	0.712	1e-111
Q6IP09	633	Polyadenylate-binding pro	N/A	N/A	0.806	0.428	0.716	1e-111
Q6DEY7	629	Embryonic polyadenylate-b	no	N/A	0.806	0.430	0.687	1e-108

>sp|P21187|PABP_DROME Polyadenylate-binding protein OS=Drosophila melanogaster GN=pAbp PE=1 SV=3

 Score =  424 bits (1089), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 210/276 (76%), Positives = 237/276 (85%), Gaps = 4/276 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD ++ +PIRIMWSQRDPSLR+SGVGNVFIKNLD++I
Sbjct: 44  GYAYVNFQQP--ADAERALDTMNFDLVRNKPIRIMWSQRDPSLRRSGVGNVFIKNLDRAI 101

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKA+YDTFSAFG+ILSCKVA DE+GNSKGYGFVHFETEEAAN SI+KVNGMLLN K V+
Sbjct: 102 DNKAIYDTFSAFGNILSCKVATDEKGNSKGYGFVHFETEEAANTSIDKVNGMLLNGKKVY 161

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGK 241
           VGKFIPRKEREKELGEKAKLFTNVY+KNF EDF+DEKLKE FEPYG ITSY+VM+  DGK
Sbjct: 162 VGKFIPRKEREKELGEKAKLFTNVYVKNFTEDFDDEKLKEFFEPYGKITSYKVMSKEDGK 221

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEV-DGKILYVGRAQKKAERTQELKRRFEMLKIERL 300
           S+GFGFVA+E+ E AE AVQA NGK++ +GK LYV RAQKKAER QELKR+FE LK +R 
Sbjct: 222 SKGFGFVAFETTEAAEAAVQALNGKDMGEGKSLYVARAQKKAERQQELKRKFEELKQKRH 281

Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
               GVNLYVKNLDD+IDD+RLR  F+P+G ITSAK
Sbjct: 282 ESVFGVNLYVKNLDDTIDDDRLRIAFSPYGNITSAK 317

Binds the poly(A) tail of mRNA.
Drosophila melanogaster (taxid: 7227)

>sp|Q13310|PABP4_HUMAN Polyadenylate-binding protein 4 OS=Homo sapiens GN=PABPC4 PE=1 SV=1

 Score =  405 bits (1040), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 199/275 (72%), Positives = 230/275 (83%), Gaps = 4/275 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KG+PIRIMWSQRDPSLRKSGVGNVFIKNLDKSI
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKA+YDTFSAFG+ILSCKV  DE G SKGY FVHFET+EAA+K+IEK+NGMLLN + VF
Sbjct: 111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYAFVHFETQEAADKAIEKMNGMLLNDRKVF 169

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGK 241
           VG+F  RKERE ELG KAK FTNVYIKNFGE+ +DE LKE+F  +G   S +VM + +GK
Sbjct: 170 VGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKELFSQFGKTLSVKVMRDPNGK 229

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
           S+GFGFV+YE  E A KAV+  NGKE+ GKI++VGRAQKK ER  ELKR+FE LK ER++
Sbjct: 230 SKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFVGRAQKKVERQAELKRKFEQLKQERIS 289

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           RYQGVNLY+KNLDD+IDDE+LRKEF+PFG+ITSAK
Sbjct: 290 RYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAK 324

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo.

Homo sapiens (taxid: 9606)

>sp|P20965|PABPA_XENLA Polyadenylate-binding protein 1-A OS=Xenopus laevis GN=pabpc1-a PE=1 SV=3

 Score =  404 bits (1039), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 198/275 (72%), Positives = 228/275 (82%), Gaps = 4/275 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KGRP+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDVIKGRPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+EAA ++I+K+NGMLLN + VF
Sbjct: 111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIDKMNGMLLNDRKVF 169

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GK 241
           VG+F  RKERE ELG +AK FTNVYIKNFG+D NDE+LKEMF  YG   S +VM +D GK
Sbjct: 170 VGRFKSRKEREAELGARAKEFTNVYIKNFGDDMNDERLKEMFGKYGPALSVKVMTDDNGK 229

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
           S+GFGFV++E  E A+KAV   NGK+++GK ++VGRAQKK ER  ELKR+FE +K +R+ 
Sbjct: 230 SKGFGFVSFERHEDAQKAVDEMNGKDMNGKSMFVGRAQKKVERQTELKRKFEQMKQDRIT 289

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           RYQGVNLYVKNLDD IDDERLRKEF PFGTITSAK
Sbjct: 290 RYQGVNLYVKNLDDGIDDERLRKEFLPFGTITSAK 324

Binds the poly(A) tail of mRNA. Prevents mRNA deadenylation and confers poly(A) stability. Stimulates the translation of mRNAs to which it is bound, acting, at least in part, with dazl.

Xenopus laevis (taxid: 8355)

>sp|P29341|PABP1_MOUSE Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2

 Score =  404 bits (1037), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 197/275 (71%), Positives = 229/275 (83%), Gaps = 4/275 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KG+P+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+EAA ++IEK+NGMLLN + VF
Sbjct: 111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GK 241
           VG+F  RKERE ELG +AK FTNVYIKNFGED +DE+LKE+F  +G   S +VM ++ GK
Sbjct: 170 VGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSVKVMTDESGK 229

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
           S+GFGFV++E  E A+KAV   NGKE++GK +YVGRAQKK ER  ELKR+FE +K +R+ 
Sbjct: 230 SKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRIT 289

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           RYQGVNLYVKNLDD IDDERLRKEF+PFGTITSAK
Sbjct: 290 RYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAK 324

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Mus musculus (taxid: 10090)

>sp|Q9EPH8|PABP1_RAT Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=2 SV=1

 Score =  403 bits (1036), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 197/275 (71%), Positives = 229/275 (83%), Gaps = 4/275 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KG+P+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+EAA ++IEK+NGMLLN + VF
Sbjct: 111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GK 241
           VG+F  RKERE ELG +AK FTNVYIKNFGED +DE+LKE+F  +G   S +VM ++ GK
Sbjct: 170 VGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSVKVMTDESGK 229

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
           S+GFGFV++E  E A+KAV   NGKE++GK +YVGRAQKK ER  ELKR+FE +K +R+ 
Sbjct: 230 SKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRIT 289

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           RYQGVNLYVKNLDD IDDERLRKEF+PFGTITSAK
Sbjct: 290 RYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAK 324

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Rattus norvegicus (taxid: 10116)

>sp|Q5R8F7|PABP1_PONAB Polyadenylate-binding protein 1 OS=Pongo abelii GN=PABPC1 PE=2 SV=1

 Score =  403 bits (1035), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 196/275 (71%), Positives = 229/275 (83%), Gaps = 4/275 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KG+P+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+EAA ++IEK+NGMLLN + VF
Sbjct: 111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GK 241
           VG+F  RKERE ELG +AK FTNVYIKNFGED +DE+LK++F  +G   S +VM ++ GK
Sbjct: 170 VGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGK 229

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
           S+GFGFV++E  E A+KAV   NGKE++GK +YVGRAQKK ER  ELKR+FE +K +R+ 
Sbjct: 230 SKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRIT 289

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           RYQGVNLYVKNLDD IDDERLRKEF+PFGTITSAK
Sbjct: 290 RYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAK 324

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Pongo abelii (taxid: 9601)

>sp|P11940|PABP1_HUMAN Polyadenylate-binding protein 1 OS=Homo sapiens GN=PABPC1 PE=1 SV=2

 Score =  402 bits (1034), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 196/275 (71%), Positives = 229/275 (83%), Gaps = 4/275 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KG+P+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+EAA ++IEK+NGMLLN + VF
Sbjct: 111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GK 241
           VG+F  RKERE ELG +AK FTNVYIKNFGED +DE+LK++F  +G   S +VM ++ GK
Sbjct: 170 VGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGK 229

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
           S+GFGFV++E  E A+KAV   NGKE++GK +YVGRAQKK ER  ELKR+FE +K +R+ 
Sbjct: 230 SKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRIT 289

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           RYQGVNLYVKNLDD IDDERLRKEF+PFGTITSAK
Sbjct: 290 RYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAK 324

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Homo sapiens (taxid: 9606)

>sp|P61286|PABP1_BOVIN Polyadenylate-binding protein 1 OS=Bos taurus GN=PABPC1 PE=2 SV=1

 Score =  402 bits (1034), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 196/275 (71%), Positives = 229/275 (83%), Gaps = 4/275 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KG+P+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+EAA ++IEK+NGMLLN + VF
Sbjct: 111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GK 241
           VG+F  RKERE ELG +AK FTNVYIKNFGED +DE+LK++F  +G   S +VM ++ GK
Sbjct: 170 VGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGK 229

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
           S+GFGFV++E  E A+KAV   NGKE++GK +YVGRAQKK ER  ELKR+FE +K +R+ 
Sbjct: 230 SKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRIT 289

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           RYQGVNLYVKNLDD IDDERLRKEF+PFGTITSAK
Sbjct: 290 RYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAK 324

Binds the poly(A) tail of mRNA. May be involved in cytoplasmic regulatory processes of mRNA metabolism such as pre-mRNA splicing. Its function in translational initiation regulation can either be enhanced by PAIP1 or repressed by PAIP2. Can probably bind to cytoplasmic RNA sequences other than poly(A) in vivo. Involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain. Involved in regulation of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons; for the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed.

Bos taurus (taxid: 9913)

>sp|Q6IP09|PABPB_XENLA Polyadenylate-binding protein 1-B OS=Xenopus laevis GN=pabpc1-b PE=2 SV=1

 Score =  402 bits (1034), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 197/275 (71%), Positives = 228/275 (82%), Gaps = 4/275 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KG+P+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+EAA ++I+K+NGMLLN + VF
Sbjct: 111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIDKMNGMLLNDRKVF 169

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GK 241
           VG+F  RKERE ELG +AK FTNVYIKNFGED +DE+LKE F  YG   S +VM +D GK
Sbjct: 170 VGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKEWFGQYGAALSVKVMTDDHGK 229

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
           SRGFGFV++E  E A+KAV   NGK+++GK ++VGRAQKK ER  ELKR+FE +K +R+ 
Sbjct: 230 SRGFGFVSFERHEDAQKAVDDMNGKDLNGKAIFVGRAQKKVERQTELKRKFEQMKQDRIT 289

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           RYQGVNLYVKNLDD IDDERLRKEFTPFG+ITSAK
Sbjct: 290 RYQGVNLYVKNLDDGIDDERLRKEFTPFGSITSAK 324

Binds the poly(A) tail of mRNA. Prevents mRNA deadenylation and confers poly(A) stability. Stimulates the translation of mRNAs to which it is bound, acting, at least in part, with dazl.

Xenopus laevis (taxid: 8355)

>sp|Q6DEY7|EPAB_XENTR Embryonic polyadenylate-binding protein OS=Xenopus tropicalis GN=epabp PE=2 SV=1

 Score =  390 bits (1002), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 189/275 (68%), Positives = 225/275 (81%), Gaps = 4/275 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   +   QP   D ERALDTMNF+ +KGRPIRIMWSQRDP LRKSGVGNVFIKNLD+SI
Sbjct: 53  GYAYINFQQP--ADAERALDTMNFEVIKGRPIRIMWSQRDPGLRKSGVGNVFIKNLDESI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKA+YDTFSAFG+ILSCKV  DE G S+GYGFVHFET+EAAN++I+ +NGMLLN + VF
Sbjct: 111 DNKALYDTFSAFGNILSCKVVCDEHG-SRGYGFVHFETQEAANRAIQTMNGMLLNDRKVF 169

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GK 241
           VG F  R+ERE E G K   FTNVYIKNFGED +D++L+E+F  +G   S +VM +D G+
Sbjct: 170 VGHFKSRRERELEYGAKVMEFTNVYIKNFGEDMDDKRLREIFSAFGNTLSVKVMMDDTGR 229

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
           SRGFGFV Y + E A+KAV   NGKEV+G+++YVGRAQK+ ER  ELKR+FE +K ER+N
Sbjct: 230 SRGFGFVNYGNHEEAQKAVSEMNGKEVNGRMIYVGRAQKRIERQGELKRKFEQIKQERIN 289

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           RYQGVNLYVKNLDD IDD+RLRKEF+P+GTITSAK
Sbjct: 290 RYQGVNLYVKNLDDGIDDDRLRKEFSPYGTITSAK 324

Binds and protects the poly(A) tail of mRNA with or without an AU-rich element (ARE) and prevents mRNA deadenylation. Stimulates the translation of mRNAs to which it is bound during early development.

Xenopus tropicalis (taxid: 8364)

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	336
157125851	628	polyadenylate-binding protein [Aedes aeg	0.809	0.433	0.832	1e-129
91095037	607	PREDICTED: similar to poly A binding pro	0.809	0.448	0.826	1e-129
307165845	635	Polyadenylate-binding protein 1 [Campono	0.809	0.428	0.826	1e-129
340719918	630	PREDICTED: polyadenylate-binding protein	0.809	0.431	0.826	1e-128
380019828	630	PREDICTED: polyadenylate-binding protein	0.809	0.431	0.826	1e-128
340719922	621	PREDICTED: polyadenylate-binding protein	0.809	0.438	0.826	1e-128
332030568	678	Polyadenylate-binding protein 1 [Acromyr	0.788	0.390	0.821	1e-128
340719924	612	PREDICTED: polyadenylate-binding protein	0.809	0.444	0.826	1e-128
332374002	634	unknown [Dendroctonus ponderosae]	0.809	0.429	0.822	1e-128
170044609	628	polyadenylate-binding protein 1 [Culex q	0.809	0.433	0.825	1e-128

>gi|157125851|ref|XP_001654419.1| polyadenylate-binding protein [Aedes aegypti] gi|157125853|ref|XP_001654420.1| polyadenylate-binding protein [Aedes aegypti] gi|94468824|gb|ABF18261.1| polyadenylate-binding protein [Aedes aegypti] gi|108873484|gb|EAT37709.1| AAEL010318-PB [Aedes aegypti] gi|108873485|gb|EAT37710.1| AAEL010318-PA [Aedes aegypti]

 Score =  468 bits (1204), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 229/275 (83%), Positives = 246/275 (89%), Gaps = 3/275 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KGRPIRIMWSQRDPSLRKSGVGNVFIKNLDK+I
Sbjct: 44  GYAYVNFQQP--ADAERALDTMNFDLIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKNI 101

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKAMYDTFSAFG+ILSCKVAQDE+GNSKGYGFVHFETEE+AN SIEKVNGMLLN K V+
Sbjct: 102 DNKAMYDTFSAFGNILSCKVAQDEKGNSKGYGFVHFETEESANTSIEKVNGMLLNGKKVY 161

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKS 242
           VG+FIPRKEREKELGEKAKLFTNVY+KNFG++ NDE LKEMFE YGTITS+RVM  DGKS
Sbjct: 162 VGRFIPRKEREKELGEKAKLFTNVYVKNFGDELNDETLKEMFEKYGTITSHRVMIKDGKS 221

Query: 243 RGFGFVAYESPEFAEKAVQAWNGKEV-DGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
           RGFGFVA+E+PE AE AVQ  NGKE+ +GKILYVGRAQKK ER  ELKRRFE LK+ERL 
Sbjct: 222 RGFGFVAFENPESAEHAVQELNGKELGEGKILYVGRAQKKNERQMELKRRFEQLKMERLT 281

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           RYQGVNLYVKNLDDSIDDERLRKEF+PFGTITSAK
Sbjct: 282 RYQGVNLYVKNLDDSIDDERLRKEFSPFGTITSAK 316

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91095037|ref|XP_975975.1| PREDICTED: similar to poly A binding protein isoform 4 [Tribolium castaneum] gi|270014772|gb|EFA11220.1| hypothetical protein TcasGA2_TC005185 [Tribolium castaneum]

 Score =  468 bits (1204), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 228/276 (82%), Positives = 248/276 (89%), Gaps = 4/276 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KGRPIRIMWSQRDPSLRKSGVGNVFIKNLD+SI
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDLIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDRSI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKAMYDTFSAFG+ILSCKVAQDE G SKGYGFVHFETEEAANKSIEKVNGMLLN K V+
Sbjct: 111 DNKAMYDTFSAFGNILSCKVAQDENGTSKGYGFVHFETEEAANKSIEKVNGMLLNGKKVY 170

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGK 241
           VG+FIPRKEREKELGEKAKLFTNVY+KNFGED  +E+L+ MFE YG ITSY++M+ +DGK
Sbjct: 171 VGRFIPRKEREKELGEKAKLFTNVYVKNFGEDLTEEQLRTMFEKYGKITSYKIMSKDDGK 230

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKE-VDGKILYVGRAQKKAERTQELKRRFEMLKIERL 300
           S+GFGFVA+ESPE AE AV+A NGKE +DGK LYVGRAQKKAER QELKRRFE LK+ERL
Sbjct: 231 SKGFGFVAFESPEAAETAVEALNGKEIIDGKPLYVGRAQKKAERQQELKRRFEALKMERL 290

Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           NRYQGVNLYVKNLDD+IDDERLRKEF+PFGTITSAK
Sbjct: 291 NRYQGVNLYVKNLDDTIDDERLRKEFSPFGTITSAK 326

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307165845|gb|EFN60208.1| Polyadenylate-binding protein 1 [Camponotus floridanus]

 Score =  466 bits (1198), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 228/276 (82%), Positives = 248/276 (89%), Gaps = 4/276 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KGRPIRIMWSQRDPSLRKSGVGNVFIKNLDK+I
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDMIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKNI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKAMYDTFSAFG+ILSCKVAQDE G SKGYGFVHFETEEAANKSI+KVNGMLLN K V+
Sbjct: 111 DNKAMYDTFSAFGNILSCKVAQDESGASKGYGFVHFETEEAANKSIDKVNGMLLNGKKVY 170

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGK 241
           VGKFIPRKEREKELGEKAKLFTNVY+KNFGED  D+KLKEMFE YGTITS++VM+ +DGK
Sbjct: 171 VGKFIPRKEREKELGEKAKLFTNVYVKNFGEDMTDDKLKEMFEKYGTITSHKVMSKDDGK 230

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEV-DGKILYVGRAQKKAERTQELKRRFEMLKIERL 300
           SRGFGFVA+E P+ AE+AV   NGK++ +GK +YVGRAQKKAER QELKR+FE LKIERL
Sbjct: 231 SRGFGFVAFEDPDAAEQAVLELNGKDISEGKCMYVGRAQKKAERQQELKRKFEQLKIERL 290

Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           NRYQGVNLYVKNLDD+IDDERLRKEFTPFGTITSAK
Sbjct: 291 NRYQGVNLYVKNLDDTIDDERLRKEFTPFGTITSAK 326

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340719918|ref|XP_003398391.1| PREDICTED: polyadenylate-binding protein 1-like isoform 1 [Bombus terrestris]

 Score =  465 bits (1196), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 228/276 (82%), Positives = 246/276 (89%), Gaps = 4/276 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KGRPIRIMWSQRDPSLRKSGVGNVFIKNLDK+I
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDMIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKNI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKAMYDTFSAFG+ILSCKVAQDE G SKGYGFVHFETEEAANKSI++VNGMLLN K V+
Sbjct: 111 DNKAMYDTFSAFGNILSCKVAQDESGVSKGYGFVHFETEEAANKSIDRVNGMLLNGKKVY 170

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGK 241
           VGKFIPRKEREKELGEKAKLFTNVY+KNFGED  D+KLKEMFE YGTITS++VM  +DGK
Sbjct: 171 VGKFIPRKEREKELGEKAKLFTNVYVKNFGEDMTDDKLKEMFEKYGTITSHKVMIKDDGK 230

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEV-DGKILYVGRAQKKAERTQELKRRFEMLKIERL 300
           SRGFGFVA+E P+ AE+AV   NGKEV +GK +YVGRAQKKAER QELKR+FE LK+ERL
Sbjct: 231 SRGFGFVAFEDPDAAEQAVLELNGKEVAEGKCMYVGRAQKKAERQQELKRKFEQLKLERL 290

Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           NRYQGVNLYVKNLDDSIDDERLRKEF PFGTITSAK
Sbjct: 291 NRYQGVNLYVKNLDDSIDDERLRKEFAPFGTITSAK 326

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380019828|ref|XP_003693803.1| PREDICTED: polyadenylate-binding protein 1-like [Apis florea]

 Score =  464 bits (1195), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 228/276 (82%), Positives = 246/276 (89%), Gaps = 4/276 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KGRPIRIMWSQRDPSLRKSGVGNVFIKNLDK+I
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDMIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKNI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKAMYDTFSAFG+ILSCKVAQDE G SKGYGFVHFETEEAANKSI++VNGMLLN K V+
Sbjct: 111 DNKAMYDTFSAFGNILSCKVAQDESGVSKGYGFVHFETEEAANKSIDRVNGMLLNGKKVY 170

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGK 241
           VGKFIPRKEREKELGEKAKLFTNVY+KNFGED  D+KLKEMFE YGTITS++VM  +DGK
Sbjct: 171 VGKFIPRKEREKELGEKAKLFTNVYVKNFGEDMTDDKLKEMFEKYGTITSHKVMIKDDGK 230

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEV-DGKILYVGRAQKKAERTQELKRRFEMLKIERL 300
           SRGFGFVA+E P+ AE+AV   NGKEV +GK +YVGRAQKKAER QELKR+FE LK+ERL
Sbjct: 231 SRGFGFVAFEDPDAAEQAVLELNGKEVAEGKCMYVGRAQKKAERQQELKRKFEQLKLERL 290

Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           NRYQGVNLYVKNLDDSIDDERLRKEF PFGTITSAK
Sbjct: 291 NRYQGVNLYVKNLDDSIDDERLRKEFAPFGTITSAK 326

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340719922|ref|XP_003398393.1| PREDICTED: polyadenylate-binding protein 1-like isoform 3 [Bombus terrestris]

 Score =  464 bits (1194), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 228/276 (82%), Positives = 246/276 (89%), Gaps = 4/276 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KGRPIRIMWSQRDPSLRKSGVGNVFIKNLDK+I
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDMIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKNI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKAMYDTFSAFG+ILSCKVAQDE G SKGYGFVHFETEEAANKSI++VNGMLLN K V+
Sbjct: 111 DNKAMYDTFSAFGNILSCKVAQDESGVSKGYGFVHFETEEAANKSIDRVNGMLLNGKKVY 170

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGK 241
           VGKFIPRKEREKELGEKAKLFTNVY+KNFGED  D+KLKEMFE YGTITS++VM  +DGK
Sbjct: 171 VGKFIPRKEREKELGEKAKLFTNVYVKNFGEDMTDDKLKEMFEKYGTITSHKVMIKDDGK 230

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEV-DGKILYVGRAQKKAERTQELKRRFEMLKIERL 300
           SRGFGFVA+E P+ AE+AV   NGKEV +GK +YVGRAQKKAER QELKR+FE LK+ERL
Sbjct: 231 SRGFGFVAFEDPDAAEQAVLELNGKEVAEGKCMYVGRAQKKAERQQELKRKFEQLKLERL 290

Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           NRYQGVNLYVKNLDDSIDDERLRKEF PFGTITSAK
Sbjct: 291 NRYQGVNLYVKNLDDSIDDERLRKEFAPFGTITSAK 326

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332030568|gb|EGI70256.1| Polyadenylate-binding protein 1 [Acromyrmex echinatior]

 Score =  464 bits (1193), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 226/275 (82%), Positives = 247/275 (89%), Gaps = 10/275 (3%)

Query: 72  PYMLD--------TERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSID 123
           P MLD         ERALDTMNFD +KGRPIRIMWSQRDPSLRKSGVGNVFIKNLDK+ID
Sbjct: 95  PTMLDPRPHSTVNAERALDTMNFDMIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKNID 154

Query: 124 NKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
           NKAMYDTFSAFG+ILSCKVAQDE G SKGYGFVHFETEEAANKSI+KVNGMLLN K V+V
Sbjct: 155 NKAMYDTFSAFGNILSCKVAQDESGASKGYGFVHFETEEAANKSIDKVNGMLLNGKKVYV 214

Query: 184 GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKS 242
           GKFIPRKEREKELGEKAKLFTNVY+KNFGED  ++KLK+MFE YGTITS++VM+ +DGKS
Sbjct: 215 GKFIPRKEREKELGEKAKLFTNVYVKNFGEDMTEDKLKDMFEKYGTITSHKVMSKDDGKS 274

Query: 243 RGFGFVAYESPEFAEKAVQAWNGKEV-DGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
           RGFGFVA+E P+ AE+AV   NGKE+ +GK +YVGRAQKKAER QELKR+FE LKIERLN
Sbjct: 275 RGFGFVAFEDPDAAEQAVLELNGKEIAEGKCMYVGRAQKKAERQQELKRKFEQLKIERLN 334

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           RYQGVNLYVKNLDD+IDDERLRKEFTPFGTITSAK
Sbjct: 335 RYQGVNLYVKNLDDTIDDERLRKEFTPFGTITSAK 369

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340719924|ref|XP_003398394.1| PREDICTED: polyadenylate-binding protein 1-like isoform 4 [Bombus terrestris]

 Score =  464 bits (1193), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 228/276 (82%), Positives = 246/276 (89%), Gaps = 4/276 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KGRPIRIMWSQRDPSLRKSGVGNVFIKNLDK+I
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDMIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKNI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKAMYDTFSAFG+ILSCKVAQDE G SKGYGFVHFETEEAANKSI++VNGMLLN K V+
Sbjct: 111 DNKAMYDTFSAFGNILSCKVAQDESGVSKGYGFVHFETEEAANKSIDRVNGMLLNGKKVY 170

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGK 241
           VGKFIPRKEREKELGEKAKLFTNVY+KNFGED  D+KLKEMFE YGTITS++VM  +DGK
Sbjct: 171 VGKFIPRKEREKELGEKAKLFTNVYVKNFGEDMTDDKLKEMFEKYGTITSHKVMIKDDGK 230

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEV-DGKILYVGRAQKKAERTQELKRRFEMLKIERL 300
           SRGFGFVA+E P+ AE+AV   NGKEV +GK +YVGRAQKKAER QELKR+FE LK+ERL
Sbjct: 231 SRGFGFVAFEDPDAAEQAVLELNGKEVAEGKCMYVGRAQKKAERQQELKRKFEQLKLERL 290

Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           NRYQGVNLYVKNLDDSIDDERLRKEF PFGTITSAK
Sbjct: 291 NRYQGVNLYVKNLDDSIDDERLRKEFAPFGTITSAK 326

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332374002|gb|AEE62142.1| unknown [Dendroctonus ponderosae]

 Score =  464 bits (1193), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 227/276 (82%), Positives = 247/276 (89%), Gaps = 4/276 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD ++GRPIRIMWSQRDPSLRKSGVGNVFIKNLD+SI
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDLIRGRPIRIMWSQRDPSLRKSGVGNVFIKNLDRSI 110

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKAMYDTFSAFG+ILSCKVAQDE G SKGYGFVHFETEEAANKSIEKVNGMLLN K V+
Sbjct: 111 DNKAMYDTFSAFGNILSCKVAQDENGTSKGYGFVHFETEEAANKSIEKVNGMLLNGKKVY 170

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGK 241
           VG+FIPRKEREKELGEKAKLFTNVY+KNFGED ++E+L+ MFE +G ITSY+VM+ +DGK
Sbjct: 171 VGRFIPRKEREKELGEKAKLFTNVYVKNFGEDLSEEQLRNMFEKFGKITSYKVMSKDDGK 230

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKE-VDGKILYVGRAQKKAERTQELKRRFEMLKIERL 300
           S+GFGFVA+ESPE AE AV A NGKE V+GK LYVGRAQKKAER QELKRRFE LK+ERL
Sbjct: 231 SKGFGFVAFESPEAAETAVDALNGKELVEGKPLYVGRAQKKAERQQELKRRFEALKMERL 290

Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           NRYQGVNLYVKNLDD+IDDERLRKEF PFGTITSAK
Sbjct: 291 NRYQGVNLYVKNLDDTIDDERLRKEFAPFGTITSAK 326

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170044609|ref|XP_001849934.1| polyadenylate-binding protein 1 [Culex quinquefasciatus] gi|167867688|gb|EDS31071.1| polyadenylate-binding protein 1 [Culex quinquefasciatus]

 Score =  464 bits (1193), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 227/275 (82%), Positives = 245/275 (89%), Gaps = 3/275 (1%)

Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KGRPIRIMWSQRDPSLRKSGVGNVFIKNLDK+I
Sbjct: 44  GYAYVNFQQP--ADAERALDTMNFDLIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKNI 101

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKAMYDTFSAFG+ILSCKVAQDE+GNSKGYGFVHFETEE+AN SIEKVNGMLLN+K VF
Sbjct: 102 DNKAMYDTFSAFGNILSCKVAQDEKGNSKGYGFVHFETEESANTSIEKVNGMLLNAKKVF 161

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKS 242
           VG+FIPRKEREKELGEKAKLFTNVY+KNFG++  DE LKEMFE YGTITS+RVM  + KS
Sbjct: 162 VGRFIPRKEREKELGEKAKLFTNVYVKNFGDELTDESLKEMFEKYGTITSHRVMIKENKS 221

Query: 243 RGFGFVAYESPEFAEKAVQAWNGKEV-DGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
           RGFGFVA+E+PE AE AVQ  NGKE+ DGK+LYVGRAQKK ER  ELKRRFE LK+ERL 
Sbjct: 222 RGFGFVAFENPESAEVAVQELNGKELGDGKVLYVGRAQKKNERQMELKRRFEQLKMERLT 281

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           RYQGVNLYVKNLDDSIDDERLRKEF+PFGTITSAK
Sbjct: 282 RYQGVNLYVKNLDDSIDDERLRKEFSPFGTITSAK 316

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	336
ZFIN|ZDB-GENE-050308-1	634	pabpc1b "poly A binding protei	0.806	0.427	0.723	1.4e-103
UNIPROTKB|B1ANR0	615	PABPC4 "Polyadenylate-binding	0.806	0.440	0.723	1.3e-102
UNIPROTKB|Q13310	644	PABPC4 "Polyadenylate-binding	0.806	0.420	0.723	1.3e-102
UNIPROTKB|P20965	633	pabpc1-a "Polyadenylate-bindin	0.806	0.428	0.72	1.3e-102
ZFIN|ZDB-GENE-030131-3238	634	pabpc1a "poly A binding protei	0.806	0.427	0.723	1.6e-102
UNIPROTKB|E2R9I0	631	PABPC4 "Uncharacterized protei	0.806	0.429	0.72	2e-102
UNIPROTKB|F1SV06	631	PABPC4 "Uncharacterized protei	0.806	0.429	0.72	2e-102
UNIPROTKB|A4IFC3	645	PABPC4 "Uncharacterized protei	0.806	0.420	0.72	2.6e-102
MGI|MGI:1349722	636	Pabpc1 "poly(A) binding protei	0.806	0.426	0.716	4.2e-102
RGD|619838	636	Pabpc1 "poly(A) binding protei	0.806	0.426	0.716	4.2e-102

ZFIN|ZDB-GENE-050308-1 pabpc1b "poly A binding protein, cytoplasmic 1 b" [Danio rerio (taxid:7955)]

 Score = 1026 (366.2 bits), Expect = 1.4e-103, P = 1.4e-103
 Identities = 199/275 (72%), Positives = 230/275 (83%)

Query:    63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
             G   V   QP   D ERALDTMNFD +KGRP+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct:    53 GYAYVNFQQP--ADAERALDTMNFDVIKGRPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 110

Query:   123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
             DNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+EAA ++IEK+NGMLLN + VF
Sbjct:   111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169

Query:   183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GK 241
             VG+F  RKERE ELG +AK FTNVYIKNFGED +D+KLK++F  YG   S RVM ++ GK
Sbjct:   170 VGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDDKLKDIFSKYGNAMSIRVMTDENGK 229

Query:   242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
             SRGFGFV++E  E A++AV   NGKE++GK++YVGRAQKK ER  ELKR+FE +K +R+ 
Sbjct:   230 SRGFGFVSFERHEDAQRAVDEMNGKEMNGKLIYVGRAQKKVERQTELKRKFEQMKQDRMT 289

Query:   302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             RYQGVNLYVKNLDD IDDERLRKEF+PFGTITSAK
Sbjct:   290 RYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAK 324

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|B1ANR0 PABPC4 "Polyadenylate-binding protein 4" [Homo sapiens (taxid:9606)]

 Score = 1017 (363.1 bits), Expect = 1.3e-102, P = 1.3e-102
 Identities = 199/275 (72%), Positives = 230/275 (83%)

Query:    63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
             G   V   QP   D ERALDTMNFD +KG+PIRIMWSQRDPSLRKSGVGNVFIKNLDKSI
Sbjct:    53 GYAYVNFQQP--ADAERALDTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 110

Query:   123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
             DNKA+YDTFSAFG+ILSCKV  DE G SKGY FVHFET+EAA+K+IEK+NGMLLN + VF
Sbjct:   111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYAFVHFETQEAADKAIEKMNGMLLNDRKVF 169

Query:   183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGK 241
             VG+F  RKERE ELG KAK FTNVYIKNFGE+ +DE LKE+F  +G   S +VM + +GK
Sbjct:   170 VGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKELFSQFGKTLSVKVMRDPNGK 229

Query:   242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
             S+GFGFV+YE  E A KAV+  NGKE+ GKI++VGRAQKK ER  ELKR+FE LK ER++
Sbjct:   230 SKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFVGRAQKKVERQAELKRKFEQLKQERIS 289

Query:   302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             RYQGVNLY+KNLDD+IDDE+LRKEF+PFG+ITSAK
Sbjct:   290 RYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAK 324

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q13310 PABPC4 "Polyadenylate-binding protein 4" [Homo sapiens (taxid:9606)]

 Score = 1017 (363.1 bits), Expect = 1.3e-102, P = 1.3e-102
 Identities = 199/275 (72%), Positives = 230/275 (83%)

Query:    63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
             G   V   QP   D ERALDTMNFD +KG+PIRIMWSQRDPSLRKSGVGNVFIKNLDKSI
Sbjct:    53 GYAYVNFQQP--ADAERALDTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 110

Query:   123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
             DNKA+YDTFSAFG+ILSCKV  DE G SKGY FVHFET+EAA+K+IEK+NGMLLN + VF
Sbjct:   111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYAFVHFETQEAADKAIEKMNGMLLNDRKVF 169

Query:   183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGK 241
             VG+F  RKERE ELG KAK FTNVYIKNFGE+ +DE LKE+F  +G   S +VM + +GK
Sbjct:   170 VGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKELFSQFGKTLSVKVMRDPNGK 229

Query:   242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
             S+GFGFV+YE  E A KAV+  NGKE+ GKI++VGRAQKK ER  ELKR+FE LK ER++
Sbjct:   230 SKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFVGRAQKKVERQAELKRKFEQLKQERIS 289

Query:   302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             RYQGVNLY+KNLDD+IDDE+LRKEF+PFG+ITSAK
Sbjct:   290 RYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAK 324

GO:0000166 "nucleotide binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

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

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0017130 "poly(C) RNA binding" evidence=IDA

GO:0006401 "RNA catabolic process" evidence=TAS

GO:0006396 "RNA processing" evidence=TAS

GO:0006412 "translation" evidence=TAS

GO:0007596 "blood coagulation" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|P20965 pabpc1-a "Polyadenylate-binding protein 1-A" [Xenopus laevis (taxid:8355)]

 Score = 1017 (363.1 bits), Expect = 1.3e-102, P = 1.3e-102
 Identities = 198/275 (72%), Positives = 228/275 (82%)

Query:    63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
             G   V   QP   D ERALDTMNFD +KGRP+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct:    53 GYAYVNFQQP--ADAERALDTMNFDVIKGRPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 110

Query:   123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
             DNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+EAA ++I+K+NGMLLN + VF
Sbjct:   111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIDKMNGMLLNDRKVF 169

Query:   183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GK 241
             VG+F  RKERE ELG +AK FTNVYIKNFG+D NDE+LKEMF  YG   S +VM +D GK
Sbjct:   170 VGRFKSRKEREAELGARAKEFTNVYIKNFGDDMNDERLKEMFGKYGPALSVKVMTDDNGK 229

Query:   242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
             S+GFGFV++E  E A+KAV   NGK+++GK ++VGRAQKK ER  ELKR+FE +K +R+ 
Sbjct:   230 SKGFGFVSFERHEDAQKAVDEMNGKDMNGKSMFVGRAQKKVERQTELKRKFEQMKQDRIT 289

Query:   302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             RYQGVNLYVKNLDD IDDERLRKEF PFGTITSAK
Sbjct:   290 RYQGVNLYVKNLDDGIDDERLRKEFLPFGTITSAK 324

GO:0005515 "protein binding" evidence=IPI

GO:0005844 "polysome" evidence=IDA

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

GO:0031370 "eukaryotic initiation factor 4G binding" evidence=IPI

GO:0043621 "protein self-association" evidence=IPI

GO:0048255 "mRNA stabilization" evidence=IDA

GO:0060212 "negative regulation of nuclear-transcribed mRNA poly(A) tail shortening" evidence=IDA

ZFIN|ZDB-GENE-030131-3238 pabpc1a "poly A binding protein, cytoplasmic 1 a" [Danio rerio (taxid:7955)]

 Score = 1016 (362.7 bits), Expect = 1.6e-102, P = 1.6e-102
 Identities = 199/275 (72%), Positives = 228/275 (82%)

Query:    63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
             G   V   QP   D ERALDTMNFD +KGRP+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct:    53 GYAYVNFQQP--ADAERALDTMNFDVIKGRPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 110

Query:   123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
             DNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET EAA ++IEK+NGMLLN + VF
Sbjct:   111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETHEAAERAIEKMNGMLLNDRKVF 169

Query:   183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GK 241
             VG+F  RKERE E+G +AK FTNVYIKNFGED +DEKLKE+F  YG   S RVM +D GK
Sbjct:   170 VGRFKSRKEREAEMGARAKEFTNVYIKNFGEDMDDEKLKEIFCKYGPALSIRVMTDDSGK 229

Query:   242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
             S+GFGFV++E  E A++AV   NGKE++GK +YVGRAQKK ER  ELKR+FE +K +R+ 
Sbjct:   230 SKGFGFVSFERHEDAQRAVDEMNGKEMNGKQVYVGRAQKKGERQTELKRKFEQMKQDRMT 289

Query:   302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             RYQGVNLYVKNLDD +DDERLRKEF+PFGTITSAK
Sbjct:   290 RYQGVNLYVKNLDDGLDDERLRKEFSPFGTITSAK 324

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0007507 "heart development" evidence=IMP

UNIPROTKB|E2R9I0 PABPC4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1015 (362.4 bits), Expect = 2.0e-102, P = 2.0e-102
 Identities = 198/275 (72%), Positives = 229/275 (83%)

Query:    63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
             G   V   QP   D ERALDTMNFD +KG+PIRIMWSQRDPSLRKSGVGNVFIKNLDKSI
Sbjct:    53 GYAYVNFQQP--ADAERALDTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 110

Query:   123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
             DNKA+YDTFSAFG+ILSCKV  DE G SKGY FVHFET+EAA+K+IEK+NGMLLN + VF
Sbjct:   111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYAFVHFETQEAADKAIEKMNGMLLNDRKVF 169

Query:   183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGK 241
             VG+F  RKERE ELG KAK FTNVYIKNFGE+ +DE LKE+F  +G   S +VM +  GK
Sbjct:   170 VGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKELFSQFGKTLSVKVMRDPSGK 229

Query:   242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
             S+GFGFV+YE  E A KAV+  NGKE+ GK+++VGRAQKK ER  ELKR+FE LK ER++
Sbjct:   230 SKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQAELKRKFEQLKQERIS 289

Query:   302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             RYQGVNLY+KNLDD+IDDE+LRKEF+PFG+ITSAK
Sbjct:   290 RYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAK 324

GO:0010494 "cytoplasmic stress granule" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1SV06 PABPC4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 1015 (362.4 bits), Expect = 2.0e-102, P = 2.0e-102
 Identities = 198/275 (72%), Positives = 229/275 (83%)

Query:    63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
             G   V   QP   D ERALDTMNFD +KG+PIRIMWSQRDPSLRKSGVGNVFIKNLDKSI
Sbjct:    53 GYAYVNFQQP--ADAERALDTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 110

Query:   123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
             DNKA+YDTFSAFG+ILSCKV  DE G SKGY FVHFET+EAA+K+IEK+NGMLLN + VF
Sbjct:   111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYAFVHFETQEAADKAIEKMNGMLLNDRKVF 169

Query:   183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGK 241
             VG+F  RKERE ELG KAK FTNVYIKNFGE+ +DE LKE+F  +G   S +VM +  GK
Sbjct:   170 VGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDENLKELFSQFGKTLSVKVMRDPSGK 229

Query:   242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
             S+GFGFV+YE  E A KAV+  NGKE+ GK+++VGRAQKK ER  ELKR+FE LK ER++
Sbjct:   230 SKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQAELKRKFEQLKQERIS 289

Query:   302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             RYQGVNLY+KNLDD+IDDE+LRKEF+PFG+ITSAK
Sbjct:   290 RYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAK 324

GO:0010494 "cytoplasmic stress granule" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|A4IFC3 PABPC4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 1014 (362.0 bits), Expect = 2.6e-102, P = 2.6e-102
 Identities = 198/275 (72%), Positives = 229/275 (83%)

Query:    63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
             G   V   QP   D ERALDTMNFD +KG+PIRIMWSQRDPSLRKSGVGNVFIKNLDKSI
Sbjct:    53 GYAYVNFQQP--ADAERALDTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 110

Query:   123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
             DNKA+YDTFSAFG+ILSCKV  DE G SKGY FVHFET+EAA+K+IEK+NGMLLN + VF
Sbjct:   111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYAFVHFETQEAADKAIEKMNGMLLNDRKVF 169

Query:   183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGK 241
             VG+F  RKERE ELG KAK FTNVYIKNFGE+ +DE LKE+F  +G   S +VM +  GK
Sbjct:   170 VGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDENLKELFSQFGKTLSVKVMRDPSGK 229

Query:   242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
             S+GFGFV+YE  E A KAV+  NGKE+ GK+++VGRAQKK ER  ELKR+FE LK ER++
Sbjct:   230 SKGFGFVSYEKHEDANKAVEEMNGKEITGKVIFVGRAQKKVERQAELKRKFEQLKQERIS 289

Query:   302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             RYQGVNLY+KNLDD+IDDE+LRKEF+PFG+ITSAK
Sbjct:   290 RYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAK 324

GO:0010494 "cytoplasmic stress granule" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:1349722 Pabpc1 "poly(A) binding protein, cytoplasmic 1" [Mus musculus (taxid:10090)]

 Score = 1012 (361.3 bits), Expect = 4.2e-102, P = 4.2e-102
 Identities = 197/275 (71%), Positives = 229/275 (83%)

Query:    63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
             G   V   QP   D ERALDTMNFD +KG+P+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct:    53 GYAYVNFQQP--ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 110

Query:   123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
             DNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+EAA ++IEK+NGMLLN + VF
Sbjct:   111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169

Query:   183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GK 241
             VG+F  RKERE ELG +AK FTNVYIKNFGED +DE+LKE+F  +G   S +VM ++ GK
Sbjct:   170 VGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSVKVMTDESGK 229

Query:   242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
             S+GFGFV++E  E A+KAV   NGKE++GK +YVGRAQKK ER  ELKR+FE +K +R+ 
Sbjct:   230 SKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRIT 289

Query:   302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             RYQGVNLYVKNLDD IDDERLRKEF+PFGTITSAK
Sbjct:   290 RYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAK 324

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003729 "mRNA binding" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008022 "protein C-terminus binding" evidence=ISO

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=ISO

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

GO:2000623 "negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=ISO

RGD|619838 Pabpc1 "poly(A) binding protein, cytoplasmic 1" [Rattus norvegicus (taxid:10116)]

 Score = 1012 (361.3 bits), Expect = 4.2e-102, P = 4.2e-102
 Identities = 197/275 (71%), Positives = 229/275 (83%)

Query:    63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
             G   V   QP   D ERALDTMNFD +KG+P+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct:    53 GYAYVNFQQP--ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 110

Query:   123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
             DNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+EAA ++IEK+NGMLLN + VF
Sbjct:   111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169

Query:   183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GK 241
             VG+F  RKERE ELG +AK FTNVYIKNFGED +DE+LKE+F  +G   S +VM ++ GK
Sbjct:   170 VGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKELFGKFGPALSVKVMTDESGK 229

Query:   242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLN 301
             S+GFGFV++E  E A+KAV   NGKE++GK +YVGRAQKK ER  ELKR+FE +K +R+ 
Sbjct:   230 SKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRIT 289

Query:   302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             RYQGVNLYVKNLDD IDDERLRKEF+PFGTITSAK
Sbjct:   290 RYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAK 324

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0003729 "mRNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=ISO

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008022 "protein C-terminus binding" evidence=ISO

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

GO:0008380 "RNA splicing" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=ISO;ISS

GO:0030529 "ribonucleoprotein complex" evidence=ISO;ISS

GO:0071013 "catalytic step 2 spliceosome" evidence=ISO

GO:2000623 "negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=ISO;ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6CDH3	PABP_YARLI	No assigned EC number	0.5419	0.7767	0.4149	yes	N/A
A2Q848	PABP_ASPNC	No assigned EC number	0.6068	0.7767	0.3570	yes	N/A
Q6FKG4	PABP_CANGA	No assigned EC number	0.5310	0.7648	0.4438	yes	N/A
Q13310	PABP4_HUMAN	No assigned EC number	0.7236	0.8065	0.4208	yes	N/A
Q6CSV3	PABP_KLULA	No assigned EC number	0.5289	0.7678	0.4358	yes	N/A
Q4WK03	PABP_ASPFU	No assigned EC number	0.6106	0.7767	0.3466	yes	N/A
Q5R8F7	PABP1_PONAB	No assigned EC number	0.7127	0.8065	0.4261	yes	N/A
P31209	PABP_SCHPO	No assigned EC number	0.6022	0.7827	0.4027	yes	N/A
P0CP46	PABP_CRYNJ	No assigned EC number	0.5572	0.7767	0.3878	yes	N/A
A3LXL0	PABP_PICST	No assigned EC number	0.5871	0.7827	0.4161	yes	N/A
Q9EPH8	PABP1_RAT	No assigned EC number	0.7163	0.8065	0.4261	yes	N/A
Q54BM2	PAP1A_DICDI	No assigned EC number	0.5900	0.7440	0.4424	yes	N/A
P04147	PABP_YEAST	No assigned EC number	0.5598	0.7678	0.4471	yes	N/A
Q6BI95	PABP_DEBHA	No assigned EC number	0.5839	0.7767	0.4162	yes	N/A
P29341	PABP1_MOUSE	No assigned EC number	0.7163	0.8065	0.4261	yes	N/A
P21187	PABP_DROME	No assigned EC number	0.7608	0.8095	0.4290	yes	N/A
Q2UK72	PABP_ASPOR	No assigned EC number	0.6068	0.7767	0.3411	yes	N/A
Q74ZS6	PABP_ASHGO	No assigned EC number	0.5598	0.7678	0.4410	yes	N/A
Q5B630	PABP_EMENI	No assigned EC number	0.6	0.7708	0.3538	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	336
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-138
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-56
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	6e-52
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	5e-42
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-41
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-29
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-23
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	5e-23
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	4e-21
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	3e-20
smart00360	73	smart00360, RRM, RNA recognition motif	1e-19
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-19
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	1e-18
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-18
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-18
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-17
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-17
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-17
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-17
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	6e-17
smart00360	73	smart00360, RRM, RNA recognition motif	6e-17
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-16
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-16
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-16
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	6e-16
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-15
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	5e-15
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-14
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	4e-14
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	2e-13
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-13
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	6e-13
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-12
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-12
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	3e-12
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	6e-12
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	6e-12
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	7e-12
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	9e-12
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	9e-12
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-11
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-11
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-11
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-11
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	2e-11
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	2e-11
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-11
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-11
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	6e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	8e-11
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	1e-10
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	1e-10
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-10
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-10
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-10
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	3e-10
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	4e-10
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	5e-10
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	6e-10
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	6e-10
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	7e-10
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	7e-10
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	7e-10
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	7e-10
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	9e-10
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	9e-10
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	9e-10
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	1e-09
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	1e-09
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-09
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-09
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-09
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	1e-09
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-09
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	2e-09
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	2e-09
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-09
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	3e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-09
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	4e-09
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	4e-09
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	5e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	5e-09
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	5e-09
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	5e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	5e-09
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	6e-09
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	6e-09
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	6e-09
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	7e-09
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	7e-09
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	7e-09
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	7e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	8e-09
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	8e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	8e-09
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	8e-09
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	8e-09
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-08
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-08
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-08
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-08
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-08
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-08
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-08
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-08
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-08
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-08
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	2e-08
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	3e-08
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	3e-08
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	3e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	4e-08
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	6e-08
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	7e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	7e-08
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	9e-08
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	9e-08
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	9e-08
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	9e-08
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	9e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-07
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	1e-07
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	1e-07
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	1e-07
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	1e-07
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-07
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	2e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-07
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	2e-07
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-07
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-07
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-07
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	2e-07
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-07
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-07
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-07
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-07
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	2e-07
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	2e-07
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-07
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	3e-07
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	3e-07
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	3e-07
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	3e-07
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	4e-07
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	4e-07
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	4e-07
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-07
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	5e-07
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	5e-07
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	6e-07
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	6e-07
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	6e-07
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	7e-07
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	7e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	7e-07
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	8e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	8e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	9e-07
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	9e-07
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	9e-07
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	9e-07
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	1e-06
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	1e-06
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-06
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	1e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-06
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	1e-06
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	1e-06
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-06
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-06
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-06
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-06
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-06
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-06
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-06
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-06
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	2e-06
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	2e-06
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-06
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-06
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	2e-06
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	3e-06
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-06
cd12487	78	cd12487, RRM1_DND1, RNA recognition motif 1 found	3e-06
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-06
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	3e-06
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	3e-06
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	3e-06
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	3e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	4e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-06
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	4e-06
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	4e-06
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	4e-06
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	4e-06
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	4e-06
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	4e-06
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	4e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-06
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	5e-06
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	5e-06
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	5e-06
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	5e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-06
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	5e-06
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	5e-06
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	6e-06
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	6e-06
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	6e-06
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	7e-06
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	7e-06
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	8e-06
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	8e-06
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	9e-06
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	9e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	9e-06
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-05
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	1e-05
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	1e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	1e-05
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	1e-05
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	1e-05
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	1e-05
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	1e-05
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	1e-05
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-05
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	1e-05
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	1e-05
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	1e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-05
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	2e-05
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-05
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	2e-05
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	2e-05
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	2e-05
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-05
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-05
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	2e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-05
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	2e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	2e-05
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	2e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-05
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-05
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	3e-05
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	3e-05
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	3e-05
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	3e-05
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	3e-05
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	3e-05
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	3e-05
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	3e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-05
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	3e-05
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	3e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	3e-05
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	4e-05
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	4e-05
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	4e-05
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	4e-05
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	4e-05
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	4e-05
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	4e-05
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	5e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	5e-05
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	5e-05
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	5e-05
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	5e-05
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	5e-05
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	6e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	6e-05
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	6e-05
smart00360	73	smart00360, RRM, RNA recognition motif	7e-05
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	7e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	7e-05
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	7e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	7e-05
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	7e-05
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	7e-05
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	7e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	8e-05
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	8e-05
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	8e-05
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	8e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	8e-05
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	8e-05
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	8e-05
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	8e-05
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	9e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	9e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	9e-05
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	1e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-04
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	1e-04
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	1e-04
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	1e-04
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	1e-04
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	1e-04
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	1e-04
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	1e-04
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-04
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	2e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	2e-04
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	2e-04
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	2e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-04
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	2e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	2e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	3e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	3e-04
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	3e-04
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	3e-04
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	3e-04
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	3e-04
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	3e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-04
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	3e-04
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	4e-04
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	4e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	4e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	4e-04
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	4e-04
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	5e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	5e-04
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	5e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	5e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	5e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	6e-04
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	6e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	7e-04
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	7e-04
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	7e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	7e-04
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	7e-04
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	7e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	8e-04
cd12668	98	cd12668, RRM3_RAVER2, RNA recognition motif 3 foun	8e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	8e-04
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	8e-04
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	9e-04
cd12288	93	cd12288, RRM_La_like_plant, RNA recognition motif	9e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	9e-04
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	9e-04
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	0.001
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	0.001
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	0.001
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.001
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	0.001
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.001
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	0.001
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	0.001
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	0.001
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	0.001
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.001
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	0.001
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.001
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	0.001
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	0.001
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	0.001
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	0.001
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	0.001
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	0.001
cd12295	74	cd12295, RRM_YRA2, RNA recognition motif in yeast	0.001
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	0.001
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	0.001
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	0.001
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	0.002
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	0.002
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	0.002
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	0.002
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	0.002
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.002
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.002
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	0.002
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	0.002
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	0.002
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	0.002
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	0.002
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	0.002
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	0.002
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.003
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	0.003
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	0.003
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	0.003
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	0.003
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	0.003
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	0.003
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	0.003
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	0.003
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	0.003
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	0.003
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.003
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	0.003
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	0.004
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	0.004
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	0.004
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	0.004
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	0.004
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	0.004

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

 Score =  403 bits (1036), Expect = e-138
 Identities = 165/266 (62%), Positives = 204/266 (76%), Gaps = 8/266 (3%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
           D ERAL+TMNF  L G+PIRIMWSQRDPSLR+SGVGN+F+KNLDKS+DNKA++DTFS FG
Sbjct: 54  DAERALETMNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFG 113

Query: 136 SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKE 195
           +ILSCKVA DE G S+GYGFVHFE EE+A  +I+KVNGMLLN K V+VG+FI + ERE  
Sbjct: 114 NILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHERE-- 171

Query: 196 LGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPE 254
                K FTN+Y+KN     N++KL+E+F  +G ITS  VM +  G+SRGF FV +E  E
Sbjct: 172 -AAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHE 230

Query: 255 FAEKAVQAWNGKEVD----GKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYV 310
            A KAV+  NGK++     GK LYVGRAQK+AER  EL+R+FE L+ ER  + QGVNLYV
Sbjct: 231 DAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYV 290

Query: 311 KNLDDSIDDERLRKEFTPFGTITSAK 336
           KNLDD++ DE+LR+ F+  G ITSAK
Sbjct: 291 KNLDDTVTDEKLRELFSECGEITSAK 316

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

 Score =  192 bits (490), Expect = 1e-56
 Identities = 77/196 (39%), Positives = 116/196 (59%), Gaps = 15/196 (7%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           N+++KNLD S++   + + F+ FG I S  V +D  G S+G+ FV+FE  E A K++E++
Sbjct: 180 NLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 172 NG----MLLNSKIVFVGKFIPRKEREKELGEKAK----------LFTNVYIKNFGEDFND 217
           NG    +    K ++VG+   R ERE EL  K +             N+Y+KN  +   D
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTD 299

Query: 218 EKLKEMFEPYGTITSYRVMNND-GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG 276
           EKL+E+F   G ITS +VM ++ G SRGFGFV + +PE A +AV   +G+ + GK LYV 
Sbjct: 300 EKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVA 359

Query: 277 RAQKKAERTQELKRRF 292
            AQ+K +R   L+ +F
Sbjct: 360 LAQRKEQRRAHLQDQF 375

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

 Score =  165 bits (421), Expect = 6e-52
 Identities = 65/77 (84%), Positives = 70/77 (90%)

Query: 109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSI 168
           GVGN+FIKNLDKSIDNKA+YDTFSAFG+ILSCKVA DE G SKGYGFVHFETEEAA ++I
Sbjct: 1   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAI 60

Query: 169 EKVNGMLLNSKIVFVGK 185
           EKVNGMLLN K VFVG 
Sbjct: 61  EKVNGMLLNDKKVFVGP 77

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

 Score =  140 bits (355), Expect = 5e-42
 Identities = 54/80 (67%), Positives = 67/80 (83%), Gaps = 1/80 (1%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQ 261
           FTNVY+KN GED +DEKLKE+F  YG ITS +VM +++GKS+GFGFV +E+ E A+KAV+
Sbjct: 1   FTNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVE 60

Query: 262 AWNGKEVDGKILYVGRAQKK 281
             NGKEV+GK LYVGRAQKK
Sbjct: 61  ELNGKEVNGKKLYVGRAQKK 80

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

 Score =  152 bits (385), Expect = 1e-41
 Identities = 76/226 (33%), Positives = 123/226 (54%), Gaps = 21/226 (9%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV 171
           +++ +LD  +    +YD F  FG +LS +V +D     S GYG+V+F+    A +++E +
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 172 NGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTIT 231
           N   L  K + +       +R+  L        N+++KN  +  +++ L + F  +G I 
Sbjct: 63  NFKRLGGKPIRIMW----SQRDPSLRRSGV--GNIFVKNLDKSVDNKALFDTFSKFGNIL 116

Query: 232 SYRVM-NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKR 290
           S +V  + +GKSRG+GFV +E  E A+ A+Q  NG  ++ K +YVGR  KK ER     +
Sbjct: 117 SCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREAAPLK 176

Query: 291 RFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           +F              NLYVKNLD S+++++LR+ F  FG ITSA 
Sbjct: 177 KF-------------TNLYVKNLDPSVNEDKLRELFAKFGEITSAA 209

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

 Score =  108 bits (272), Expect = 1e-29
 Identities = 40/77 (51%), Positives = 55/77 (71%), Gaps = 1/77 (1%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQAW 263
           N+Y+KN  +  +DE+L+E F P+GTITS +VM +  G+S+GFGFV + SPE A KAV   
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 264 NGKEVDGKILYVGRAQK 280
           NG+ + GK LYV  AQ+
Sbjct: 63  NGRIIGGKPLYVALAQR 79

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

 Score = 97.7 bits (242), Expect = 2e-23
 Identities = 58/256 (22%), Positives = 103/256 (40%), Gaps = 13/256 (5%)

Query: 94  IRIMWSQRDPSLRKSGVGN-VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKG 152
                 +   S  +S     +    L + +  +       A    L+ +V   +  +   
Sbjct: 1   KESKNLKGPHSSFESVKPEDIESGKLTELLLKEEYGGLEEANSKELNLEVNSRKIESEIS 60

Query: 153 YGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKA----KLFTNVYI 208
                        +  E+      + +  +  +F     R  E  +      +    +++
Sbjct: 61  PPSKKRLLSSERKEENEREMEEQNDGERGYTKEFEEELFRSSESPKSRQKSKEENNTLFV 120

Query: 209 KNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWNGK 266
            N   D  +E L+E+F+ +G +   R++ +   GKSRGF FV +ES E AEKA++  NGK
Sbjct: 121 GNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGK 180

Query: 267 EVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRY------QGVNLYVKNLDDSIDDE 320
           E++G+ L V +AQ  ++   EL    +    ++L+R       +  NLYV NL     +E
Sbjct: 181 ELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEE 240

Query: 321 RLRKEFTPFGTITSAK 336
            L   F   G I  A 
Sbjct: 241 ELADLFKSRGDIVRAS 256

Length = 306

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

 Score = 90.7 bits (226), Expect = 5e-23
 Identities = 33/74 (44%), Positives = 55/74 (74%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           NV++KNL + +D++ + + F  +G I S KV +D++G SKG+GFV+FE  EAA K++E++
Sbjct: 3   NVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 172 NGMLLNSKIVFVGK 185
           NG  +N K ++VG+
Sbjct: 63  NGKEVNGKKLYVGR 76

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

 Score = 85.4 bits (212), Expect = 4e-21
 Identities = 33/73 (45%), Positives = 52/73 (71%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           N+++KNLD SID++ + + FS FG+I S KV  DE+G SKG+GFV F + E A K++ ++
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 172 NGMLLNSKIVFVG 184
           NG ++  K ++V 
Sbjct: 63  NGRIIGGKPLYVA 75

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

 Score = 83.1 bits (206), Expect = 3e-20
 Identities = 34/74 (45%), Positives = 52/74 (70%), Gaps = 2/74 (2%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSIL-SCKVAQDEQ-GNSKGYGFVHFETEEAANKSIE 169
           N+FI NLD  +D K +YDTFSAFG IL + K+ +D   GNSKG+ F+ +++ EA++ +IE
Sbjct: 3   NLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62

Query: 170 KVNGMLLNSKIVFV 183
            +NG  L ++ + V
Sbjct: 63  AMNGQYLCNRPITV 76

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|214636 smart00360, RRM, RNA recognition motif

 Score = 81.1 bits (201), Expect = 1e-19
 Identities = 32/73 (43%), Positives = 50/73 (68%), Gaps = 2/73 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQA 262
            +++ N   D  +E+L+E+F  +G + S R++ +   GKS+GF FV +ES E AEKA++A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 263 WNGKEVDGKILYV 275
            NGKE+DG+ L V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 79.6 bits (197), Expect = 4e-19
 Identities = 29/70 (41%), Positives = 46/70 (65%), Gaps = 1/70 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           +++ N   D  +E LK++F  +G I S R++ +  G+S+GF FV +E  E AEKA++A N
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 265 GKEVDGKILY 274
           GKE+ G+ L 
Sbjct: 61  GKELGGRELR 70

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

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

 Score = 78.7 bits (195), Expect = 1e-18
 Identities = 25/74 (33%), Positives = 47/74 (63%), Gaps = 1/74 (1%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           N++IKN  +  +++ L + F  +G I S +V  + +G S+G+GFV +E+ E A +A++  
Sbjct: 4   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 264 NGKEVDGKILYVGR 277
           NG  ++ K ++VG 
Sbjct: 64  NGMLLNDKKVFVGP 77

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

 Score = 85.7 bits (212), Expect = 2e-18
 Identities = 47/194 (24%), Positives = 90/194 (46%), Gaps = 8/194 (4%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKV 171
           VF+  L      + +Y+ FS  G +   +  +D     SKG  +V F   E+  K++  +
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-L 150

Query: 172 NGMLLNSKIVFVGKFIPRKERE----KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPY 227
            G +L  + + V      K R              F  +Y+ N   +  +++L+++FEP+
Sbjct: 151 TGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPF 210

Query: 228 GTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERT 285
           G I   ++  +   G+S+GFGF+ +   E A++A++  NG E+ G+ + VG AQ      
Sbjct: 211 GDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLL 270

Query: 286 QELKRRFEMLKIER 299
                  ++ K ++
Sbjct: 271 DAANTFEDIDKQQQ 284

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

 Score = 82.7 bits (204), Expect = 9e-18
 Identities = 43/157 (27%), Positives = 86/157 (54%), Gaps = 11/157 (7%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L +++  + +   F++ G I SCK+ +D+  G S GYGFV++   E A K++  
Sbjct: 5   NLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS 64

Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTI 230
           +NG+ L +K + V    P  +  K          N+Y+    +     +L+ +F P+G I
Sbjct: 65  LNGLRLQNKTIKVSYARPSSDSIKG--------ANLYVSGLPKTMTQHELESIFSPFGQI 116

Query: 231 TSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNG 265
            + R+++++  G S+G GF+ ++  + A++A++  NG
Sbjct: 117 ITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNG 153

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

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

 Score = 75.7 bits (187), Expect = 1e-17
 Identities = 28/69 (40%), Positives = 41/69 (59%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ NL      + + D FS FG I S ++ +DE G SKG+ FV FE EE A K++E +N
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 173 GMLLNSKIV 181
           G  L  + +
Sbjct: 61  GKELGGREL 69

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

>gnl|CDD|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 = 76.1 bits (188), Expect = 1e-17
 Identities = 24/79 (30%), Positives = 49/79 (62%), Gaps = 2/79 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
             +++        +++L+ +F  +G +    +M +   G+SRGFGFV +ES E A+ A++
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 262 AWNGKEVDGKILYVGRAQK 280
             NGKE++G+++ V +A++
Sbjct: 62  DLNGKELEGRVIKVEKAKR 80

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

 Score = 74.6 bits (184), Expect = 3e-17
 Identities = 35/71 (49%), Positives = 51/71 (71%), Gaps = 1/71 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           +++ N   D  +E L+E+F  +G I S R++ + DGKS+GF FV +ESPE AEKA++A N
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 265 GKEVDGKILYV 275
           GKE+DG+ L V
Sbjct: 61  GKELDGRKLKV 71

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

 Score = 81.4 bits (201), Expect = 5e-17
 Identities = 31/90 (34%), Positives = 56/90 (62%)

Query: 107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANK 166
           K+   N+++KNLD ++ ++ + + FS  G I S KV  DE+G S+G+GFV F   E AN+
Sbjct: 282 KAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANR 341

Query: 167 SIEKVNGMLLNSKIVFVGKFIPRKEREKEL 196
           ++ +++G +L  K ++V     +++R   L
Sbjct: 342 AVTEMHGRMLGGKPLYVALAQRKEQRRAHL 371

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

 Score = 74.2 bits (183), Expect = 6e-17
 Identities = 30/32 (93%), Positives = 32/32 (100%)

Query: 305 GVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           GVNLYVKNLDDSIDDERLR+EF+PFGTITSAK
Sbjct: 1   GVNLYVKNLDDSIDDERLREEFSPFGTITSAK 32

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|214636 smart00360, RRM, RNA recognition motif

 Score = 73.8 bits (182), Expect = 6e-17
 Identities = 26/73 (35%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
            +F+ NL      + + + FS FG + S ++ +D++ G SKG+ FV FE+EE A K++E 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 171 VNGMLLNSKIVFV 183
           +NG  L+ + + V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 73.1 bits (180), Expect = 1e-16
 Identities = 26/71 (36%), Positives = 43/71 (60%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ NL      + + + FS FG I S ++ +D+ G SKG+ FV FE+ E A K++E +N
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 173 GMLLNSKIVFV 183
           G  L+ + + V
Sbjct: 61  GKELDGRKLKV 71

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

 Score = 80.5 bits (198), Expect = 1e-16
 Identities = 43/154 (27%), Positives = 82/154 (53%), Gaps = 6/154 (3%)

Query: 131 FSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK--FI 187
           F  FG I S  ++ D   G  KG+ FV +E  EAA  ++E++NG +L  + + VG+   +
Sbjct: 128 FDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM 187

Query: 188 PRKERE-KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRG 244
           P+ +     + E+AK F  +Y+ +   D ++  +K +FE +G I   ++         +G
Sbjct: 188 PQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKG 247

Query: 245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA 278
           +GF+ Y + +   +A+ + N  ++ G+ L VG+ 
Sbjct: 248 YGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC 281

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

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

 Score = 71.5 bits (176), Expect = 6e-16
 Identities = 30/78 (38%), Positives = 47/78 (60%), Gaps = 2/78 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQA 262
           N+Y+ N   +  +E LK++F  +G +TS RV+ +   G+SRGFGFV  E+ E A  A++ 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 263 WNGKEVDGKILYVGRAQK 280
            NG +  G+ L V  A+ 
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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 77.4 bits (190), Expect = 6e-16
 Identities = 45/167 (26%), Positives = 82/167 (49%), Gaps = 11/167 (6%)

Query: 101 RDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFE 159
            D +   +   N+ +  L + + ++ +Y  F   G I +C++ +D + G S GY FV F 
Sbjct: 98  SDDNDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFG 157

Query: 160 TEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEK 219
           +E  + ++I+ +NG+ + +K + V    P  E  K+        TN+Y+ N      D++
Sbjct: 158 SEADSQRAIKNLNGITVRNKRLKVSYARPGGESIKD--------TNLYVTNLPRTITDDQ 209

Query: 220 LKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWN 264
           L  +F  YG I    ++ +   G  RG  FV +   E A++A+ A N
Sbjct: 210 LDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALN 256

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|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 = 69.2 bits (170), Expect = 3e-15
 Identities = 28/64 (43%), Positives = 44/64 (68%), Gaps = 2/64 (3%)

Query: 214 DFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK 271
           +F D+ L ++F P+G + S +V    N G+S+ FGFV+Y++PE A+ A++A NG +V GK
Sbjct: 9   EFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGK 68

Query: 272 ILYV 275
            L V
Sbjct: 69  RLKV 72

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

 Score = 68.6 bits (168), Expect = 5e-15
 Identities = 31/69 (44%), Positives = 48/69 (69%), Gaps = 2/69 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQA 262
            +++ N     +DE LK  FE +GT+   RV+ +   G+SRGFG+V +ESPE A+KA++A
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 263 WNGKEVDGK 271
            +GKE+DG+
Sbjct: 61  MDGKELDGR 69

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 67.2 bits (165), Expect = 1e-14
 Identities = 26/66 (39%), Positives = 40/66 (60%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +Y++N      +E L+E F PYG +   R++ N  + RGF FV + SPE AE A++  NG
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 266 KEVDGK 271
             +DG+
Sbjct: 61  LVLDGR 66

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

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

 Score = 66.3 bits (162), Expect = 4e-14
 Identities = 22/73 (30%), Positives = 41/73 (56%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +++ N    F D  L++MF  +G I    ++ N+  S+GFGFV + +   A++A +  +G
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGSKGFGFVTFANSADADRAREKLHG 62

Query: 266 KEVDGKILYVGRA 278
             V+G+ + V  A
Sbjct: 63  TVVEGRKIEVNNA 75

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

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

 Score = 64.2 bits (157), Expect = 2e-13
 Identities = 25/71 (35%), Positives = 46/71 (64%), Gaps = 1/71 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           ++++N       + LK++F   G +    V  +NDG+S+GFG V +ESPE A++A++ +N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 265 GKEVDGKILYV 275
           G +++G+ L V
Sbjct: 61  GYDLEGRELEV 71

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

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

 Score = 63.8 bits (156), Expect = 2e-13
 Identities = 26/69 (37%), Positives = 42/69 (60%), Gaps = 2/69 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
           TNVYI+    +  DE L+++ +P+G I S + +      K +G+GFV ++SPE A KA++
Sbjct: 1   TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

Query: 262 AWNGKEVDG 270
             NG+ V  
Sbjct: 61  GLNGRGVQA 69

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

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

 Score = 63.3 bits (155), Expect = 6e-13
 Identities = 23/28 (82%), Positives = 26/28 (92%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDP 103
           D ERALDT+NFD +KG+PIRIMWSQRDP
Sbjct: 53  DAERALDTLNFDVIKGKPIRIMWSQRDP 80

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

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

 Score = 61.6 bits (150), Expect = 2e-12
 Identities = 27/77 (35%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    +D   E+L+ +FE  G I S +++     G+S G+GFV Y     A+KA+ 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 262 AWNGKEVDGKILYVGRA 278
             NG E+  K L V  A
Sbjct: 61  TLNGFEIRNKRLKVSYA 77

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

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

 Score = 61.2 bits (149), Expect = 2e-12
 Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 1/69 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
           ++F+ +L   ID + +   F+ FG I   +V +D Q G SKGYGFV F  +E A  +I+ 
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 171 VNGMLLNSK 179
           +NG  L  +
Sbjct: 61  MNGQWLGGR 69

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

 Score = 60.7 bits (148), Expect = 3e-12
 Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 207 YIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWN 264
            + N   +F DE+ +E+  P+G +    ++ ++  G+S+G+GFV Y S   A KA    +
Sbjct: 3   CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 265 GKEVDGKILYV 275
           GK++ G+ L V
Sbjct: 63  GKQIGGRKLQV 73

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

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

 Score = 60.4 bits (147), Expect = 6e-12
 Identities = 24/75 (32%), Positives = 47/75 (62%), Gaps = 2/75 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
           +Y+ +   D +++ +K +FE +G I S  +  +   GK +G+GF+ YE+P+ A+ A+ + 
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 264 NGKEVDGKILYVGRA 278
           N  ++ G+ L VG+A
Sbjct: 63  NLFDLGGQQLRVGKA 77

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

>gnl|CDD|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 = 60.2 bits (146), Expect = 6e-12
 Identities = 33/83 (39%), Positives = 50/83 (60%), Gaps = 6/83 (7%)

Query: 200 AKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAE 257
            KLF    I     D N++ L+++F  YG I+   V+ +    +SRGFGFV +E+P+ A+
Sbjct: 1   GKLF----IGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAK 56

Query: 258 KAVQAWNGKEVDGKILYVGRAQK 280
            A+ A NGK VDG+ + V +A K
Sbjct: 57  DAMMAMNGKSVDGRQIRVDQAGK 79

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

>gnl|CDD|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 = 59.9 bits (146), Expect = 7e-12
 Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 4/70 (5%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           T VY+ N      +E+L+  F P+G I   RV     K +G+ FV +++ E A  A+ A 
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVF----KDKGYAFVRFDTHEAAATAIVAV 56

Query: 264 NGKEVDGKIL 273
           NG  ++G+ +
Sbjct: 57  NGTSINGQTV 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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 59.7 bits (145), Expect = 9e-12
 Identities = 26/68 (38%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQA 262
           TN+YI N     +++ L+ M +PYG + S R++ ++ G+SRG GF   ES E  E  +  
Sbjct: 1   TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISK 60

Query: 263 WNGKEVDG 270
           +NGK + G
Sbjct: 61  FNGKYLKG 68

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

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

 Score = 59.5 bits (145), Expect = 9e-12
 Identities = 26/67 (38%), Positives = 43/67 (64%), Gaps = 1/67 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQA 262
           + + +KN  +   +++L+E FE  G +T  +VM   DGKSR FGFV ++S E A++AV+ 
Sbjct: 1   SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKY 60

Query: 263 WNGKEVD 269
           +N   +D
Sbjct: 61  FNKTFID 67

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 26/68 (38%), Positives = 40/68 (58%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ NL  S +   + + F   G ++  ++AQD+ G SKG+G V F TEE A K++EK  
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKSG 61

Query: 173 GMLLNSKI 180
             LL  +I
Sbjct: 62  EELLGREI 69

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

 Score = 59.1 bits (144), Expect = 1e-11
 Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 6/64 (9%)

Query: 214 DFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQA----WNGKE 267
           D  +E L+E F  YG +    +M +   G+SRGFGFV +  P   +K + A     +G+E
Sbjct: 9   DTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKPHVLDGRE 68

Query: 268 VDGK 271
           +D K
Sbjct: 69  IDPK 72

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

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

 Score = 58.9 bits (143), Expect = 2e-11
 Identities = 23/69 (33%), Positives = 44/69 (63%), Gaps = 2/69 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQA 262
           ++++ +   + + E L+  F P+G I+  RV+ +   GKS+G+GFV++   E AE A+Q+
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 263 WNGKEVDGK 271
            NG+ + G+
Sbjct: 61  MNGQWLGGR 69

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

 Score = 59.6 bits (145), Expect = 2e-11
 Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 207 YIKNFGEDFND-EKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           ++    + F D   L+++F   G  T  ++ +  +G+ RGF FV Y + E AE+A QA N
Sbjct: 6   FVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALN 65

Query: 265 GKEVDG 270
           G  + G
Sbjct: 66  GHSLQG 71

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

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

 Score = 58.7 bits (142), Expect = 2e-11
 Identities = 24/69 (34%), Positives = 41/69 (59%), Gaps = 1/69 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
           N+F+ +L   + +  ++  FSAF S    +V  D + G S+GYGFV F +++ A  +I +
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 171 VNGMLLNSK 179
           +NG  L S+
Sbjct: 61  MNGKWLGSR 69

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

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

 Score = 58.7 bits (143), Expect = 2e-11
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQA 262
           + +++ NF   F+   ++++FE YG I S R  +    K+R F +V + SPE A  AV  
Sbjct: 1   STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVAL 60

Query: 263 WNGKEVDG 270
            NGK  +G
Sbjct: 61  LNGKLGEG 68

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|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 = 58.4 bits (142), Expect = 3e-11
 Identities = 22/68 (32%), Positives = 40/68 (58%), Gaps = 1/68 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKV 171
           +FI +L     ++ +Y  F+ FG+++S KV  D+    SK +GFV ++  E+A  +I+ +
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 172 NGMLLNSK 179
           NG  +  K
Sbjct: 61  NGFQVGGK 68

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

 Score = 58.6 bits (142), Expect = 3e-11
 Identities = 25/71 (35%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
            +F+ NL  S+D++ +   F  FG+++  +V  D E G S+G+G+V FE+ E A K+IE 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 171 VNGMLLNSKIV 181
           ++G  L+ + +
Sbjct: 61  MDGKELDGRPI 71

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

 Score = 57.7 bits (140), Expect = 5e-11
 Identities = 23/72 (31%), Positives = 44/72 (61%), Gaps = 2/72 (2%)

Query: 207 YIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWN 264
           Y+ N   +  ++ L+ +FEP+G I   ++  +   G+S+G+GF+ +   E A+KA++  N
Sbjct: 2   YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 265 GKEVDGKILYVG 276
           G E+ G+ + VG
Sbjct: 62  GFELAGRPIKVG 73

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

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

 Score = 57.6 bits (139), Expect = 6e-11
 Identities = 26/73 (35%), Positives = 47/73 (64%), Gaps = 2/73 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQA 262
           N++I +  ++F D +L +MF P+G + S +V  +    +S+ FGFV++++P  A+ A+QA
Sbjct: 6   NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA 65

Query: 263 WNGKEVDGKILYV 275
            NG ++  K L V
Sbjct: 66  MNGFQIGMKRLKV 78

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

>gnl|CDD|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 = 57.2 bits (139), Expect = 8e-11
 Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIE 169
             +F+  L      K +   FS FG +    + +D E G S+G+GFV FE+ E A+ +I 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 170 KVNGMLLNSKIVFV 183
            +NG  L  +++ V
Sbjct: 62  DLNGKELEGRVIKV 75

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

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

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 2/79 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSA-FGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           +F+ +L   +D+  +Y+ FS  + S    KV  D+ GNS+GYGFV F  E    +++ ++
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQNGNSRGYGFVRFSDESEQKRALTEM 63

Query: 172 NGML-LNSKIVFVGKFIPR 189
            G   L  K + V   IP+
Sbjct: 64  QGASGLGGKPIRVSLAIPK 82

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

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

 Score = 56.3 bits (136), Expect = 1e-10
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           VY   F   F    +K +FE  G +    +++     +   F+ +E+ E A+ A++  NG
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSR--TVQPHAFITFENLEAAQLAIETLNG 59

Query: 266 KEVDGKILYVGR 277
             VDG  + V R
Sbjct: 60  ASVDGNCIKVQR 71

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|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 = 55.7 bits (135), Expect = 2e-10
 Identities = 27/70 (38%), Positives = 39/70 (55%), Gaps = 5/70 (7%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            V++ NL   +  + +  TFS FG+I   +V +D     KGY FV F+T EAA  +I  V
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAV 56

Query: 172 NGMLLNSKIV 181
           NG  +N + V
Sbjct: 57  NGTSINGQTV 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|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 55.7 bits (135), Expect = 2e-10
 Identities = 23/70 (32%), Positives = 40/70 (57%), Gaps = 6/70 (8%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +Y++N      +E+L+E+F  YG +   RV     K + + FV +E  + A KA++  NG
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVE--RVK----KIKDYAFVHFEERDDAVKAMEEMNG 57

Query: 266 KEVDGKILYV 275
           KE++G  + V
Sbjct: 58  KELEGSPIEV 67

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

 Score = 55.7 bits (135), Expect = 2e-10
 Identities = 25/68 (36%), Positives = 35/68 (51%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+  +      + + D FS FGS+   K+  D  G SKGYGFV FET+E A K +   N
Sbjct: 5   IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAMGN 64

Query: 173 GMLLNSKI 180
                 K+
Sbjct: 65  LNFRGKKL 72

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

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

 Score = 55.4 bits (134), Expect = 3e-10
 Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L + +  + +   F A G I SCK+ +D   G S GYGFV +  E  A K+I  
Sbjct: 2   NLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINT 61

Query: 171 VNGMLLNSK 179
           +NG  + +K
Sbjct: 62  LNGFEIRNK 70

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

 Score = 54.9 bits (133), Expect = 4e-10
 Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           + +KNL K +    + + F + G +   KV +   G S+ +GFV F++EE A ++++  N
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFN 62

Query: 173 GMLLN-SKIV 181
              ++ SKI 
Sbjct: 63  KTFIDTSKIS 72

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 55.0 bits (133), Expect = 5e-10
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 6/75 (8%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRV----MNNDGKSR-GFGFVAYESPEFAEKAV 260
           +Y++N     +++ L+ +F  +G + S R+        G+   GF FV ++    AE A+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 261 QAWNGKEVDGKILYV 275
           Q  NG E+ G+ + V
Sbjct: 63  QL-NGTELGGRKISV 76

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

 Score = 54.6 bits (132), Expect = 6e-10
 Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 208 IKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWNGK 266
           ++N      +  LK++F P+G +    +    DGK +GF FV + S   AEKA++  NGK
Sbjct: 4   VRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGK 63

Query: 267 EVDGK 271
           ++ G+
Sbjct: 64  KIKGR 68

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

 Score = 54.7 bits (132), Expect = 6e-10
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L +++    +   FS+ G I SCK+ +D   G S GYGFV++   E A K+I  
Sbjct: 3   NLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINT 62

Query: 171 VNGMLLNSKIVFV 183
           +NG+ L +K + V
Sbjct: 63  LNGLRLQNKTIKV 75

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

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

 Score = 54.2 bits (131), Expect = 7e-10
 Identities = 22/77 (28%), Positives = 46/77 (59%), Gaps = 2/77 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           +++ N       + L+E F+  G +   R+  ++DG+S+GFG V + + E A+KA++  +
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEK-S 60

Query: 265 GKEVDGKILYVGRAQKK 281
           G+E+ G+ + V  A ++
Sbjct: 61  GEELLGREIRVDLATER 77

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

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

 Score = 54.6 bits (132), Expect = 7e-10
 Identities = 25/63 (39%), Positives = 42/63 (66%), Gaps = 1/63 (1%)

Query: 208 IKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQAWNGK 266
           +KN  +   ++KL+++FE +GTIT  ++    DGK R FGFV Y++ E A+KA++ +N  
Sbjct: 5   VKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNS 64

Query: 267 EVD 269
            +D
Sbjct: 65  FID 67

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

 Score = 59.5 bits (144), Expect = 7e-10
 Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
           +YI N      ++++KE+ E +G + ++ ++ +   G S+G+ F  Y+ P   + A+ A 
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 264 NGKEVDGKILYVGRA 278
           NGK+     L+V RA
Sbjct: 358 NGKDTGDNKLHVQRA 372

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

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

 Score = 54.3 bits (131), Expect = 7e-10
 Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 2/77 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
           TN+ I    +   DE+ + +F   G + + +++ +   G S GFGFV Y+S E A++A++
Sbjct: 1   TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 262 AWNGKEVDGKILYVGRA 278
             NG ++  K + V  A
Sbjct: 61  TLNGLQLQNKRIKVAYA 77

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

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

 Score = 54.2 bits (131), Expect = 9e-10
 Identities = 27/63 (42%), Positives = 40/63 (63%), Gaps = 1/63 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           N+++ NL  ++  + + D F  FG + S +V  D E G S+G+GFV  ET E AN +IEK
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 171 VNG 173
           +NG
Sbjct: 61  LNG 63

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

 Score = 54.2 bits (131), Expect = 9e-10
 Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 2/78 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG--KSRGFGFVAYESPEFAEKAVQAW 263
           ++++N   D  DE+L+E F   G I    V+ + G  K RGFG+V +   E A++A++  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 264 NGKEVDGKILYVGRAQKK 281
              +  G+ ++V  A+KK
Sbjct: 62  KKTKFGGRKIHVEFAKKK 79

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

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

 Score = 54.2 bits (131), Expect = 9e-10
 Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 4/76 (5%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKV----AQDEQGNSKGYGFVHFETEEAANKS 167
            ++I NLD  +    +   FS +G I         +   +G  +GY FV FET+E A K+
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 168 IEKVNGMLLNSKIVFV 183
           ++ +NG     K + V
Sbjct: 61  LKSLNGKTALGKKLVV 76

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

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

 Score = 53.4 bits (129), Expect = 1e-09
 Identities = 26/71 (36%), Positives = 40/71 (56%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F++NL  S+  + + D F   G++L   V  D  G SKG+G V FE+ E A ++IE  N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 173 GMLLNSKIVFV 183
           G  L  + + V
Sbjct: 61  GYDLEGRELEV 71

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

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

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 24/56 (42%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 131 FSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK 185
           F AFG I SC +A D E G  KGYGF+ +E  ++A  +I  +N   L  + + VGK
Sbjct: 21  FEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQQLRVGK 76

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

 Score = 53.7 bits (129), Expect = 1e-09
 Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQA 262
           N+++ +   +  D  L   F  + + +  RVM     G+SRG+GFV++ S + AE A+  
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 263 WNGKEVDGK 271
            NGK +  +
Sbjct: 61  MNGKWLGSR 69

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

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

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 22/58 (37%), Positives = 36/58 (62%), Gaps = 1/58 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIE 169
           VFI+NL      + + + FS FG +   ++ +D+  G+SKG  FV F+T+E+A K +E
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

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|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 = 53.8 bits (130), Expect = 1e-09
 Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAW 263
           V++ N   D  +E+L E+F   G + S+R++   + GK +G+GF  +E  E A  A++  
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 264 NGKEVDGKILYVGRA 278
           NG E +G+ L V  A
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|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 2/68 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQA 262
           N+Y+    +    ++L+ +F PYG I + R++  N  G SRG GF+ ++    AE+A++A
Sbjct: 2   NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 263 WNGKEVDG 270
            NG    G
Sbjct: 62  LNGTIPPG 69

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

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 54.0 bits (129), Expect = 1e-09
 Identities = 25/64 (39%), Positives = 40/64 (62%), Gaps = 1/64 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQA 262
           TN+YI N     ++++L+ M +P+G + S R++ + +G SRG GF   ES E  E  +Q 
Sbjct: 2   TNLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQH 61

Query: 263 WNGK 266
           +NGK
Sbjct: 62  FNGK 65

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

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

 Score = 57.6 bits (139), Expect = 2e-09
 Identities = 38/135 (28%), Positives = 64/135 (47%), Gaps = 20/135 (14%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    +    E+++ +F   G I S +++ +   G+S G+GFV Y  PE AEKAV 
Sbjct: 4   TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVN 63

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
           + NG  +  K + V  A+  ++                    +G NLYV  L  ++    
Sbjct: 64  SLNGLRLQNKTIKVSYARPSSDSI------------------KGANLYVSGLPKTMTQHE 105

Query: 322 LRKEFTPFGTITSAK 336
           L   F+PFG I +++
Sbjct: 106 LESIFSPFGQIITSR 120

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

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

 Score = 58.2 bits (140), Expect = 2e-09
 Identities = 47/183 (25%), Positives = 88/183 (48%), Gaps = 26/183 (14%)

Query: 163 AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKE 222
           A  +SI++V   LL        + +  ++R+++  +   +   VY+ +   +  ++ ++ 
Sbjct: 70  AMEQSIKQV---LLKQTKAHQQQQLENQQRQQQRQQALAIMCRVYVGSISFELREDTIRR 126

Query: 223 MFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR-- 277
            F+P+G I S   M+ D   GK +GF FV YE PE A+ A++  NG+ + G+ + VGR  
Sbjct: 127 AFDPFGPIKSIN-MSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS 185

Query: 278 ----AQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTIT 333
               AQ   +  QE  ++F        NR     +YV ++   + +  ++  F  FG I 
Sbjct: 186 NMPQAQPIIDMVQEEAKKF--------NR-----IYVASVHPDLSETDIKSVFEAFGEIV 232

Query: 334 SAK 336
             +
Sbjct: 233 KCQ 235

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

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

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 20/65 (30%), Positives = 34/65 (52%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           N++I NL   +D + +      +G ++S ++ +D +G S+G GF   E+ E     I K 
Sbjct: 2   NLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKF 61

Query: 172 NGMLL 176
           NG  L
Sbjct: 62  NGKYL 66

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

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

 Score = 52.9 bits (128), Expect = 2e-09
 Identities = 23/72 (31%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAW 263
           +++     + N + LKE+F  YGT+    +  +      RG+ +V +ESPE AEKA++  
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 264 NGKEVDGKILYV 275
           +G ++DG+ + V
Sbjct: 61  DGGQIDGQEVTV 72

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

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

 Score = 52.5 bits (127), Expect = 3e-09
 Identities = 29/76 (38%), Positives = 44/76 (57%), Gaps = 6/76 (7%)

Query: 208 IKNFGEDFNDEKLKEMFEPYGTITSYRVM----NNDGKSRGFGFVAYESPEFAEKAVQAW 263
           + N  ED +++ L+E+F P+G I+  RV        G+SRGF FV + + E AE+A++  
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPIS--RVYLAKDKETGQSRGFAFVTFHTREDAERAIEKL 61

Query: 264 NGKEVDGKILYVGRAQ 279
           NG   D  IL V  A+
Sbjct: 62  NGFGYDNLILSVEWAK 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|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 53.1 bits (127), Expect = 3e-09
 Identities = 24/66 (36%), Positives = 39/66 (59%), Gaps = 1/66 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQA 262
           TN+YI N     ++++L+ M +P+G + S R++ +  G SRG GF   ES E  E  +  
Sbjct: 1   TNLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCEAIITH 60

Query: 263 WNGKEV 268
           +NGK +
Sbjct: 61  FNGKYI 66

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 52.2 bits (126), Expect = 4e-09
 Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 115 IKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKVNG 173
           + NL +  D   + + F  FG I    +A+D E G S+G+ FV F T E A ++IEK+NG
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

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

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

 Score = 52.3 bits (126), Expect = 4e-09
 Identities = 20/58 (34%), Positives = 34/58 (58%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
           VF+ NLD S+    +   FS  G I   ++ ++ +G SKGY +V FE EE+  ++++ 
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKL 59

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

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 52.8 bits (126), Expect = 4e-09
 Identities = 24/64 (37%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQA 262
           TN+YI N     ++++L+ M +P+G + S R++ ++ G SRG GF   ES E  E  +  
Sbjct: 1   TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISH 60

Query: 263 WNGK 266
           +NGK
Sbjct: 61  FNGK 64

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

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

 Score = 52.3 bits (126), Expect = 5e-09
 Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQ 261
             +++ N   D ++  L ++F P+G +T+ +V+      K +G+GFV   + E A  A+ 
Sbjct: 2   WCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIA 61

Query: 262 AWNGKEVDGKILYV 275
           + NG  + G++L V
Sbjct: 62  SLNGYRLGGRVLQV 75

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

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

 Score = 52.0 bits (125), Expect = 5e-09
 Identities = 17/71 (23%), Positives = 37/71 (52%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+  L  S+  + +   F   G + S ++  +  G  KG  +V +E E +A++++ K++
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMD 64

Query: 173 GMLLNSKIVFV 183
           G  +  K + V
Sbjct: 65  GTEIKEKTISV 75

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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 52.4 bits (125), Expect = 5e-09
 Identities = 28/81 (34%), Positives = 46/81 (56%), Gaps = 2/81 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW 263
           ++I N G+D ++  L +MF P+G +T+ +V+   N  K +GFGFV   + E A  A+ + 
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           NG  +  KIL V     K+ +
Sbjct: 64  NGYRLGDKILQVSFKTSKSHK 84

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 52.4 bits (125), Expect = 5e-09
 Identities = 28/79 (35%), Positives = 47/79 (59%), Gaps = 2/79 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQA 262
           N++I +  ++F D+ L +MF P+G + S +V        S+ FGFV+Y++P  A+ A+QA
Sbjct: 9   NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQA 68

Query: 263 WNGKEVDGKILYVGRAQKK 281
            NG ++  K L V   + K
Sbjct: 69  MNGFQIGMKRLKVQLKRSK 87

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

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

 Score = 51.9 bits (125), Expect = 5e-09
 Identities = 24/72 (33%), Positives = 43/72 (59%), Gaps = 3/72 (4%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           VF   L      + + + FS +G I   +V  D++ G S+G+GFV+FE+ E A ++ E++
Sbjct: 4   VF--GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 172 NGMLLNSKIVFV 183
           NGM ++ + + V
Sbjct: 62  NGMEIDGRRIRV 73

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

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

 Score = 52.0 bits (125), Expect = 6e-09
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAW 263
           +++     D  +E+ KE F  +G +   ++M  ++ G+SRGFGFV ++S    E+   A 
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA- 60

Query: 264 NGKEVDGKILYVGRA 278
              E+ GK + V RA
Sbjct: 61  GMLELGGKQVEVKRA 75

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

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

 Score = 51.7 bits (124), Expect = 6e-09
 Identities = 22/70 (31%), Positives = 41/70 (58%), Gaps = 6/70 (8%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +Y++ F  D ++  ++E+F PYG +   ++++N      F FV +ES E A +A  + +G
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMISN------FAFVEFESLESAIRAKDSVHG 55

Query: 266 KEVDGKILYV 275
           K ++   LYV
Sbjct: 56  KVLNNNPLYV 65

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

 Score = 51.9 bits (124), Expect = 6e-09
 Identities = 26/74 (35%), Positives = 44/74 (59%), Gaps = 2/74 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
            N++I +  ++F D  L + F P+G + S +V        S+ FGFV+Y++P+ A+ A+Q
Sbjct: 5   CNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQ 64

Query: 262 AWNGKEVDGKILYV 275
           A NG ++  K L V
Sbjct: 65  AMNGFQIGTKRLKV 78

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

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

 Score = 51.5 bits (124), Expect = 7e-09
 Identities = 25/64 (39%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
           NV+I+ L  +  ++ +      FG I+S K   D++    KGYGFV F++ EAA K+IE 
Sbjct: 2   NVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEG 61

Query: 171 VNGM 174
           +NG 
Sbjct: 62  LNGR 65

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

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

 Score = 51.5 bits (124), Expect = 7e-09
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 3/77 (3%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
           T +++        D+ L++ F  +G I    V+     GKSRG+GFV ++  E AE+A +
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 262 AWNGKEVDGKILYVGRA 278
             N   +DG+   V  A
Sbjct: 61  DPN-PIIDGRKANVNLA 76

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

>gnl|CDD|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 = 51.8 bits (125), Expect = 7e-09
 Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 2/54 (3%)

Query: 215 FNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGK 266
             +E ++ +FE YG I    ++   + G+S+G  FV + S E A+KA++A +GK
Sbjct: 11  ATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGK 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|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 51.6 bits (124), Expect = 7e-09
 Identities = 20/64 (31%), Positives = 35/64 (54%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ NLD  +  K + + F   G ++   + +D++G S+G G V FE    A ++I   N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 173 GMLL 176
           G +L
Sbjct: 61  GQML 64

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

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

 Score = 51.6 bits (124), Expect = 8e-09
 Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 5/79 (6%)

Query: 198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYR-VMNNDGKSRGFGFVAYESPEFA 256
           EK KLF    +         E+L+++F+ +G + S R V N  GK +G  +V YE+   A
Sbjct: 1   EKHKLF----VSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSA 56

Query: 257 EKAVQAWNGKEVDGKILYV 275
            +AV   +G E+  K + V
Sbjct: 57  SQAVLKMDGTEIKEKTISV 75

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

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

 Score = 51.5 bits (124), Expect = 8e-09
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           +++  L + +D K ++  F  FG I   ++  D +    +G+ FV FE  E A  +I+ +
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 172 NGMLLNSKIVFV 183
           N   L  + + V
Sbjct: 61  NESELFGRTIRV 72

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|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 = 51.5 bits (124), Expect = 8e-09
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 207 YIKNFGEDFNDEKLKEMFEPYGTI--TSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           +++N      +E+L+E+FE +G I      +     +S+GF FV++  PE A KA    +
Sbjct: 3   FVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELD 62

Query: 265 GKEVDGKILYV 275
           G    G++L+V
Sbjct: 63  GSIFQGRLLHV 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|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 51.4 bits (124), Expect = 8e-09
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           + + N   D  +E L+E+F   G +   ++  +  G+S G   V +E  E AE+A++ +N
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFN 62

Query: 265 GKEVDGKILYV 275
           G  +DG+ + V
Sbjct: 63  GVLLDGQPMQV 73

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|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 51.5 bits (124), Expect = 8e-09
 Identities = 20/75 (26%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYR-VMNND-GKSRGFGFVAYESPEFAEKAVQAW 263
           ++I       +++++KE+ E +G + ++  V ++  G S+G+ F  Y  P   ++A+   
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 264 NGKEVDGKILYVGRA 278
           NG ++  K L V RA
Sbjct: 63  NGMQLGDKKLTVQRA 77

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

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

 Score = 55.4 bits (133), Expect = 1e-08
 Identities = 37/131 (28%), Positives = 59/131 (45%), Gaps = 20/131 (15%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    +D  D +L  +F   G I + R+M +   G S G+ FV + S   +++A++
Sbjct: 108 TNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIK 167

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
             NG  V  K L V  A+   E  ++                   NLYV NL  +I D++
Sbjct: 168 NLNGITVRNKRLKVSYARPGGESIKD------------------TNLYVTNLPRTITDDQ 209

Query: 322 LRKEFTPFGTI 332
           L   F  +G I
Sbjct: 210 LDTIFGKYGQI 220

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           +F++NL     ++ + + FS  G I  C V +D      +G+G+V F  EE A +++E+ 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 172 NGMLLNSKIVFV 183
                  + + V
Sbjct: 62  KKTKFGGRKIHV 73

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

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

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 6/70 (8%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +++ N  +    E+L+ +FE YGT+T   V+ N      +GFV  E  E AE A++A NG
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN------YGFVHMEEEEDAEDAIKALNG 55

Query: 266 KEVDGKILYV 275
            E  GK + V
Sbjct: 56  YEFMGKRINV 65

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

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

 Score = 52.7 bits (126), Expect = 1e-08
 Identities = 27/72 (37%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           +FI  L    D+ ++ D F+ FG ++  KV  D E G S+G+GFV+F  E AA  +I ++
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 172 NGMLLNSKIVFV 183
           +G  LN + + V
Sbjct: 97  DGKELNGRHIRV 108

Length = 144

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

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 114 FIKNLDKS-IDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           F+  L K+  D   +   FS  G    C++A    G  +G+ FV + T E A ++ + +N
Sbjct: 6   FVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAEEAQQALN 65

Query: 173 GMLLN 177
           G  L 
Sbjct: 66  GHSLQ 70

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

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

 Score = 50.9 bits (122), Expect = 2e-08
 Identities = 23/73 (31%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
           N+ I  L +++ ++     F A G + +CK+ +D++ G S G+GFV +++ E A ++I  
Sbjct: 2   NLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT 61

Query: 171 VNGMLLNSKIVFV 183
           +NG+ L +K + V
Sbjct: 62  LNGLQLQNKRIKV 74

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

 Score = 50.4 bits (121), Expect = 2e-08
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 5/76 (6%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-----GKSRGFGFVAYESPEFAEKA 259
            ++I N      +  L ++F  YG I  +  + +      G+ RG+ FV +E+ E AEKA
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 260 VQAWNGKEVDGKILYV 275
           +++ NGK   GK L V
Sbjct: 61  LKSLNGKTALGKKLVV 76

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

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

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           +F+  L     + ++   FS FG I    V  D Q G S+GYGFV F+ +E+A ++ +  
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDP 62

Query: 172 N 172
           N
Sbjct: 63  N 63

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

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

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-----NNDGKSRGFGFVAYESPEFAEK 258
           TN+Y+ N      +E L + F  +G + S ++M         ++R  GFVA+ +   AE+
Sbjct: 2   TNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAER 61

Query: 259 AVQAWNGKEVDGKILYVG 276
           A+   +GK+V G  L +G
Sbjct: 62  ALDELDGKDVMGYELKLG 79

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 3/66 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           VY+ N G      +L++ FE YG + S  V  N     GF FV +E P  AE AV+A +G
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARN---PPGFAFVEFEDPRDAEDAVRALDG 58

Query: 266 KEVDGK 271
           + + G 
Sbjct: 59  RRICGN 64

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

 Score = 50.2 bits (120), Expect = 2e-08
 Identities = 23/72 (31%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAW 263
           +YI +    F +++LK+ F  +GT+ + RV  +   G S+ +GF+ + +PE A  A ++ 
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 264 NGKEVDGKILYV 275
           N   + GK+L V
Sbjct: 62  NNYLLMGKVLQV 73

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

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

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 4/70 (5%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +++ N   D  +E+ KE+F  YG ++   V  N  K  GFGF+  ++   AEKA    +G
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVS--EVFLNKEK--GFGFIRLDTRTNAEKAKAELDG 59

Query: 266 KEVDGKILYV 275
               G+ L V
Sbjct: 60  IMRKGRQLRV 69

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

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

 Score = 50.4 bits (120), Expect = 2e-08
 Identities = 24/66 (36%), Positives = 40/66 (60%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           ++++N   D   +KLKE F   G +    +   +GKS+G G V ++SPE AEKA +  NG
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKMENGKSKGCGTVRFDSPESAEKACRLMNG 61

Query: 266 KEVDGK 271
            +++G+
Sbjct: 62  IKINGR 67

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

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

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 18/68 (26%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
           N+++  L K++  + +   FS +G I++ ++  D   G S+G GF+ F+    A ++I+ 
Sbjct: 2   NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 171 VNGMLLNS 178
           +NG +   
Sbjct: 62  LNGTIPPG 69

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

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

 Score = 50.0 bits (119), Expect = 3e-08
 Identities = 24/69 (34%), Positives = 43/69 (62%), Gaps = 1/69 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEK 170
           N+FI +L +   +  +  TF  FG+++S KV  D+Q N SK +GFV ++  ++A  +I+ 
Sbjct: 6   NLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQA 65

Query: 171 VNGMLLNSK 179
           +NG  + +K
Sbjct: 66  MNGFQIGTK 74

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

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

 Score = 50.0 bits (120), Expect = 3e-08
 Identities = 20/54 (37%), Positives = 36/54 (66%), Gaps = 1/54 (1%)

Query: 131 FSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
           FS FG I SC+V +D++ G+S  Y F+ FET+E   ++  K++ +L++ + + V
Sbjct: 24  FSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRIHV 77

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

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

 Score = 49.9 bits (120), Expect = 4e-08
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 7/77 (9%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSR-------GFGFVAYESPEFA 256
           T +++KN      +E LK+ FE  G + S  +               G+GFV ++S E A
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 257 EKAVQAWNGKEVDGKIL 273
           +KA++   G  +DG  L
Sbjct: 61  QKALKRLQGTVLDGHAL 77

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

 Score = 49.2 bits (118), Expect = 6e-08
 Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           +F+  L      + + + FS +G I   ++ +D   G SKGY FV +E E  A ++    
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 172 NGMLLNSKIVFV 183
           + ++++   +FV
Sbjct: 66  HKLVIDGSEIFV 77

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

 Score = 48.7 bits (117), Expect = 7e-08
 Identities = 17/30 (56%), Positives = 24/30 (80%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           N+YVKNL + +DDE+L++ F  +G ITSAK
Sbjct: 3   NVYVKNLGEDMDDEKLKELFGKYGKITSAK 32

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

 Score = 48.7 bits (117), Expect = 7e-08
 Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           V+I +L        +   FS FG++   ++++  + G SKGY FV FE+ E A    E +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 172 NGMLLNSKIV 181
           N  LL  +++
Sbjct: 62  NNYLLFERLL 71

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score = 48.3 bits (115), Expect = 9e-08
 Identities = 22/71 (30%), Positives = 41/71 (57%), Gaps = 7/71 (9%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ N+D+    + +   F A+G++LSC V        + + FVH   E AA+++IE++N
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVM-------RQFAFVHLRGEAAADRAIEELN 55

Query: 173 GMLLNSKIVFV 183
           G  L+ + + V
Sbjct: 56  GRELHGRKLVV 66

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

 Score = 48.5 bits (116), Expect = 9e-08
 Identities = 18/58 (31%), Positives = 30/58 (51%)

Query: 115 IKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +KNL   + N+ +   FS FG +    V  D++G S G G V F  +  A  +I++ +
Sbjct: 4   VKNLSPFVSNELLEQAFSQFGEVERAVVIVDDRGRSTGEGIVEFSRKPGAQAAIKRCS 61

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

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

 Score = 48.6 bits (116), Expect = 9e-08
 Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 4/75 (5%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQA 262
           VY+ +   +  ++ +++ F P+G I S   M+ D    K +GF FV YE PE A+ A++ 
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSID-MSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 263 WNGKEVDGKILYVGR 277
            NG  + G+ + VGR
Sbjct: 62  MNGVMLGGRNIKVGR 76

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

 Score = 48.7 bits (116), Expect = 9e-08
 Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 218 EKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG 276
            KLK++F  YG +    +     GK  GF FV  +  + AE A++  NG E+DG+ + V 
Sbjct: 16  VKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVD 75

Query: 277 RAQKK 281
            A +K
Sbjct: 76  WAVQK 80

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

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

 Score = 48.6 bits (116), Expect = 9e-08
 Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 3/64 (4%)

Query: 217 DEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILY 274
           D  L+  F  YG +T   VM   N  +SRGFGF+ + S + A++A++A     +DG  + 
Sbjct: 16  DSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA-QPHSIDGNQIE 74

Query: 275 VGRA 278
           + RA
Sbjct: 75  LKRA 78

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

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

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 7/71 (9%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ NL  +  ++ +   F  +G++  C V        K YGFVH E EE A  +I+ +N
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVV-------KNYGFVHMEEEEDAEDAIKALN 54

Query: 173 GMLLNSKIVFV 183
           G     K + V
Sbjct: 55  GYEFMGKRINV 65

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

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

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 6/71 (8%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVA------QDEQGNSKGYGFVHFETEEAANK 166
           +F+KNL+     + +   F   G + S  +A         +  S GYGFV F+++EAA K
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 167 SIEKVNGMLLN 177
           +++++ G +L+
Sbjct: 63  ALKRLQGTVLD 73

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|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 = 48.3 bits (115), Expect = 1e-07
 Identities = 25/75 (33%), Positives = 45/75 (60%), Gaps = 2/75 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
           V++ N   +  +E+LK++F   G + S+R++ +   GK +G+GF  Y+  E A  A++  
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 264 NGKEVDGKILYVGRA 278
           NG E++G+ L V  A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

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

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +++ NLD+++    + + FS  G I SCK+ ++   +   Y FV +    +A  +++ +N
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP--YAFVEYYDHRSAAAALQTMN 58

Query: 173 GMLLNSKIVFVG 184
           G L+  + + V 
Sbjct: 59  GRLILGQEIKVN 70

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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 48.0 bits (114), Expect = 1e-07
 Identities = 23/66 (34%), Positives = 40/66 (60%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           ++++N   DF  + LK+ F   G +    +   +GKS+G G V +ESPE AE+A +  NG
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVRFESPEVAERACRMMNG 61

Query: 266 KEVDGK 271
            +++G+
Sbjct: 62  YKLNGR 67

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 48.1 bits (115), Expect = 2e-07
 Identities = 24/80 (30%), Positives = 48/80 (60%), Gaps = 3/80 (3%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTI-TSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
           N++I N   + +++ L + F  +G I  + ++M +   G S+GF F++Y+S E ++ A++
Sbjct: 3   NLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62

Query: 262 AWNGKEVDGKILYVGRAQKK 281
           A NG+ +  + + V  A KK
Sbjct: 63  AMNGQYLCNRPITVSYAFKK 82

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

 Score = 47.5 bits (114), Expect = 2e-07
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 207 YIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWN 264
           Y+ +   D  +  L E+F P G + S RV  +    +S G+ +V +++P  AE+A+   N
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 265 GKEVDGKILYVGRAQK 280
              + GK + +  +Q+
Sbjct: 63  FDVIKGKPIRIMWSQR 78

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 23/55 (41%), Positives = 33/55 (60%), Gaps = 1/55 (1%)

Query: 131 FSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG 184
           F  FG I   ++ +D E G SKGYGF+ F   E A K++E++NG  L  + + VG
Sbjct: 19  FEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFELAGRPIKVG 73

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

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 4/72 (5%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKV--AQDEQGNSK--GYGFVHFETEEAANKSI 168
           ++++NLD  +D   +   FS FG + S ++   QDE+      G+ FV F+   +A  ++
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 169 EKVNGMLLNSKI 180
           +     L   KI
Sbjct: 63  QLNGTELGGRKI 74

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|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 = 47.6 bits (114), Expect = 2e-07
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           VF+ N+      + + + FS  G ++S ++  D + G  KGYGF  FE  E A  +I  +
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 172 NGMLLNSKIVFVG 184
           NG   N + + V 
Sbjct: 61  NGYEFNGRALRVD 73

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|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 47.8 bits (113), Expect = 2e-07
 Identities = 21/67 (31%), Positives = 36/67 (53%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           N++I NL  S+D + + +    FG ++S ++ +D  G S+G GF   E+ E     I+  
Sbjct: 3   NLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQHF 62

Query: 172 NGMLLNS 178
           NG  L +
Sbjct: 63  NGKYLKT 69

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRV-MNND-GKSRGFGFVAYESPEFAEKAVQAW 263
           +Y+    E+ +++ L   F P+G I   ++ ++ +  K RGF FV +E PE A  A+   
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 264 NGKEVDGKILYV 275
           N  E+ G+ + V
Sbjct: 61  NESELFGRTIRV 72

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 19/68 (27%), Positives = 35/68 (51%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           + + NL   +  + + + F   G +   K+  D  G S+G   V FE  E A ++I++ N
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQFN 62

Query: 173 GMLLNSKI 180
           G+LL+ + 
Sbjct: 63  GVLLDGQP 70

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

 Score = 47.5 bits (113), Expect = 2e-07
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 6/70 (8%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +++ N  ED + E+L+ +FE YG + S  VM      R F FV       A++A++  NG
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVM------RQFAFVHLRGEAAADRAIEELNG 56

Query: 266 KEVDGKILYV 275
           +E+ G+ L V
Sbjct: 57  RELHGRKLVV 66

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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 48.3 bits (114), Expect = 2e-07
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
           TN+YI+    +  D+ L ++ +PYG I S + +      K +G+GFV ++SP  A+KAV 
Sbjct: 8   TNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVS 67

Query: 262 AWNGKEVDGKI 272
           A     V  ++
Sbjct: 68  ALKASGVQAQM 78

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 1/69 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           +F+ NL  ++ +K + + FS FG + SC V  D E G SKGYGFV F + +    +++K 
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQKQ 61

Query: 172 NGMLLNSKI 180
             +L  +K+
Sbjct: 62  KHILEGNKL 70

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

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

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 24/62 (38%), Positives = 33/62 (53%), Gaps = 6/62 (9%)

Query: 216 NDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQA----WNGKEVD 269
            D+ LK  F  +G IT   VM   N  +SRGFGFV + S    + A+ A     +G+EV+
Sbjct: 12  TDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNARPHKVDGREVE 71

Query: 270 GK 271
            K
Sbjct: 72  PK 73

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

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 24/67 (35%), Positives = 41/67 (61%), Gaps = 2/67 (2%)

Query: 118 LDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLL 176
           L+  +D   +Y  F+  G + S K+ +++Q G S GYGFV F T EAA ++++ +NG  +
Sbjct: 7   LEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPI 66

Query: 177 -NSKIVF 182
            N++  F
Sbjct: 67  PNTQQRF 73

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

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

 Score = 47.1 bits (113), Expect = 2e-07
 Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 220 LKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV 275
           L ++F P+G +   +++    K  GF FV + + E AEKAVQ  NG    G+ L V
Sbjct: 1   LYKLFSPFGNVEKIKLL---KKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 53

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

 Score = 47.6 bits (113), Expect = 2e-07
 Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 2/69 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
            N+Y+    +    ++L+++F  YG I + R++ +   G SRG GF+ ++    AE+A++
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 262 AWNGKEVDG 270
             NG++ +G
Sbjct: 61  GLNGQKPEG 69

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

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

 Score = 52.3 bits (125), Expect = 2e-07
 Identities = 58/237 (24%), Positives = 95/237 (40%), Gaps = 60/237 (25%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           VF+  + + +    +   F   G I   ++  D  G ++GY FV F  +E A ++++ +N
Sbjct: 61  VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLN 120

Query: 173 ------GMLLNSKI------VFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKL 220
                 G LL   I      +FVG     K+RE+ L E +K+   V              
Sbjct: 121 NYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVV------------- 167

Query: 221 KEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKA--------VQAWNGKEVDGKI 272
                    +  Y    +  K+RGF FV YES   A  A        +Q W      G +
Sbjct: 168 --------DVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLW------GHV 213

Query: 273 LYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPF 329
           + V  A+ + E  +++      +KI          LYV+NL  +  +E + K F+ F
Sbjct: 214 IAVDWAEPEEEVDEDV---MAKVKI----------LYVRNLMTTTTEEIIEKSFSEF 257

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

 Score = 47.8 bits (113), Expect = 2e-07
 Identities = 30/75 (40%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW 263
           ++I     +  DE L+  FE +GT+T   VM   N  +SRGFGFV Y S E  + A+ A 
Sbjct: 5   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNAR 64

Query: 264 NGKEVDGKILYVGRA 278
             K VDG+++   RA
Sbjct: 65  PHK-VDGRVVEPKRA 78

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

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

 Score = 47.2 bits (113), Expect = 3e-07
 Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 7/80 (8%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYR-VMNND-GKSRGFGFVAYESPEFAEKAVQAW 263
           V+I+N   D  +E+LKE+F  +G +   R V +   G S+G  FV +++ E A+K ++A 
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 264 NGKE-----VDGKILYVGRA 278
           +  E     +DG+ L V  A
Sbjct: 63  DNAEDSGLSLDGRRLIVTLA 82

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

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 47.4 bits (112), Expect = 3e-07
 Identities = 20/67 (29%), Positives = 35/67 (52%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           N++I NL  S+D + + +    FG ++S ++ +D  G S+G GF   E+ E     I   
Sbjct: 2   NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISHF 61

Query: 172 NGMLLNS 178
           NG  + +
Sbjct: 62  NGKFIKT 68

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

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

 Score = 47.0 bits (112), Expect = 3e-07
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           +++ N       +KLKE+F+  G +    +  + +GKSRG G V +E P  A +A+  +N
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAISMFN 60

Query: 265 GKEVDGKILYV 275
           G+ +  + + V
Sbjct: 61  GQMLFDRPMRV 71

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

>gnl|CDD|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 = 47.3 bits (113), Expect = 3e-07
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 208 IKNFGEDFNDEKLKEMF-EPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +KN      + +LKE F +  G IT  +++   DGKSR   F+ Y++ E A+KA   +N 
Sbjct: 5   VKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYFNN 64

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|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 47.1 bits (111), Expect = 3e-07
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
           TN+YI+       D+ L ++ +PYG I S + +   N  + +G+GFV ++SP  A+KAV 
Sbjct: 5   TNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVA 64

Query: 262 AWNGKEVDGKI 272
           +     V  ++
Sbjct: 65  SLKANGVQAQM 75

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

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

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANKSIEK 170
            +F+ NL    D   ++  FS FG++ + KV +D   N  KGYGFV     E A  +I  
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 171 VNGMLLNSKIVFV 183
           +NG  L  +++ V
Sbjct: 63  LNGYRLGGRVLQV 75

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

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 46.7 bits (110), Expect = 4e-07
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
           TN+YI+       D+ L ++ +PYG I S + +      K +G+GFV ++SP  A+KAV 
Sbjct: 2   TNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 61

Query: 262 AWNGKEVDGKI 272
           A     V  ++
Sbjct: 62  ALKASGVQAQM 72

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

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

 Score = 46.9 bits (111), Expect = 4e-07
 Identities = 19/71 (26%), Positives = 39/71 (54%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ NL+  +  + +Y+ F   G +    + +D++G  K +GFV F+  E+   +I  +N
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63

Query: 173 GMLLNSKIVFV 183
           G+ L  + + V
Sbjct: 64  GIRLYGRPIKV 74

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

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

 Score = 47.0 bits (111), Expect = 4e-07
 Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 1/78 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L +++  + +   F + G I SCK+ +D+  G S GYGFV++   + A K+I  
Sbjct: 6   NLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 65

Query: 171 VNGMLLNSKIVFVGKFIP 188
           +NG+ L +K + V    P
Sbjct: 66  LNGLRLQTKTIKVSYARP 83

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

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

 Score = 46.4 bits (110), Expect = 5e-07
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 4/75 (5%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAW 263
           ++I     +  D+ L+E F  +G +T   VM +   G+SRGFGF+ ++ P+   + ++  
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 264 NGKEVDGKILYVGRA 278
           +   +DGKI+   RA
Sbjct: 61  H--ILDGKIIDPKRA 73

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

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

 Score = 46.4 bits (110), Expect = 5e-07
 Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 2/64 (3%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
           TN+Y+ N      +++L+++FE YG I    ++ +   G  RG  FV Y+  E A+ A+ 
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 262 AWNG 265
           + NG
Sbjct: 61  SLNG 64

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

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

 Score = 46.4 bits (110), Expect = 6e-07
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEK 170
           N+FI +L +   +  +   F  FG+++S KV  D   N SK +GFV F+   +A  +I+ 
Sbjct: 6   NLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA 65

Query: 171 VNGMLLNSK 179
           +NG  +  K
Sbjct: 66  MNGFQIGMK 74

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

>gnl|CDD|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 = 46.4 bits (111), Expect = 6e-07
 Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           +F+  L K+   + +   F  +G+I    + +D+  G SKG  FV F + E A K+IE +
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 172 NGM 174
           +G 
Sbjct: 62  HGK 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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 46.3 bits (110), Expect = 6e-07
 Identities = 25/75 (33%), Positives = 42/75 (56%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+  +D   +   +   FS +G++   K+  D  G SKGYGFV FET+E A K +++ N
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEAN 64

Query: 173 GMLLNSKIVFVGKFI 187
            +    K + +G+ I
Sbjct: 65  RLCFRDKKLNIGQAI 79

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

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

 Score = 46.1 bits (109), Expect = 7e-07
 Identities = 29/77 (37%), Positives = 45/77 (58%), Gaps = 3/77 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GKSRGFGFVAYESPEFAEKAVQAWN 264
           +++K   ED  +E LKE F+  G+I +  V + D G S+GFGFV + S E A+ A +A  
Sbjct: 3   LFVKGLSEDTTEETLKESFD--GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAME 60

Query: 265 GKEVDGKILYVGRAQKK 281
             E+DG  + +  A+ K
Sbjct: 61  DGEIDGNKVTLDFAKPK 77

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

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 46.2 bits (109), Expect = 7e-07
 Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 2/81 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW 263
           +++ N   D ++  L +MF P+G +T+ +V+   N  K +GFGFV   + + A  A+ + 
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           NG  +  ++L V     K  +
Sbjct: 66  NGYRLGDRVLQVSFKTNKTHK 86

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 46.0 bits (109), Expect = 7e-07
 Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           +F++NL  S+  + + D FS    I    V  D + G S+GYGFV F   E A +++ K+
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 172 NGMLLNSKIV 181
               L+ +I+
Sbjct: 62  KNKKLHGRIL 71

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

 Score = 50.5 bits (120), Expect = 8e-07
 Identities = 28/118 (23%), Positives = 54/118 (45%), Gaps = 10/118 (8%)

Query: 80  ALDTMNFDALKGRPIRIMWSQRDPSLRK---------SGVGNVFIKNLDKSIDNKAMYDT 130
           AL+ MN   L GR I++      P  +               +++ ++   +    +   
Sbjct: 165 ALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSV 224

Query: 131 FSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI 187
           F AFG I+ C++A+   G   KGYGF+ +   ++ +++I  +N   L  + + VGK +
Sbjct: 225 FEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV 282

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

>gnl|CDD|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 = 45.8 bits (109), Expect = 8e-07
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 6/69 (8%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           VF+  LD ++    +   F  FG I+  K+        KG GFV F    AA  +I+++ 
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIP-----PGKGCGFVQFVHRAAAEAAIQQLQ 58

Query: 173 G-MLLNSKI 180
           G ++  S+I
Sbjct: 59  GTIIGGSRI 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 45.2 bits (108), Expect = 9e-07
 Identities = 16/67 (23%), Positives = 42/67 (62%), Gaps = 1/67 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           ++++NL  S+  + + + FS +G +   ++ +++    +G+ FV F + E A  +++K+N
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59

Query: 173 GMLLNSK 179
           G++L+ +
Sbjct: 60  GLVLDGR 66

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

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

 Score = 45.8 bits (109), Expect = 9e-07
 Identities = 21/69 (30%), Positives = 38/69 (55%)

Query: 115 IKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGM 174
           +KNL K I    +   F AFG+I   ++   + G  + +GFV ++TEE A K+++  N  
Sbjct: 5   VKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNS 64

Query: 175 LLNSKIVFV 183
            +++  + V
Sbjct: 65  FIDTSKITV 73

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

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

 Score = 46.2 bits (109), Expect = 9e-07
 Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIE 169
            N+FI +L +   ++ +   F  FG+++S KV  D+Q N SK +GFV ++   +A  +I+
Sbjct: 8   ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 67

Query: 170 KVNGMLLNSK 179
            +NG  +  K
Sbjct: 68  AMNGFQIGMK 77

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

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

 Score = 45.7 bits (109), Expect = 9e-07
 Identities = 26/62 (41%), Positives = 39/62 (62%), Gaps = 2/62 (3%)

Query: 216 NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
            +  L+E+F  YG I   +V+     G+SRGFGFV +ES E A++A +  NG E+DG+ +
Sbjct: 12  TERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRRI 71

Query: 274 YV 275
            V
Sbjct: 72  RV 73

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

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

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    ++   ++++ +F   G I S +++     G+S G+GFV Y  PE AEKA+ 
Sbjct: 2   TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61

Query: 262 AWNGKEVDGKILYVGRA 278
             NG  +  K + V  A
Sbjct: 62  TLNGLRLQNKTIKVSYA 78

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

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 45.8 bits (108), Expect = 1e-06
 Identities = 20/62 (32%), Positives = 32/62 (51%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           N++I NL  S+D + +      FG ++S ++ +D  G S+G GF   E+ E     I   
Sbjct: 2   NLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCEAIITHF 61

Query: 172 NG 173
           NG
Sbjct: 62  NG 63

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

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

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 20/71 (28%), Positives = 42/71 (59%), Gaps = 2/71 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYR-VMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           V++ N      +++L+++F   G IT  R V N  GKS+G+ +V +E+ E  ++A+   +
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEAL-KLD 60

Query: 265 GKEVDGKILYV 275
            + + G+ ++V
Sbjct: 61  RELIKGRPMFV 71

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

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 45.4 bits (107), Expect = 1e-06
 Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANKSIEKV 171
           +FI NL +  D   ++  F  FG++ + KV +D   N  KG+GFV     E A  +I  +
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 172 NGMLLNSKIVFV 183
           NG  L  KI+ V
Sbjct: 64  NGYRLGDKILQV 75

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 6/56 (10%)

Query: 218 EKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
           E L+E+F  YG I    +       +G+GFV +++ E A  AV   NG+E+ G+ L
Sbjct: 16  EDLEEIFSKYGKILGISL------HKGYGFVQFDNEEDARAAVAGENGREIAGQKL 65

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

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

 Score = 44.9 bits (107), Expect = 1e-06
 Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 8/68 (11%)

Query: 113 VFIKNLDKSIDNKA-MYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           VF+ NL+    +K  + + FS +G IL   +        KGYGFV F+ EE A  ++   
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISL-------HKGYGFVQFDNEEDARAAVAGE 55

Query: 172 NGMLLNSK 179
           NG  +  +
Sbjct: 56  NGREIAGQ 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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 214 DFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK 271
           D  + KL+  FE YG I   R++ +   GK RG+ F+ +E     + A +  +GK++DG+
Sbjct: 12  DTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYADGKKIDGR 71

Query: 272 ILYV----GRAQK 280
            + V    GR  K
Sbjct: 72  RVLVDVERGRTVK 84

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

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 2/61 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTI--TSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           VY++   ++   E LK +F  YGT+   S     + G  +GF F+ +E+PE A+KA +  
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 264 N 264
           N
Sbjct: 62  N 62

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 19/60 (31%), Positives = 33/60 (55%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+  L K  +   +   F+ FGSI  C V +D+ G S+G  FV F + + A  +I+ ++
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMH 63

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 15/30 (50%), Positives = 21/30 (70%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           N+++KNLD SID++ L   F+ FG I S K
Sbjct: 4   NIFIKNLDKSIDNKALYDTFSAFGNILSCK 33

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

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 114 FIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVN 172
            + NL     ++   +  S FG++  C +   E  G SKGYGFV + ++ +A K+  +++
Sbjct: 3   CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 173 GMLLNSKIVFV 183
           G  +  + + V
Sbjct: 63  GKQIGGRKLQV 73

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

>gnl|CDD|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 = 45.2 bits (107), Expect = 2e-06
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIE 169
           G +FI  L    + +++   FS +G I    V +D +   S+G+GFV FE  + A  ++ 
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 170 KVNGMLLNSKIVFV 183
            +NG  ++ + + V
Sbjct: 61  AMNGKSVDGRQIRV 74

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

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

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 23/69 (33%), Positives = 41/69 (59%), Gaps = 2/69 (2%)

Query: 214 DFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKI 272
           D  +E+L++ F  +G++   +++ +  G S+G+GFV +E+ E AEK +   N     GK 
Sbjct: 13  DTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILAMGN-LNFRGKK 71

Query: 273 LYVGRAQKK 281
           L +G A +K
Sbjct: 72  LNIGPAIRK 80

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

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 23/70 (32%), Positives = 40/70 (57%), Gaps = 2/70 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAW 263
           VYI +    F + +L++ F  +GT+T  R+  +   GKS+G+ FV +ESPE A+   +  
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 264 NGKEVDGKIL 273
           N   +  ++L
Sbjct: 62  NNYLLFERLL 71

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score = 44.5 bits (105), Expect = 2e-06
 Identities = 19/63 (30%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
           N+++  L K++  K +   FS +G I++ ++ +D+  G S+G GF+ F+    A ++I+ 
Sbjct: 2   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKG 61

Query: 171 VNG 173
           +NG
Sbjct: 62  LNG 64

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

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

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 2/78 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    ++   E+LK +F   G I S +++ +   G+S G+GFV Y  P+ AEKA+ 
Sbjct: 5   TNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 64

Query: 262 AWNGKEVDGKILYVGRAQ 279
             NG  +  K + V  A+
Sbjct: 65  TLNGLRLQTKTIKVSYAR 82

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

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

 Score = 44.9 bits (106), Expect = 2e-06
 Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
           N+++ NL + +    +   F A+G+I+ C + +D+  G  +G  FV ++  E A  +I  
Sbjct: 2   NLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 171 VNGML 175
           +NG +
Sbjct: 62  LNGTI 66

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

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 45.1 bits (106), Expect = 2e-06
 Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L +++  +     F + G I SCK+ +D+  G S GYGFV++     A+K+I  
Sbjct: 5   NLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

Query: 171 VNGMLLNSKIVFVGKFIP 188
           +NG+ L +K + V    P
Sbjct: 65  LNGLKLQTKTIKVSYARP 82

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 2/67 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKV 171
           +FI    KS+    + + F+ FG I    V +D+Q   SKG  +V F    +A +++E++
Sbjct: 6   LFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEM 64

Query: 172 NGMLLNS 178
           NG  L  
Sbjct: 65  NGKCLGG 71

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 27/74 (36%), Positives = 45/74 (60%), Gaps = 2/74 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSY-RVMN-NDGKSRGFGFVAYESPEFAEKAVQ 261
           T V++ N  E  +D+ ++++ E  G + S+ RV + + GK + FGF  +E PE A +A++
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 262 AWNGKEVDGKILYV 275
             NG E+ GK L V
Sbjct: 61  LLNGLELGGKKLLV 74

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

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

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 23/74 (31%), Positives = 43/74 (58%), Gaps = 2/74 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSA-FGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
           +F+ +L   + +  + +TF A + S+   KV  D   G SKGYGFV F  E+  ++++ +
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 171 VNGMLLNSKIVFVG 184
           +NG+  +S+ + V 
Sbjct: 64  MNGVYCSSRPMRVS 77

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

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

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 2/52 (3%)

Query: 213 EDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQA 262
           ED  +E L+E F  YG + S  ++ +   GK RGF FV ++  +  +K V  
Sbjct: 9   EDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

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

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYR-VMNNDGKSRGFGFVAYESPEFAEKAVQ 261
              V++     D  +++L  +FE  G I   R +M+  G +RG+ FV Y + E A++AV+
Sbjct: 1   GCEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAVK 60

Query: 262 AWNGKEVD-GKILYV 275
             +  E+  GK L V
Sbjct: 61  QLHNYEIRPGKRLGV 75

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

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

 Score = 44.8 bits (106), Expect = 2e-06
 Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGK------SRGFGFVAYESPEFAEK 258
           +++KN      ++ L + F+        RV    D K      S GFGFV +++ E A+ 
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 259 AVQAWNGKEVDGKILYVGRAQK 280
           A++A +G  +DG  L V  + +
Sbjct: 63  ALKAMDGFVLDGHTLVVKFSHR 84

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

>gnl|CDD|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 = 44.2 bits (105), Expect = 3e-06
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAF-GSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           + +KNL  S+    + + FS   G I   K+ + E G S+   F+ ++TEE A K+ +  
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKDYF 62

Query: 172 NGMLLN-SKIV 181
           N   +N SKI 
Sbjct: 63  NNTYINTSKIS 73

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

 Score = 44.7 bits (105), Expect = 3e-06
 Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L +++  +     F + G I SCK+ +D+  G S GYGFV++   + A K+I  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 171 VNGMLLNSKIVFVGKFIP 188
           +NG+ L +K + V    P
Sbjct: 64  LNGLRLQTKTIKVSYARP 81

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate dead end protein homolog 1 (DND1)

 Score = 44.4 bits (105), Expect = 3e-06
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWN 264
           V+I    +D  +++L  +F+  GT+  +R+M    G +RGF +  Y     A  A+   +
Sbjct: 4   VFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAIATLH 63

Query: 265 GKEV-DGKILYVGRA 278
             E+ +G  L V R+
Sbjct: 64  NYELPEGCCLLVCRS 78

This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 44.3 bits (105), Expect = 3e-06
 Identities = 20/62 (32%), Positives = 37/62 (59%), Gaps = 1/62 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           +F+ NL    D  ++Y+ F  +G I S ++  D + G  KG+G+V F ++EAA  +++ +
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 172 NG 173
            G
Sbjct: 61  GG 62

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

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

 Score = 44.3 bits (104), Expect = 3e-06
 Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 5/69 (7%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           V+   +   +  + M  TFS FG I+  +V  D     KGY FV F + E+A  +I  VN
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD-----KGYSFVRFNSHESAAHAIVSVN 57

Query: 173 GMLLNSKIV 181
           G  +   +V
Sbjct: 58  GTTIEGHVV 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|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 44.3 bits (104), Expect = 3e-06
 Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L +++    +   FS+ G + S K+ +D+  G+S GYGFV++   + A ++I  
Sbjct: 3   NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT 62

Query: 171 VNGMLLNSKIVFV 183
           +NG+ L SK + V
Sbjct: 63  LNGLRLQSKTIKV 75

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

>gnl|CDD|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 = 44.1 bits (105), Expect = 3e-06
 Identities = 19/60 (31%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQA 262
           T + ++N   +   ++L+E+F P+G + S R+    DG  RGF FV + + + A+ A++A
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEA 60

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

 Score = 44.3 bits (104), Expect = 3e-06
 Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
           ++I     +  D+ L+E FE +GT+T   VM +    +SRGFGFV Y   E  + A+ A 
Sbjct: 5   LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSAR 64

Query: 264 NGKEVDGKILYVGRA 278
             K VDG+++   RA
Sbjct: 65  PHK-VDGRVVEPKRA 78

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

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

 Score = 44.1 bits (105), Expect = 4e-06
 Identities = 17/67 (25%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 114 FIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVN 172
           ++ +L   +    +Y+ FS  G +LS +V +D     S GY +V+F+    A ++++ +N
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 173 GMLLNSK 179
             ++  K
Sbjct: 63  FDVIKGK 69

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

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

 Score = 43.4 bits (103), Expect = 4e-06
 Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 114 FIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVN 172
           F++NL  +   + + + F AFG I    +  D++   SKG+ FV F   E A K+  +++
Sbjct: 3   FVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELD 62

Query: 173 GMLLNSKIVFV 183
           G +   +++ V
Sbjct: 63  GSIFQGRLLHV 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|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           +FI  L   +    + +   +FG + +  + +D   G SKGY F  +      +++I  +
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 172 NGMLLNSKIVFV 183
           NGM L  K + V
Sbjct: 63  NGMQLGDKKLTV 74

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

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

 Score = 43.6 bits (103), Expect = 4e-06
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 130 TFSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK 185
            FS FG I S  ++ D      KG+ FV +E  EAA  ++E++NG++L  + + VG+
Sbjct: 20  AFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIKVGR 76

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

 Score = 43.7 bits (103), Expect = 4e-06
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 7/67 (10%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ N+  +  +  +   F  FG ++ C          K Y FVH E EE A  +IE +N
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKV-------KDYAFVHMEREEEALAAIEALN 55

Query: 173 GMLLNSK 179
           G  +  +
Sbjct: 56  GKEVKGR 62

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|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 43.8 bits (103), Expect = 4e-06
 Identities = 24/71 (33%), Positives = 38/71 (53%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           VF+ NLD  +  K + + FS  G ++   + +D+ G S+G G V FE    A ++I   N
Sbjct: 3   VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISMFN 62

Query: 173 GMLLNSKIVFV 183
           G LL  + + V
Sbjct: 63  GQLLFDRPMHV 73

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 44.3 bits (104), Expect = 4e-06
 Identities = 21/81 (25%), Positives = 42/81 (51%), Gaps = 2/81 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW 263
           +++ N   D ++  L ++F P+G + + +V+   N  K +GFGFV   + + A  A+ + 
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           NG  +  ++L V     K  +
Sbjct: 66  NGYRLGDRVLQVSFKTNKTHK 86

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 19/69 (27%), Positives = 35/69 (50%)

Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
             + + NLD  + +  + + F+ FG++    V  D  G S G   V FE    A K++++
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60

Query: 171 VNGMLLNSK 179
            NG+ L+ +
Sbjct: 61  YNGVPLDGR 69

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +Y++N     + E+L ++F  YG I   R+  N  ++RG  FV YE    A+ A    +G
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRI-GNTKETRGTAFVVYEDIYDAKNACDHLSG 63

Query: 266 KEVDGKILYVG 276
             V  + L V 
Sbjct: 64  FNVANRYLVVL 74

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

 Score = 47.6 bits (113), Expect = 5e-06
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANKSIEKV 171
           +F+ NL    D   ++  F  FG++ + K+ +D   N  KGYGFV     + A  +I  +
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 172 NGMLLNSKIVFV 183
           NG  L ++++ V
Sbjct: 332 NGYTLGNRVLQV 343

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

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

 Score = 45.4 bits (107), Expect = 5e-06
 Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 2/88 (2%)

Query: 196 LGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESP 253
           LG    + T ++I       +D  L++ F  +G +   +V+     G+SRGFGFV +   
Sbjct: 27  LGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDE 86

Query: 254 EFAEKAVQAWNGKEVDGKILYVGRAQKK 281
             A  A+   +GKE++G+ + V  A  +
Sbjct: 87  GAATAAISEMDGKELNGRHIRVNPANDR 114

Length = 144

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

 Score = 43.6 bits (103), Expect = 5e-06
 Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           ++I +L      K +   FS FG++ + +VA+ ++ GNSK YGF+ F   E A  + + +
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 172 NGMLLNSKIVFV 183
           N  LL  K++ V
Sbjct: 62  NNYLLMGKVLQV 73

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

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

 Score = 43.7 bits (103), Expect = 5e-06
 Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
           ++++N       E L + F     I    V+ +   G+SRG+GFV +   E A++A+   
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 264 NGKEVDGKILYVGRAQKK 281
             K++ G+IL +  A+++
Sbjct: 62  KNKKLHGRILRLDIAERR 79

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

>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 43.3 bits (103), Expect = 5e-06
 Identities = 19/67 (28%), Positives = 37/67 (55%), Gaps = 5/67 (7%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKS-RGFGFVAYESPEFAEKAVQA-- 262
           VY+K F +D   + ++E FE +G + + R+  +  K  +G  FV +++ E A+K ++   
Sbjct: 2   VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEKEK 61

Query: 263 --WNGKE 267
             +  KE
Sbjct: 62  LKYKEKE 68

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

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

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+  L   +  + + + FS  G IL   + +     +  + F+ FE E+AA +++E  N
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTN-AFAFIKFEREQAAARAVESEN 64

Query: 173 G-MLLNSKI 180
             ML N  +
Sbjct: 65  HSMLKNKTM 73

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

 Score = 43.6 bits (103), Expect = 5e-06
 Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 6/63 (9%)

Query: 218 EKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQA----WNGKEVDGK 271
           E L+E F  +G I    VM      +SRGFGFV +  P   +K +       +GK++D K
Sbjct: 13  EGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGPHELDGKKIDPK 72

Query: 272 ILY 274
           + +
Sbjct: 73  VAF 75

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

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

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 9/73 (12%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
           +++ + G +  DE L   F  Y +    +V+ +   GKS+G+GFV++  P    KA++  
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 264 NGKEVDGKILYVG 276
           NGK       YVG
Sbjct: 69  NGK-------YVG 74

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

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

 Score = 43.3 bits (102), Expect = 6e-06
 Identities = 23/78 (29%), Positives = 45/78 (57%), Gaps = 3/78 (3%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV 171
           +FI  L+    + ++ + F  FG +  C V +D   G S+G+GF+ F+  ++ N+ ++K 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 172 NGMLLNSKIVFVGKFIPR 189
           +  +L+ KI+   + IPR
Sbjct: 61  H--ILDGKIIDPKRAIPR 76

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

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

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 4/70 (5%)

Query: 211 FGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
            G    +E LK+ F P+G I +     +  K +  GFV +E  E A++A+   NG  V G
Sbjct: 10  HGYGLTEEILKKAFSPFGNIINI----SMEKEKNCGFVTFEKMESADRAIAELNGTTVQG 65

Query: 271 KILYVGRAQK 280
             L V  A+K
Sbjct: 66  VQLKVSLARK 75

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 43.3 bits (102), Expect = 6e-06
 Identities = 18/62 (29%), Positives = 35/62 (56%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+  L+K    K + + FS +G +    + +DE   S+G  FV + ++E A  +I+ +N
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61

Query: 173 GM 174
           G+
Sbjct: 62  GV 63

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 43.3 bits (102), Expect = 7e-06
 Identities = 27/73 (36%), Positives = 44/73 (60%), Gaps = 3/73 (4%)

Query: 212 GEDF--NDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWNGKEV 268
           G DF  N+  L++ F  YGT+   +++N+  G S+G+GFV +E+ E A+K +Q  N    
Sbjct: 9   GIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEANRLCF 68

Query: 269 DGKILYVGRAQKK 281
             K L +G+A +K
Sbjct: 69  RDKKLNIGQAIRK 81

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

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

 Score = 43.1 bits (102), Expect = 7e-06
 Identities = 21/68 (30%), Positives = 40/68 (58%), Gaps = 2/68 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
           +++ N   D +++ + E F  YG I+S R+  +   G+ +GFG+V + S E A+ A+ A 
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 264 NGKEVDGK 271
            G ++ G+
Sbjct: 61  GGTDLLGR 68

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

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

 Score = 43.4 bits (102), Expect = 8e-06
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 2/80 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           +F+  L   +    + + FS FG +   +V  D+Q G  +G+GFV+F+  ++A+K+   V
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA-VV 60

Query: 172 NGMLLNSKIVFVGKFIPRKE 191
               +N   V V K +P++E
Sbjct: 61  KFHPINGHRVEVKKAVPKEE 80

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 42.7 bits (100), Expect = 8e-06
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 5/69 (7%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           V+   +   +  + M  TFS FG I+  +V  +     KGY F+ F T E+A  +I  VN
Sbjct: 3   VYCGGIASGLTEQLMRQTFSPFGQIMEIRVFPE-----KGYSFIRFSTHESAAHAIVSVN 57

Query: 173 GMLLNSKIV 181
           G  +   +V
Sbjct: 58  GTTIEGHVV 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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 43.2 bits (101), Expect = 9e-06
 Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    ++   E+ + +F   G I S +++ +   G+S G+GFV Y  P+ AEKA+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 262 AWNGKEVDGKILYVGRAQ 279
             NG  +  K + V  A+
Sbjct: 63  TLNGLRLQTKTIKVSYAR 80

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 42.7 bits (101), Expect = 9e-06
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN---DGKSRGFGFVAYESPEFAEKAVQ 261
           N+++           LK++F  YG +   +++ N    G +R FGFV   S E A K +Q
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPG-ARCFGFVTMASVEEAAKCIQ 59

Query: 262 AWNGKEVDGKILYV 275
             +  E+ G+++ V
Sbjct: 60  HLHRTELHGRVISV 73

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

>gnl|CDD|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 = 9e-06
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 208 IKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           + N       + L+ +FE YG +    +       +SRGF FV +     AE A+ A +G
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 266 KEVDGKILYV 275
           KE+DG+ L V
Sbjct: 63  KELDGRELRV 72

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

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

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 19/53 (35%), Positives = 33/53 (62%), Gaps = 1/53 (1%)

Query: 131 FSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
           F  FG IL  ++  +E+G SKG+GFV F     A+++ EK++G ++  + + V
Sbjct: 21  FGQFGPILDVEIIFNERG-SKGFGFVTFANSADADRAREKLHGTVVEGRKIEV 72

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

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

 Score = 42.5 bits (101), Expect = 1e-05
 Identities = 18/72 (25%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKV 171
           + +  L ++++   + + FS +G++    +  D + N  +GY +V FE+ E A K+I+ +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 172 NGMLLNSKIVFV 183
           +G  ++ + V V
Sbjct: 61  DGGQIDGQEVTV 72

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

>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F++NL      K + D F+  G +L   + + E G SKG G V FE+ E A ++   +N
Sbjct: 2   IFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKGCGVVRFESPEVAERACRMMN 60

Query: 173 GMLLNSK 179
           G  LN +
Sbjct: 61  GYKLNGR 67

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 5/63 (7%)

Query: 201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKA 259
           KLF  +  K      N+  ++ MF P+G+I    V+ + +G+SRG  FV + S + A  A
Sbjct: 3   KLFVGMLSKKC----NENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNA 58

Query: 260 VQA 262
           ++A
Sbjct: 59  IKA 61

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

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

 Score = 42.4 bits (99), Expect = 1e-05
 Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    ++   ++L+ +F   G + S +++ +   G S G+GFV Y + + AE+A+ 
Sbjct: 2   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61

Query: 262 AWNGKEVDGKILYVGRAQ 279
             NG  +  K + V  A+
Sbjct: 62  TLNGLRLQSKTIKVSYAR 79

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

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

 Score = 42.8 bits (100), Expect = 1e-05
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           +VF+ +L   I    +   F+ FG I   +V +D   G SKGYGFV F  +  A  +I++
Sbjct: 3   HVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 62

Query: 171 VNGMLLNSK 179
           + G  L  +
Sbjct: 63  MGGQWLGGR 71

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

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

 Score = 42.4 bits (99), Expect = 1e-05
 Identities = 21/69 (30%), Positives = 41/69 (59%), Gaps = 2/69 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQA 262
           +V++ +   +   + +K  F P+G I+  RV+ +   GKS+G+GFV++ +   AE A+Q 
Sbjct: 3   HVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 62

Query: 263 WNGKEVDGK 271
             G+ + G+
Sbjct: 63  MGGQWLGGR 71

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

>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query: 115 IKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
           +KNL   + N+ +   FS FG +    V  D++G   G GFV F  + AA K++E+
Sbjct: 4   VKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKALER 59

This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 42.8 bits (100), Expect = 1e-05
 Identities = 19/56 (33%), Positives = 32/56 (57%)

Query: 115 IKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
           ++NL   + N+ + + FS FG +    V  D++G S G G V F ++ AA K+ E+
Sbjct: 4   VRNLSPYVSNELLEEAFSQFGPVERAVVIVDDRGRSTGKGIVEFASKPAARKAFER 59

This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 80

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMF-EPYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           V+I N   D   + LK++F E  G +T   +  + +GKSRG G V ++  E  +KA++  
Sbjct: 2   VFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALETM 61

Query: 264 NGKEVDGKILYV 275
           N  E+ G+ L V
Sbjct: 62  NRYELKGRKLVV 73

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           +F+  + +    + ++D F+ FG I +  +  D + G  KGY  + +ET++ A  +IE +
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 172 NG-MLLNSKI 180
           NG  LL   I
Sbjct: 69  NGKELLGQTI 78

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|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 4/69 (5%)

Query: 207 YIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGK 266
           YI N   D N+  L+++FE +    S  ++    K  G+ FV      +A+KA++  NGK
Sbjct: 2   YIGNLSSDVNESDLRQLFEEHKIPVSSVLV----KKGGYAFVDCPDQSWADKAIEKLNGK 57

Query: 267 EVDGKILYV 275
            + GK++ V
Sbjct: 58  ILQGKVIEV 66

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 9/77 (11%)

Query: 114 FIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-------QGNSKGYGFVHFETEEAANK 166
           ++KNL K +  + +   F  F  + S    ++        +G  KG  FV F +EE A K
Sbjct: 5   YVKNLSKRVTEEDLVYIFGRF--VDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIATK 62

Query: 167 SIEKVNGMLLNSKIVFV 183
           ++  VNG +L  K + +
Sbjct: 63  ALNLVNGYVLKGKPMVI 79

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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 42.4 bits (99), Expect = 1e-05
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANKSIEKV 171
           +F+ NL    D   ++  F  FG++ + KV +D   N  KG+GFV     + A  +I  +
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 172 NGMLLNSKIVFV 183
           NG  L  +++ V
Sbjct: 64  NGYRLGDRVLQV 75

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|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 = 1e-05
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
           VY+ N      +  L ++F  YG +    ++ +    KS+G  F+ +   E A K V+A 
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 264 NGKEVDGKIL 273
           N KE+ G+ L
Sbjct: 64  NNKELFGRTL 73

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 17/69 (24%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 114 FIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVN 172
           FI  L      +++ + FS +G ++ C + +D   G S+G+GFV F    + +K +    
Sbjct: 2   FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKP 61

Query: 173 GMLLNSKIV 181
             +L+ + +
Sbjct: 62  -HVLDGREI 69

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

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANKSIEKV 171
           +F+ NL    D   ++  F  FG++ + KV +D   N  KG+GFV     + A  +I  +
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 172 NGMLLNSKIVFV 183
           NG  L  +++ V
Sbjct: 66  NGYRLGDRVLQV 77

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 2/78 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    ++   E+ K +F   G I S +++ +   G+S G+GFV Y  P  A+KA+ 
Sbjct: 4   TNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAIN 63

Query: 262 AWNGKEVDGKILYVGRAQ 279
             NG ++  K + V  A+
Sbjct: 64  TLNGLKLQTKTIKVSYAR 81

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 20/61 (32%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGK-SRGFGFVAYESPEFAEKAVQAWN 264
           +++    +   +++++E+F PYG +    +M ++ K SRG  FV Y S E A+ A++A N
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61

Query: 265 G 265
           G
Sbjct: 62  G 62

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGT----ITSYRV---MNNDGKSRGFGFVAYESPEFAEK 258
           VYI N     ++E L+E  + +      I S  V    +   +  G  +  + SPE AEK
Sbjct: 2   VYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEK 61

Query: 259 AVQAWNGKEVDGKILYV 275
            V+  NGK    + L+V
Sbjct: 62  VVKDLNGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 17/64 (26%), Positives = 37/64 (57%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ NLD  +  + +++ F   G ++  K+ +D+ G  K + FV+F+ E +   ++  +N
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLN 63

Query: 173 GMLL 176
           G+ L
Sbjct: 64  GIKL 67

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 22/74 (29%), Positives = 43/74 (58%), Gaps = 1/74 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           V++ NLD+ +  + +++ F   G +++  + +D      +GYGFV F +EE A+ +I+ +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 172 NGMLLNSKIVFVGK 185
           N + L  K + V K
Sbjct: 61  NMIKLYGKPIRVNK 74

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 115 IKNLDKSIDNKAMYDTFSAFGS--ILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKV 171
           ++ LD     + +    SA  S  I   ++ +D+    S+G+ FV F + E A + ++ +
Sbjct: 7   LRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDAL 66

Query: 172 NGML 175
           N + 
Sbjct: 67  NNLD 70

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 14/73 (19%), Positives = 34/73 (46%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            +F+ NL+ +I  + +   F  +G +    + +  +G    Y FV F   + A+++   +
Sbjct: 4   TLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 172 NGMLLNSKIVFVG 184
           +G  +    + +G
Sbjct: 64  SGQYIGRNQIKIG 76

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           VF+  L   +  + +Y+ FS  G +   ++ +D     SKG  +V F  EE+   ++  +
Sbjct: 2   VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-L 60

Query: 172 NGMLLN 177
            G  L 
Sbjct: 61  TGQRLL 66

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|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 122 IDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANK 166
              + + D FS FG +L  +V +D + G SKG+GFV F   E   K
Sbjct: 11  TTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVK 56

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

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

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 21/64 (32%), Positives = 40/64 (62%), Gaps = 3/64 (4%)

Query: 208 IKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKE 267
           + N     +++ L+E+FE     TS R+  N+G+ +G+ FV +ES E A++A+ + N  E
Sbjct: 6   VNNLSYSASEDSLQEVFE---KATSIRIPQNNGRPKGYAFVEFESAEDAKEALNSCNNTE 62

Query: 268 VDGK 271
           ++G+
Sbjct: 63  IEGR 66

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

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRV--MNNDGKSRGFGFVAYESPEFAEKA 259
           +++ N   D  +++LKE F+ +G +   R+      G+   FGFV ++ PE  +K 
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

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

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 20/64 (31%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIE 169
            N+++  L K++  K M   FS +G I++ ++  D+  G S+G GF+ F+    A ++I+
Sbjct: 2   ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIK 61

Query: 170 KVNG 173
            +NG
Sbjct: 62  GLNG 65

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

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

 Score = 44.9 bits (106), Expect = 3e-05
 Identities = 19/81 (23%), Positives = 43/81 (53%), Gaps = 2/81 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW 263
           +++ N   D ++  L ++F P+G + + +++      + +G+GFV+  + + A  A+ + 
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           NG  +  ++L V     KA R
Sbjct: 332 NGYTLGNRVLQVSFKTNKAYR 352

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

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 18/61 (29%), Positives = 30/61 (49%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           + ++NL        +   FS FG +    + +   G  KG+ FV F ++  A K+I+ VN
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 173 G 173
           G
Sbjct: 62  G 62

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 40.6 bits (96), Expect = 3e-05
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 4/56 (7%)

Query: 128 YDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
           Y  FS FG++   K+         G+ FV F TEEAA K+++ +NG+L   + + V
Sbjct: 2   YKLFSPFGNVEKIKL----LKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRV 53

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

 Score = 45.4 bits (107), Expect = 3e-05
 Identities = 37/141 (26%), Positives = 68/141 (48%), Gaps = 17/141 (12%)

Query: 145 DEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI------PRKEREKELGE 198
            ++  ++G+ FV +E+  AA  +  K    L+  +I   G  I      P +E ++++  
Sbjct: 176 ADKKKNRGFAFVEYESHRAAAMARRK----LMPGRIQLWGHVIAVDWAEPEEEVDEDVMA 231

Query: 199 KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEK 258
           K K+   +Y++N      +E +++ F  +      RV     K R + FV +E  E A K
Sbjct: 232 KVKI---LYVRNLMTTTTEEIIEKSFSEFKPGKVERVK----KIRDYAFVHFEDREDAVK 284

Query: 259 AVQAWNGKEVDGKILYVGRAQ 279
           A+   NGKE++G  + V  A+
Sbjct: 285 AMDELNGKELEGSEIEVTLAK 305

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

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

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD----EQGN--SKGYGFVHFETEEAANK 166
           +F+KNL+ S  N+ + D F      +  +V         G   S G+GFV F+T+E A  
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 167 SIEKVNGMLLNSKIVFV 183
           +++ ++G +L+   + V
Sbjct: 63  ALKAMDGFVLDGHTLVV 79

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

>gnl|CDD|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 41.1 bits (96), Expect = 3e-05
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQA 262
           + V++ N       +KLKE+F   G +    ++ + DGKSRG G V +E P  A +A+  
Sbjct: 1   STVFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAISM 60

Query: 263 WNGKEVDGKILYV 275
           +NG+ +  + ++V
Sbjct: 61  FNGQLLFDRPMHV 73

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|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 = 3e-05
 Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYG--TITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
           + ++       +E + +         I   R++ +   G SRGF FV + S E A + + 
Sbjct: 5   LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64

Query: 262 AWNGK---EVDGKILYV 275
           A N      +DG+++ V
Sbjct: 65  ALNNLDPFVIDGRVVRV 81

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

 Score = 41.5 bits (97), Expect = 3e-05
 Identities = 18/65 (27%), Positives = 40/65 (61%), Gaps = 2/65 (3%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQA 262
           N+Y+    +  + ++++++F  YG I + R++ +   G SRG GF+ ++    AE+A++ 
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKG 62

Query: 263 WNGKE 267
            NG++
Sbjct: 63  LNGQK 67

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

>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 41.9 bits (98), Expect = 3e-05
 Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
           N++I  L +++  K + D FS FG I++ +V  D+  G S+G  F+ F+    A ++I  
Sbjct: 2   NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 171 VNG 173
            NG
Sbjct: 62  FNG 64

This subgroup corresponds to the RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 41.5 bits (97), Expect = 3e-05
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQA 262
           N+YI         + +++MF  +G I + RV+     G SRG  F+ ++    AE+A+ +
Sbjct: 2   NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 263 WNGKEVDG 270
           +NG +  G
Sbjct: 62  FNGHKPPG 69

This subgroup corresponds to the RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 41.5 bits (97), Expect = 3e-05
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 5/72 (6%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIE-- 169
           +FI  L      K + D FS FG ++ C +  D   G S+G+GFV F+  E+ +K ++  
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 170 --KVNGMLLNSK 179
             K+NG +++ K
Sbjct: 61  EHKLNGKVIDPK 72

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 41.6 bits (98), Expect = 3e-05
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITS--YRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           ++I+N      +E L+++F  YG ++     +     K +GF FV Y  PE A KA    
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 264 NGKEVDGKILYV 275
           +G    G++L++
Sbjct: 65  DGTVFQGRLLHL 76

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 20/68 (29%), Positives = 40/68 (58%), Gaps = 2/68 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQA 262
           N+Y+    +    ++L+++F  YG I + R++ +   G SRG GF+ ++    AE+A++ 
Sbjct: 4   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63

Query: 263 WNGKEVDG 270
            NG++  G
Sbjct: 64  LNGQKPSG 71

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

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 1/71 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           +++ N      +E L E+F   G +   ++  + +GK + F FV ++       A+Q  N
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63

Query: 265 GKEVDGKILYV 275
           G  + G+ L +
Sbjct: 64  GIRLFGRELRI 74

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

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 3/67 (4%)

Query: 207 YIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGK 266
           +++N   +  DE+L+ +FE +G I   R +    K RGF  V+Y     A +A +A  G 
Sbjct: 5   FVRNINSNVEDEELRALFEQFGDI---RTLYTACKHRGFIMVSYYDIRAARRAKRALQGT 61

Query: 267 EVDGKIL 273
           E+ G+ L
Sbjct: 62  ELGGRKL 68

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

 Score = 40.8 bits (96), Expect = 4e-05
 Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 3/64 (4%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           +F+  L   +  +   + FS FG ++  ++ QD + G S+G+GFV F++E A  +     
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFS-- 59

Query: 172 NGML 175
            GML
Sbjct: 60  AGML 63

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

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 41.2 bits (96), Expect = 4e-05
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANKSIEKV 171
           +F+ NL    D   ++  F  FG++ + KV +D   N  KG+GFV     + A  +I  +
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 172 NGMLLNSKIVFV 183
           NG  L  +++ V
Sbjct: 66  NGYRLGDRVLQV 77

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 19/64 (29%), Positives = 35/64 (54%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ NLD  +  + +Y+ F   G +   K+ +D  G  K + FV F+ E +   +I+ +N
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQLLN 63

Query: 173 GMLL 176
           G+ L
Sbjct: 64  GIRL 67

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|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 41.2 bits (96), Expect = 4e-05
 Identities = 21/64 (32%), Positives = 34/64 (53%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ NLD  +  K + + FS  G++    + +D+ G S+G G V FE    A ++I   N
Sbjct: 3   IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISMFN 62

Query: 173 GMLL 176
           G  L
Sbjct: 63  GQFL 66

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWN 264
           V++     D  +++L  +FE  G I   R+M + DGK+RG+ FV Y     A++AV+  N
Sbjct: 4   VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELN 63

Query: 265 GKEV-DGKILYV 275
             E+  G++L V
Sbjct: 64  NYEIRPGRLLGV 75

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIE-- 169
           +FI  L      K + +  S FG +L C +  D   G S+G+GFV F+   + +K +E  
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61

Query: 170 --KVNGMLLNSK 179
             K++G L++ K
Sbjct: 62  EHKLDGKLIDPK 73

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

>gnl|CDD|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 = 40.8 bits (96), Expect = 4e-05
 Identities = 16/71 (22%), Positives = 35/71 (49%), Gaps = 2/71 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           + +  +D S+    + + FS  G +   ++  D Q +++ + FV F   E+A  ++  ++
Sbjct: 3   IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR-FAFVEFADAESALSAL-NLS 60

Query: 173 GMLLNSKIVFV 183
           G LL    + V
Sbjct: 61  GTLLGGHPLRV 71

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

 Score = 41.1 bits (97), Expect = 5e-05
 Identities = 20/55 (36%), Positives = 33/55 (60%), Gaps = 2/55 (3%)

Query: 214 DFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWNGK 266
             ++  +   F   G +TS +++ N   GKS G+GFV + + E AE+A+Q+ NGK
Sbjct: 10  WMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGK 64

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

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

 Score = 41.3 bits (96), Expect = 5e-05
 Identities = 20/68 (29%), Positives = 40/68 (58%), Gaps = 2/68 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQA 262
           N+Y+    +    ++L+++F  YG I + R++ +   G SRG GF+ ++    AE+A++ 
Sbjct: 7   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 66

Query: 263 WNGKEVDG 270
            NG++  G
Sbjct: 67  LNGQKPPG 74

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

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 40.9 bits (96), Expect = 5e-05
 Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 6/71 (8%)

Query: 113 VFIKNLDKSID----NKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSI 168
           VF+ +L  S        A+ + FS +G+++  KV +D +   + Y FV F  ++ A  ++
Sbjct: 5   VFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWRQ--RPYAFVQFTNDDDAKNAL 62

Query: 169 EKVNGMLLNSK 179
            K  G +L+ +
Sbjct: 63  AKGQGTILDGR 73

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 40.7 bits (95), Expect = 5e-05
 Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEK 258
           +++ N   D +  +LKE F+ YG +   R+ N+ GK   FGFV ++  E  +K
Sbjct: 6   LFVGNLPHDVDKSELKEFFQQYGNVVELRI-NSGGKLPNFGFVVFDDSEPVQK 57

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

>gnl|CDD|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 = 40.5 bits (95), Expect = 5e-05
 Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 7/71 (9%)

Query: 206 VYIKNFGED-FNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           +++  F      +E ++++FEP+G +    +       + F FV +E  E A KA++A +
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDI------RKTFAFVEFEDSEDATKALEALH 55

Query: 265 GKEVDGKILYV 275
           G  +DG +L V
Sbjct: 56  GSRIDGSVLTV 66

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

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +++KN   +   ++LKE+FE    I        DG S+G  ++ +++   AEKA++   G
Sbjct: 6   LFVKNLPYNITVDELKEVFEDAVDIRL--PSGKDGSSKGIAYIEFKTEAEAEKALEEKQG 63

Query: 266 KEVDGKILYV 275
            EVDG+ + V
Sbjct: 64  AEVDGRSIVV 73

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

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

 Score = 40.6 bits (95), Expect = 6e-05
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           VF+ N+      + + D FS  G ++S ++  D E G  KGYGF  ++ +E A  ++  +
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 172 NGMLLNSK 179
           NG  LN +
Sbjct: 61  NGYELNGR 68

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

 Score = 40.6 bits (96), Expect = 6e-05
 Identities = 18/69 (26%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           VF+ NL   I+ + +   F   G + + ++ +D + G  KG+G+V F+T+++   +++  
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLN 61

Query: 172 NGMLLNSKI 180
              L   KI
Sbjct: 62  GIKLKGRKI 70

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

>gnl|CDD|240726 cd12280, RRM_FET, RNA recognition motif in the FET family of RNA-binding proteins

 Score = 40.8 bits (96), Expect = 6e-05
 Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 9/79 (11%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYR---------VMNNDGKSRGFGFVAYESPEFA 256
           +YI    +D  ++ L E+F   G I   +           + + + +G   V Y+ P  A
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 257 EKAVQAWNGKEVDGKILYV 275
           + A++ +NG E  G  + V
Sbjct: 61  QAAIEWFNGYEFRGNKIKV 79

This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. . Length = 81

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

 Score = 40.3 bits (95), Expect = 7e-05
 Identities = 11/30 (36%), Positives = 17/30 (56%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            L+V NL     +E LR+ F+ FG + S +
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVR 30

Length = 73

>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 40.6 bits (95), Expect = 7e-05
 Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 8/73 (10%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           VF+  +D  +D   +   F+ +GS+   K+  D  G SKGYGFV F  +    K +E   
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRTGVSKGYGFVSFYDDVDVQKIVE--- 64

Query: 173 GMLLNSKIVFVGK 185
                S+I F GK
Sbjct: 65  -----SQINFHGK 72

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

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

 Score = 40.5 bits (94), Expect = 7e-05
 Identities = 21/69 (30%), Positives = 40/69 (57%), Gaps = 2/69 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQA 262
           +V++ +   +   E +K  F P+G I+  RV+ +   GKS+G+GFV++ +   AE A+  
Sbjct: 3   HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 62

Query: 263 WNGKEVDGK 271
             G+ + G+
Sbjct: 63  MGGQWLGGR 71

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

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

 Score = 40.3 bits (95), Expect = 7e-05
 Identities = 15/71 (21%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 208 IKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKE 267
           +++   + +++  +++ + +G  +S RVM+  GK +   F  +++ + A +A+   +  +
Sbjct: 4   VRHLPPELSEDDKEDLLKHFG-ASSVRVMSRRGKLKNTAFATFDNEQAASQALSRLHQLK 62

Query: 268 VDGKILYVGRA 278
           + GK L V  A
Sbjct: 63  ILGKRLVVEYA 73

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

 Score = 40.3 bits (94), Expect = 7e-05
 Identities = 21/61 (34%), Positives = 38/61 (62%), Gaps = 2/61 (3%)

Query: 217 DEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILY 274
           +  L+E+F  YG +    V+ +   G+SRGF FV +E  + +++A++  NG E+DG+ + 
Sbjct: 13  ERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIR 72

Query: 275 V 275
           V
Sbjct: 73  V 73

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

>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 40.4 bits (94), Expect = 7e-05
 Identities = 17/56 (30%), Positives = 32/56 (57%)

Query: 115 IKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
           +KNL + + N+ + + FS FG +    V  D++G   G G V F  + +A K++++
Sbjct: 4   VKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKALDR 59

This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

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

 Score = 40.2 bits (94), Expect = 7e-05
 Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +Y+ N   D  ++ L+++F  YG I    + N  G    F FV +E P  AE AV   NG
Sbjct: 2   IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRG-LVPFAFVRFEDPRDAEDAVFGRNG 60

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

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

 Score = 40.2 bits (94), Expect = 7e-05
 Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           +Y+ N      ++ LK++F+  G + + +++ + + K   +GFV Y     AE A+Q  N
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 265 GKEVDGKILYVGRA 278
           G++++   + V  A
Sbjct: 61  GRQIENNEIRVNWA 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|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar protein 3 (Npl3p) and similar proteins

 Score = 39.7 bits (93), Expect = 8e-05
 Identities = 16/71 (22%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           ++++         A+ + FS +G++   K+          + FV FE+ E+A ++ + V+
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMI-------SNFAFVEFESLESAIRAKDSVH 54

Query: 173 GMLLNSKIVFV 183
           G +LN+  ++V
Sbjct: 55  GKVLNNNPLYV 65

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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 40.5 bits (94), Expect = 8e-05
 Identities = 20/81 (24%), Positives = 43/81 (53%), Gaps = 2/81 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
           +++ N   + ++  L ++F P+G +T+ +V+ +    K +GFGFV   + + A  A+ + 
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           NG  +  ++L V     K  +
Sbjct: 64  NGYRLGDRVLQVSFKTSKQHK 84

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

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

 Score = 40.5 bits (94), Expect = 8e-05
 Identities = 19/64 (29%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIE 169
            N+++  L K++  K +   FS +G I++ ++  D+  G S+G GF+ F+    A ++I+
Sbjct: 3   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 62

Query: 170 KVNG 173
            +NG
Sbjct: 63  GLNG 66

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

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 40.5 bits (95), Expect = 8e-05
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 7/76 (9%)

Query: 206 VYIKNF----GEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKA 259
           +++K F    GED     L E F   G IT   +  +   G S+GF ++ ++S +  EKA
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 260 VQAWNGKEVDGKILYV 275
           ++  +G ++ G  L V
Sbjct: 62  LEL-DGSDLGGGNLVV 76

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 40.1 bits (94), Expect = 8e-05
 Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           V+I NL   I    + + F     I S ++A D E G  KG+G V F  EE+ + ++ K+
Sbjct: 2   VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAAL-KL 59

Query: 172 NGMLLNSKIVFVG 184
           +G +L  + + + 
Sbjct: 60  DGTVLCGRPIRIA 72

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 40.7 bits (96), Expect = 8e-05
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 17/74 (22%)

Query: 208 IKNFGEDFNDEKLKEMF---------EPYGTITSYRVM--------NNDGKSRGFGFVAY 250
           I+N  +  +++KLKE+F         +    I   ++M        N  GKS+G+GFV +
Sbjct: 5   IRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEF 64

Query: 251 ESPEFAEKAVQAWN 264
            + E A KA++A N
Sbjct: 65  TNHEHALKALRALN 78

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 40.1 bits (94), Expect = 8e-05
 Identities = 19/60 (31%), Positives = 28/60 (46%)

Query: 114 FIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG 173
           F+  L K      +   F  FG+I  C + +   GNSKG  FV F +   A  +I  ++G
Sbjct: 5   FVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALHG 64

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

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

 Score = 40.1 bits (94), Expect = 8e-05
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV--MNNDGKSRGFGFVAYESPEFAEKAVQ 261
           T + IKN       E+L ++ E  G    Y      ++G  RG  F  + SPE A+  V+
Sbjct: 2   TAIVIKNIPFSLRKEQLLDIIEDLGIPLPYAFNYHFDNGVFRGLAFANFRSPEEAQTVVE 61

Query: 262 AWNGKEVDGKILYV 275
           A NG E+ G+ L V
Sbjct: 62  ALNGYEISGRRLRV 75

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

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

 Score = 39.9 bits (94), Expect = 9e-05
 Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 4/65 (6%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           V++ NL      + + D F  +G + S  VA+    N  G+ FV FE    A  ++  ++
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVAR----NPPGFAFVEFEDPRDAEDAVRALD 57

Query: 173 GMLLN 177
           G  + 
Sbjct: 58  GRRIC 62

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

 Score = 40.5 bits (94), Expect = 9e-05
 Identities = 19/64 (29%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIE 169
            N+++  L K++  K +   FS +G I++ ++  D+  G S+G GF+ F+    A ++I+
Sbjct: 6   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 65

Query: 170 KVNG 173
            +NG
Sbjct: 66  GLNG 69

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

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

 Score = 40.1 bits (94), Expect = 9e-05
 Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 2/57 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAV 260
           +++ N   +  +++L+  F   G I   R+M   + GK +GF FV +E  EFA  A+
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 21/71 (29%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F++NL   +  + + + FS  G ++  ++   E G SKG G V F++ E+A K+   +N
Sbjct: 2   IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKM-ENGKSKGCGTVRFDSPESAEKACRLMN 60

Query: 173 GMLLNSKIVFV 183
           G+ +N + + V
Sbjct: 61  GIKINGREIDV 71

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

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

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           +VF+ +L   I  + +   F+ FG I   +V +D   G SKGYGFV F  +  A  +I  
Sbjct: 3   HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 62

Query: 171 VNGMLLNSK 179
           + G  L  +
Sbjct: 63  MGGQWLGGR 71

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

>gnl|CDD|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 17/50 (34%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 217 DEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWNG 265
           ++ ++ +FEP+GTI    ++   DG S+G  FV + S   A+ A+ A +G
Sbjct: 15  EDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALHG 64

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

>gnl|CDD|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 6/60 (10%)

Query: 220 LKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ 279
           L+  FEPYG + + R+  N      F FV YE+ E A KA+++ N  +V  +++ V  A 
Sbjct: 17  LERHFEPYGKLVNVRIRRN------FAFVQYETQEDATKALESTNMSKVLDRVISVEYAA 70

This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 70

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 20/64 (31%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWN 264
           V++     D  +++L  +FE  G I  +R+M    G++RG+ FV Y + E A+ A++  N
Sbjct: 4   VFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRILN 63

Query: 265 GKEV 268
             E+
Sbjct: 64  NYEI 67

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 23/70 (32%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +Y+ N   D   + ++++F  YG I    + N  G    F FV +E P  AE AV   +G
Sbjct: 2   IYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRGPP--FAFVEFEDPRDAEDAVYGRDG 59

Query: 266 KEVDGKILYV 275
            + DG  L V
Sbjct: 60  YDYDGYRLRV 69

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

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 6/72 (8%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAV--- 260
           +++     +  +  L++ F  +GT+T   VM  +   + RGFGF+ +ES +  ++ V   
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEH 64

Query: 261 -QAWNGKEVDGK 271
               NGK+V+ K
Sbjct: 65  FHDINGKKVEVK 76

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

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAW 263
           +YI     +  +  +  +F  YG I    ++     GKS+GF F+AYE       AV   
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 264 NGKEVDGKILYV 275
           NG ++ G+ + V
Sbjct: 72  NGIKLLGRTIRV 83

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

>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 2/50 (4%)

Query: 214 DFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
            + +E L+E F+ +G I    ++   N G+S+GFG+V +  P  A  A++
Sbjct: 11  SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 17/40 (42%), Positives = 24/40 (60%)

Query: 144 QDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
            DE G +KGY FV F T E A ++++ +NG  L+ K  F 
Sbjct: 43  VDETGKTKGYAFVEFATPEEAKEAVKALNGYKLDKKHTFA 82

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

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 16/77 (20%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKV----AQDEQGNSKGYGFVHFETEEAANKS 167
           N+++ NL+  +  + +   F  FG + S K+     ++E+  ++  GFV F     A ++
Sbjct: 3   NLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERA 62

Query: 168 IEKVNGMLLNSKIVFVG 184
           +++++G  +    + +G
Sbjct: 63  LDELDGKDVMGYELKLG 79

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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           VF+ N+ + + +  +       G +LS K  +D   G  K +GF  FE  E A +++  +
Sbjct: 3   VFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLL 62

Query: 172 NGMLLNSK 179
           NG+ L  K
Sbjct: 63  NGLELGGK 70

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 14/61 (22%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           ++++NL   I ++ +YD F  +G+I   ++   +   ++G  FV +E    A  + + ++
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTK--ETRGTAFVVYEDIYDAKNACDHLS 62

Query: 173 G 173
           G
Sbjct: 63  G 63

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQA 262
           + +++ N       +KLKE+F   GT+    +  + DGKSRG G V +E P  A +A+  
Sbjct: 1   STIFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAISM 60

Query: 263 WNGK 266
           +NG+
Sbjct: 61  FNGQ 64

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 10/72 (13%)

Query: 198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAE 257
           EK +    V  K F + F   K+  ++ P         ++  GK++G+ FV + +PE A+
Sbjct: 15  EKLEKLKKVLRKIFSK-FGVGKIVGIYMP---------VDETGKTKGYAFVEFATPEEAK 64

Query: 258 KAVQAWNGKEVD 269
           +AV+A NG ++D
Sbjct: 65  EAVKALNGYKLD 76

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

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

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 4/83 (4%)

Query: 197 GEKAKLFTNVYIKNFGEDF--NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYES 252
           G +A    N  +  FG      +  L+E+F  YG I    ++      +SRGF FV +E+
Sbjct: 1   GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 253 PEFAEKAVQAWNGKEVDGKILYV 275
            + A++A +  NG E+DG+ + V
Sbjct: 61  VDDAKEAKERANGMELDGRRIRV 83

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

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 125 KAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
           + + + FS +G I    +  D+Q   S+G+ FV+FE  + A ++ E+ NGM L+ + + V
Sbjct: 24  RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 83

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|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 20/67 (29%), Positives = 38/67 (56%), Gaps = 2/67 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
           T +++     D  +++L  +FE  G I   R+M +   G +RG+ FV + + E A++AV+
Sbjct: 2   TEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVK 61

Query: 262 AWNGKEV 268
            +N  E+
Sbjct: 62  LYNNHEI 68

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

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

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
           T++Y++N  +    + L+ +F  YG I    +  +    + RGF +V +E    AE A+ 
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 262 AWNGKEVDGKILYVGRAQ 279
             +     G+ + +  AQ
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|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 = 22/70 (31%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +Y+ N   D  +  ++++F  YG I +  + N       F FV +E P  AE AV+  +G
Sbjct: 2   IYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRRRGP-PFAFVEFEDPRDAEDAVRGRDG 60

Query: 266 KEVDGKILYV 275
            + DG  L V
Sbjct: 61  YDFDGYRLRV 70

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

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

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 7/65 (10%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ NL      + +   F  +G +L C +        K YGFVH + + AA+++I  ++
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDII-------KNYGFVHMDDKTAADEAIRNLH 55

Query: 173 GMLLN 177
              L+
Sbjct: 56  HYKLH 60

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

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

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 7/61 (11%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           ++++NL  S   + + + FS +G +   K  +D       Y FVHFE  + A K++E++N
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEEMN 56

Query: 173 G 173
           G
Sbjct: 57  G 57

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 3/78 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +++     D   E+L E F  +G I    ++     +  F F+ +E  + A +AV++ N 
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAVESENH 65

Query: 266 KEVDGKILYVGRAQKKAE 283
             +  K ++V   Q K  
Sbjct: 66  SMLKNKTMHV---QYKEI 80

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

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 4/68 (5%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           VY         ++ +++ F P+G I   RV       +G+ F+ + + E A  A+ + NG
Sbjct: 3   VYCGGIASGLTEQLMRQTFSPFGQIMEIRVF----PEKGYSFIRFSTHESAAHAIVSVNG 58

Query: 266 KEVDGKIL 273
             ++G ++
Sbjct: 59  TTIEGHVV 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|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           V++ NL  S+ N  ++  FS +G ++   + +D E   SKG  F+ F   E A+K ++ +
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 172 NGMLLNSKIV 181
           N   L  + +
Sbjct: 64  NNKELFGRTL 73

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|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 1/67 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKV-AQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           +F+ NL   I    + + F  FG++L  ++ ++   G    +GFV F+  EA  K +   
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

Query: 172 NGMLLNS 178
                  
Sbjct: 66  PIYFRGD 72

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

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

 Score = 38.3 bits (90), Expect = 3e-04
 Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 7/74 (9%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRV----MNNDGKSRGFGFVAYESPEFAEKAVQ 261
           V++ N   D  +E+L++ FE  G + + R+        GK  GFG+V +++ +    A++
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGK--GFGYVLFKTKDSVALALK 59

Query: 262 AWNGKEVDGKILYV 275
             NG ++ G+ + V
Sbjct: 60  L-NGIKLKGRKIRV 72

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

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

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIE-- 169
           +F+  L      K + + FS FG ++ C +  D   G S+G+GFV F+   +  K ++  
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 170 --KVNGMLLNSK 179
             K++G +++ K
Sbjct: 61  EHKLDGRVIDPK 72

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

>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTF-SAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
            V + NL K +    + + F S  G I    ++ +E G S G   + F+    A K+ +K
Sbjct: 1   KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEGGKSTGIANITFKRAGDATKAYDK 60

Query: 171 VNGMLLNSK 179
            NG + +  
Sbjct: 61  FNGRIDDGN 69

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

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

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 19/61 (31%), Positives = 36/61 (59%), Gaps = 7/61 (11%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F++NL  ++  + +  +FS FG +   K  +D       Y FVHFE  +AA ++++++N
Sbjct: 4   LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEERDAAVRAMDEMN 56

Query: 173 G 173
           G
Sbjct: 57  G 57

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|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANKSIEKV 171
           +F+  L  +     +   FS FG +    +  D+Q N  +G+GFV FE+E+  +K  E +
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCE-I 60

Query: 172 NGMLLNSKIVFVGK 185
           +   +N+K+V   K
Sbjct: 61  HFHEINNKMVECKK 74

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 17/62 (27%), Positives = 36/62 (58%), Gaps = 3/62 (4%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV---MNNDGKSRGFGFVAYESPEFAEKAV 260
           + + ++N   +   ++L+E+F  +G + + R+   M   G  RGFGFV + + + A++A 
Sbjct: 1   SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAF 60

Query: 261 QA 262
           +A
Sbjct: 61  KA 62

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

 Score = 38.1 bits (88), Expect = 4e-04
 Identities = 18/68 (26%), Positives = 34/68 (50%), Gaps = 4/68 (5%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           VY         ++ +++ F P+G I   RV  +    +G+ FV + S E A  A+ + NG
Sbjct: 3   VYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD----KGYSFVRFNSHESAAHAIVSVNG 58

Query: 266 KEVDGKIL 273
             ++G ++
Sbjct: 59  TTIEGHVV 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|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQA 262
           T + + N     +D+ +KE+F  +G +    V  +  G+S G   V +E    A KA++ 
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60

Query: 263 WNGKEVDGK 271
           +NG  +DG+
Sbjct: 61  YNGVPLDGR 69

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

 Score = 38.6 bits (89), Expect = 4e-04
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 3/78 (3%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG--KSRGFGFVAYESPEFAEKAV 260
           F  ++I     +  +E L+  +E +G +T   VM +    +SRGFGFV +      + A+
Sbjct: 2   FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAM 61

Query: 261 QAWNGKEVDGKILYVGRA 278
            A     +DG+++   RA
Sbjct: 62  AA-RPHTIDGRVVEPKRA 78

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

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 15/69 (21%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           ++I +L K +  + + + F  +G I S  +        +G  +V  ET + A+++++K+ 
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIP-----PRGCAYVCMETRQDAHRALQKLR 59

Query: 173 GMLLNSKIV 181
            + L  K +
Sbjct: 60  NVKLAGKKI 68

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 38.0 bits (88), Expect = 4e-04
 Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 115 IKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNG 173
           I NL  +   +   +    FG++  C +   E  G+SKGYGFV +  +++A ++   + G
Sbjct: 4   IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 174 MLLNSKIVFV 183
             L S+ ++V
Sbjct: 64  KQLGSRTLYV 73

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

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

 Score = 41.4 bits (97), Expect = 5e-04
 Identities = 32/149 (21%), Positives = 61/149 (40%), Gaps = 9/149 (6%)

Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGF 245
             +  ++ L E  +    V++        +  L E F   G +   + +   N  +S+G 
Sbjct: 74  SGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGV 133

Query: 246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQG 305
            +V +   E   KA+    G+ + G+ + V  +Q +  R  +          +  +    
Sbjct: 134 AYVEFYDVESVIKALAL-TGQMLLGRPIIVQSSQAEKNRAAK------AATHQPGDIPNF 186

Query: 306 VNLYVKNLDDSIDDERLRKEFTPFGTITS 334
           + LYV NL  +I ++ LR+ F PFG I  
Sbjct: 187 LKLYVGNLHFNITEQELRQIFEPFGDIED 215

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

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 11/83 (13%)

Query: 216 NDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
            +E L+E+F  YG I   R++ +   G S+G+ FV YE    A +A +  +   +DG  +
Sbjct: 16  TEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKLVIDGSEI 75

Query: 274 YVGRAQKKAERTQELK----RRF 292
           +V       ER + L     RR 
Sbjct: 76  FVDF-----ERERTLPGWIPRRL 93

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|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 38.0 bits (88), Expect = 5e-04
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 208 IKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNG 265
           I N    +  ++ +E+  P+G +    ++ ++  G S+G+GFV Y   + A +A     G
Sbjct: 4   IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 266 KEVDGKILYV 275
           K++  + LYV
Sbjct: 64  KQLGSRTLYV 73

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

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

 Score = 37.9 bits (89), Expect = 5e-04
 Identities = 19/71 (26%), Positives = 29/71 (40%), Gaps = 5/71 (7%)

Query: 207 YIKNFGEDFNDEKLK----EMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
           YI N  E    ++LK     +F  +G +          K RG  FV ++  E A  A++A
Sbjct: 3   YINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTL-KMRGQAFVVFKDVESATNALRA 61

Query: 263 WNGKEVDGKIL 273
             G     K +
Sbjct: 62  LQGFPFYDKPM 72

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

 Score = 37.9 bits (88), Expect = 5e-04
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQA 262
           T + +KN   +   + ++ +F  YG + S RV    D  +RGF FV + + + A  A+ A
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNA 60

Query: 263 WNGKEVDGKIL 273
                + G+ L
Sbjct: 61  LKDTHLLGRRL 71

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

 Score = 41.0 bits (96), Expect = 6e-04
 Identities = 39/197 (19%), Positives = 74/197 (37%), Gaps = 36/197 (18%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           ++I NL   +    + +   +FG + +  + +D   G SKGY F  ++     + +I  +
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAAL 357

Query: 172 NGMLLNSKIVFVGKFIPRKEREK----------------------ELGEKAKLFTNVYIK 209
           NG       + V +      +                        ++G K      +   
Sbjct: 358 NGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNL 417

Query: 210 NFGEDFND--------EKLKEMFEPYGTITSYRV--MNNDGKS-RGFG--FVAYESPEFA 256
             G+D  D        E +K  F  YG + +  +   N D  S  G G  F+ Y     A
Sbjct: 418 VTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSA 477

Query: 257 EKAVQAWNGKEVDGKIL 273
           EKA++  NG++ + +++
Sbjct: 478 EKAMEGMNGRKFNDRVV 494

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

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

 Score = 37.7 bits (87), Expect = 6e-04
 Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 3/65 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           VY+ N G      +L+  F  YG + +  +  N     GF FV +E P  AE AV+  +G
Sbjct: 2   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP---GFAFVEFEDPRDAEDAVRGLDG 58

Query: 266 KEVDG 270
           K + G
Sbjct: 59  KVICG 63

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

 Score = 41.1 bits (96), Expect = 7e-04
 Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 2/74 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQA 262
             V++     D  +++L  +FE  G I   R+M +  G++RG+ FV +   E A++AV+ 
Sbjct: 59  CEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKL 118

Query: 263 WNGKEV-DGKILYV 275
            N  E+  G++L V
Sbjct: 119 LNNYEIRPGRLLGV 132

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

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

 Score = 37.6 bits (88), Expect = 7e-04
 Identities = 13/69 (18%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           +F+  L + +  + + + FS +G++ S ++  D++ G  +G+ FV F+  +  +K + + 
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQK 61

Query: 172 NGMLLNSKI 180
              +   ++
Sbjct: 62  YHTINGHRV 70

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

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

 Score = 37.6 bits (87), Expect = 7e-04
 Identities = 18/60 (30%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 125 KAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
           + + + FS +G +    V  D++ G S+G+ FV+FE  + + +++E  NGM L+ + + V
Sbjct: 14  RDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMELDGRRIRV 73

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

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 37.8 bits (88), Expect = 7e-04
 Identities = 19/72 (26%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAW 263
           ++++N      ++ L+++F  +G ++   V      GKS+GF +V +  PE A KA +  
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 264 NGKEVDGKILYV 275
           +GK   G+++++
Sbjct: 65  DGKVFQGRLIHI 76

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

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

 Score = 37.2 bits (86), Expect = 7e-04
 Identities = 26/68 (38%), Positives = 35/68 (51%), Gaps = 9/68 (13%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +++ N   D  +E  K++FE YG   S   +N D   RGFGF+  ES   AE A      
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGE-PSEVFINRD---RGFGFIRLESRTLAEIA-----K 54

Query: 266 KEVDGKIL 273
            E+DG IL
Sbjct: 55  AELDGTIL 62

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 37.3 bits (87), Expect = 7e-04
 Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 5/72 (6%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRV--MNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           + I N       E L  +   YGT+ +       ++  +     V YESPE A++AV   
Sbjct: 3   IQISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETATV---NVTYESPEQAQQAVNKL 59

Query: 264 NGKEVDGKILYV 275
           NG E +G  L V
Sbjct: 60  NGHEYEGSKLKV 71

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

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

 Score = 37.3 bits (87), Expect = 8e-04
 Identities = 16/71 (22%), Positives = 36/71 (50%), Gaps = 5/71 (7%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ NL   I  +   + FS +G +    + ++     KG+GF+  +T   A K+  +++
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAELD 58

Query: 173 GMLLNSKIVFV 183
           G++   + + V
Sbjct: 59  GIMRKGRQLRV 69

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|241112 cd12668, RRM3_RAVER2, RNA recognition motif 3 found in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 38.0 bits (88), Expect = 8e-04
 Identities = 15/54 (27%), Positives = 27/54 (50%)

Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLL 176
           D++ +   FS     + C++AQDE     G+  V +ET E A +    ++G  +
Sbjct: 16  DSEELLQIFSESYKPVFCQLAQDEGSCVGGFAVVEYETAEQAEEVQLAMDGTTI 69

This subgroup corresponds to the RRM3 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 98

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

 Score = 37.3 bits (86), Expect = 8e-04
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 5/72 (6%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIE-- 169
           +F+  L      K + D F+ FG +  C +  D   G S+G+GF+ F+   +  K +E  
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 170 --KVNGMLLNSK 179
             +++G L++ K
Sbjct: 62  EHRLDGRLIDPK 73

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

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

 Score = 37.2 bits (87), Expect = 8e-04
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 4/63 (6%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           T +Y+   GE   ++ L++ F  +G I S  V+      +   FV + + E AEKA +  
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEIRSITVVPR----QQCAFVTFTTREAAEKAAERL 57

Query: 264 NGK 266
             K
Sbjct: 58  FNK 60

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

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

 Score = 37.4 bits (87), Expect = 9e-04
 Identities = 19/64 (29%), Positives = 26/64 (40%), Gaps = 5/64 (7%)

Query: 114 FIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG 173
           F+  ++  +    + D F  FG   S  V           GFV FET EAA K    ++ 
Sbjct: 6   FLFGVEDDLPEYKIRDYFEQFGKSKSVIVNHR-----AKCGFVRFETREAAEKFAAAISE 60

Query: 174 MLLN 177
             LN
Sbjct: 61  NGLN 64

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

>gnl|CDD|240734 cd12288, RRM_La_like_plant, RNA recognition motif in plant proteins related to the La autoantigen

 Score = 37.9 bits (88), Expect = 9e-04
 Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 17/76 (22%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFG---------------FV 248
           V  +N  ED + E L+E+F   G++ + R+      G                      V
Sbjct: 3   VVAENLPEDHSIENLEEIFGTVGSVKNVRICDPGRVGSGSTASKAKKPDTLVSNKLHALV 62

Query: 249 AYESPEFAEKAVQAWN 264
            YE+ E AEKAV   +
Sbjct: 63  EYETVEAAEKAVTELS 78

This subfamily corresponds to the RRM of plant La-like proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Members in this family contain an LAM domain followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 93

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

 Score = 37.3 bits (86), Expect = 9e-04
 Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 10/73 (13%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F++NL  ++  + +   F  FG +   K  +D       Y F+HF+  + A K++E++N
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 56

Query: 173 GMLL---NSKIVF 182
           G  L   N +IVF
Sbjct: 57  GKELEGENIEIVF 69

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|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 37.5 bits (88), Expect = 9e-04
 Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 2/49 (4%)

Query: 225 EPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
             +G +   +V  N     G  +V +++ E A+K +QA NG+  DG+ +
Sbjct: 33  SKFGPVEHIKVDKN--SPEGVVYVKFKTVEAAQKCIQALNGRWFDGRQI 79

This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia 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. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

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

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 12/29 (41%), Positives = 17/29 (58%)

Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           L+V NL     +E LR+ F+ FG I S +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVR 29

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

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 15/30 (50%), Positives = 20/30 (66%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            L+V NL  S+DDE L+ EF  FGT+  A+
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGAR 30

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 15/29 (51%), Positives = 19/29 (65%)

Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           L VKNL   I +++LRK F  FGTIT  +
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQ 31

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +Y+ N      ++ L E+F   G I S +++   G    + FV Y     A  A+Q  NG
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGND-PYAFVEYYDHRSAAAALQTMNG 59

Query: 266 KEVDGKILYVGRA 278
           + + G+ + V  A
Sbjct: 60  RLILGQEIKVNWA 72

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

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 37.1 bits (85), Expect = 0.001
 Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANKSI 168
           N++I+ L  +  ++ +      +G I+S K   D+  N  KGYGFV F++  AA K++
Sbjct: 9   NLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAV 66

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 37.1 bits (85), Expect = 0.001
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANKSI 168
           N++I+ L     ++ +      +G I+S K   D+  N  KGYGFV F++  AA K++
Sbjct: 6   NLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAV 63

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

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

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWN 264
           +++ N      +E L E+F   G +T   +  + +GK + FGFV ++  E    A+   N
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDKEGKPKSFGFVCFKHSESVPYAIALLN 63

Query: 265 GKEVDGKILYV 275
           G  + G+ + V
Sbjct: 64  GIRLYGRPIKV 74

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

>gnl|CDD|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 = 36.9 bits (86), Expect = 0.001
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 4/49 (8%)

Query: 217 DEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +++L+ +F P+G I   ++    GK  G GFV +     AE A+Q   G
Sbjct: 15  EDELRSLFGPFGEIVYVKIPP--GK--GCGFVQFVHRAAAEAAIQQLQG 59

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|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 = 37.2 bits (87), Expect = 0.001
 Identities = 13/43 (30%), Positives = 25/43 (58%)

Query: 131 FSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG 173
           FS FG + S ++ +   G+ +G+ FV F T++ A  ++E +  
Sbjct: 21  FSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKS 63

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

 Score = 36.8 bits (85), Expect = 0.001
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 6/72 (8%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             +++ N       ++L+ +FE +G     RV+  D K + + FV  E  E A  A++A 
Sbjct: 1   WKIFVGNVSATCTSDELRGLFEEFG-----RVVECD-KVKDYAFVHMEREEEALAAIEAL 54

Query: 264 NGKEVDGKILYV 275
           NGKEV G+ + V
Sbjct: 55  NGKEVKGRRINV 66

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

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 2/57 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAV 260
           +++     D  +  L E F  +G +    V+ +   GK RGFGFV +++ + A+KA 
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA 58

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 2/48 (4%)

Query: 214 DFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKA 259
              ++ LK+ F  +G +   +V      G+S+GFGFV +   E   K 
Sbjct: 10  KTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV 57

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

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

 Score = 36.8 bits (85), Expect = 0.001
 Identities = 15/71 (21%), Positives = 32/71 (45%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +++ NLD  +    +   F   G + + K+  D+      YGFV +     A  +++ +N
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 173 GMLLNSKIVFV 183
           G  + +  + V
Sbjct: 61  GRQIENNEIRV 71

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

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
             + +KNL      K +   FS++G + S +V +    +++G+ FV F T + A  ++  
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAMNA 60

Query: 171 VNGM-LLNSKIV 181
           +    LL  ++V
Sbjct: 61  LKDTHLLGRRLV 72

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

>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 37.5 bits (88), Expect = 0.001
 Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 7/68 (10%)

Query: 213 EDFND--EKLKEMFEPYGTITSYRV-----MNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           E++ +  E +KE    YG + S  +        D    G  FV +   E A+KA  A  G
Sbjct: 19  EEYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAG 78

Query: 266 KEVDGKIL 273
           ++ DG+ +
Sbjct: 79  RKFDGRTV 86

This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 89

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 208 IKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNG 265
           + N    F  E+ +E+   YG I    ++ ++  G S+G+GFV Y   + A KA     G
Sbjct: 4   VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63

Query: 266 KEVDGKILYV 275
           K++    L+ 
Sbjct: 64  KQLGESTLFA 73

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

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

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 18/72 (25%), Positives = 37/72 (51%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ NLD ++    +   F  FG I    + +  +G +  YGF+ FE  + A+++   ++
Sbjct: 10  LFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGRGQTSTYGFLKFENLDMAHRAKLAMS 69

Query: 173 GMLLNSKIVFVG 184
           G +L    + +G
Sbjct: 70  GKVLRRNPIKIG 81

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

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
           T V++     D  +++L  +FE  G I   R+M +   G++RG+ F+ +   E A++AV+
Sbjct: 2   TEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVK 61

Query: 262 AWNGKEV-DGKILYV 275
             +  E+  GK L V
Sbjct: 62  LCDNYEIRPGKHLGV 76

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding protein Raly

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 22/65 (33%), Positives = 34/65 (52%), Gaps = 8/65 (12%)

Query: 113 VFIKNLDKSIDNKAMYDT-FSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           VFI NL+ ++  K+  +T FS +G ++ C V        KGY FV +  E  A  ++   
Sbjct: 4   VFIGNLNTAVVKKSDVETIFSKYGRVVGCSV-------HKGYAFVQYSNERHARGAVIGE 56

Query: 172 NGMLL 176
           NG +L
Sbjct: 57  NGRVL 61

This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch. . Length = 76

>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing protein YRA2 (Yra2p) and similar proteins

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 4/71 (5%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWN 264
           + I N   D +D  ++++ + +G     +  ++ D ++  F F   E P   EK V+ +N
Sbjct: 3   LRITNIPLDVSDYTIEDLIKEFGEPVYSKFYDHKDSRTAVFEF---EDPSILEKVVEKYN 59

Query: 265 GKEVDGKILYV 275
           GKE++G  + V
Sbjct: 60  GKELNGAKIEV 70

This subfamily corresponds to the RRM of Yra2p, a nonessential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA2 gene. It may share some overlapping functions with Yra1p, and is able to complement an YRA1 deletion when overexpressed in yeast. Yra2p belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. It is a major component of endogenous Yra1p complexes. It interacts with Yra1p and functions as a negative regulator of Yra1p. Yra2p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

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

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 5/57 (8%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSI 168
           NV+I NL +S   + + +    FG I   K+ ++     K   FVHF +   A K +
Sbjct: 5   NVYIGNLPESYSEEELREDLEKFGPIDQIKIVKE-----KNIAFVHFLSIANAIKVV 56

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

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 2/57 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
           +++    ED  +  L++ FE YG I +  ++ +   GK RGFGFV ++  +  +K V
Sbjct: 3   LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIV 59

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQA 262
           ++I    +  N+  ++ MF P+G I   R++   DG SRG  FV + +   A+ A++A
Sbjct: 4   LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 61

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

>gnl|CDD|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 36.7 bits (84), Expect = 0.002
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS-KGYGFVHFETEEAANKSI 168
           N++I+ L     ++ +      +G I+S K   D+  N  KGYGFV F++  AA K++
Sbjct: 3   NLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKV 171
           +F+ +L   + ++ +   FS + S    KV +D++   SKGYGFV F       K+++++
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 172 NG 173
           NG
Sbjct: 69  NG 70

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|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTF-SAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           VFI N+   +  + + D F    G +   ++ +DE+G S+G G V F+ +E+  K++E +
Sbjct: 2   VFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALETM 61

Query: 172 N 172
           N
Sbjct: 62  N 62

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 4/73 (5%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQA 262
           +++    E+  +E + + F  +G I +   +N D   G  +G+  + YE+ + A+ A++ 
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLH-LNLDRRTGFVKGYALIEYETKKEAQAAIEG 67

Query: 263 WNGKEVDGKILYV 275
            NGKE+ G+ + V
Sbjct: 68  LNGKELLGQTISV 80

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|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 16/39 (41%), Positives = 25/39 (64%)

Query: 152 GYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRK 190
           GY FV    +  A+K+IEK+NG +L  K++ V   +P+K
Sbjct: 35  GYAFVDCPDQSWADKAIEKLNGKILQGKVIEVEHSVPKK 73

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 6/72 (8%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAW 263
           +++     +  ++ +K+ F  +G +    +M      + RGFGFV +ES +  +K  +  
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIH 61

Query: 264 ----NGKEVDGK 271
               N K V+ K
Sbjct: 62  FHEINNKMVECK 73

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 4/78 (5%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           T ++I +  +   +E LK +FE YG I S  ++      RG  +V  E+ + A +A+Q  
Sbjct: 3   TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPP----RGCAYVCMETRQDAHRALQKL 58

Query: 264 NGKEVDGKILYVGRAQKK 281
              ++ GK + V  A  K
Sbjct: 59  RNVKLAGKKIKVAWAPNK 76

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 4/60 (6%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
             + ++    +D  + K+++ FE +G   S  ++N+  K    GFV +E+ E AEK   A
Sbjct: 2   IKSFFLFGVEDDLPEYKIRDYFEQFGKSKSV-IVNHRAK---CGFVRFETREAAEKFAAA 57

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

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

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 10/70 (14%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQ--- 261
           NVYI N  E +++E+L+E  E +G I   +++    K +   FV + S   A K V    
Sbjct: 5   NVYIGNLPESYSEEELREDLEKFGPIDQIKIV----KEKNIAFVHFLSIANAIKVVTTLP 60

Query: 262 ---AWNGKEV 268
               +  + +
Sbjct: 61  CEPDYASRRI 70

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

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 2/57 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
           +++    ED  +  L++ FE YG I +  VM +   GK RGF FV ++  +  +K V
Sbjct: 3   IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIV 59

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 4/58 (6%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
           NVYI N  +   +EKL+  F  YG I S     N  + +   FV + +   A KA+  
Sbjct: 5   NVYIGNIDDSLTEEKLRNDFSQYGEIESV----NYLREKNCAFVNFTNISNAIKAIDG 58

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

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 4/62 (6%)

Query: 213 EDFNDEK-LKEMFEPYG-TITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWNGKEV 268
           E + DE  +K  F   G T+ S +++ N   G   G+ FV +     AE+ +   NGK +
Sbjct: 8   EPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHKLNGKPI 67

Query: 269 DG 270
            G
Sbjct: 68  PG 69

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

>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 36.8 bits (85), Expect = 0.002
 Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSI 168
           +F++NL      +++   FS FGS+       D+    +KG GFV F+ +   N  +
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

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

>gnl|CDD|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 206 VYIKNFGEDFNDEKLKE-MFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAW 263
           V+I N   D   + +K+ M E  G +T   +  + +GKSRG G V ++  EF +KA++  
Sbjct: 2   VFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEVM 61

Query: 264 NGKEVDGKILYV 275
           N  +++G+ L +
Sbjct: 62  NKYDLNGRPLNI 73

This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 11/29 (37%), Positives = 17/29 (58%)

Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           + VKNL   + ++RLR+ F   G +T  K
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVK 31

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 2/62 (3%)

Query: 216 NDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
            DE L+ +F  +G I S  V+ +   G S  + F+ +E+ E  E+A    +   +D + +
Sbjct: 16  TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRI 75

Query: 274 YV 275
           +V
Sbjct: 76  HV 77

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

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

 Score = 36.0 bits (83), Expect = 0.003
 Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 115 IKNLDKSI-DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG 173
           I+NL  SI     +   F  +G +    + +   G   G+ FV  +  + A  ++E  NG
Sbjct: 5   IRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENTNG 64

Query: 174 MLLNSKIVFV 183
           + ++ + V V
Sbjct: 65  LEIDGRPVAV 74

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

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

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 14/58 (24%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIE 169
           +F+  L+    +  +   F+ +G +  C V  D     S+G+GF+ F + + A++++E
Sbjct: 5   LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62

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

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 5/62 (8%)

Query: 113 VFIKNLDKSIDN----KAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKS 167
           +F+K  D S+      +++ + FS+ G I    +  D E G SKG+ ++ F++ +   K+
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 168 IE 169
           +E
Sbjct: 62  LE 63

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 35.5 bits (82), Expect = 0.003
 Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIE 169
           +F+ NL        +   F   G I   ++   E  G  KG+ FV FE  E A  +++
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALK 58

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 3/70 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTIT--SYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           +++     D + + LK+ F  +G +T  + ++  N G+SRGFGF+ ++     EK V   
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEK-VLEQ 60

Query: 264 NGKEVDGKIL 273
               +DG+++
Sbjct: 61  KEHRLDGRLI 70

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

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

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +++ NL + +    +   FS  G   SCK+  D  GN   Y FV F     A  S+  +N
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDP-YCFVEFFEHRHAAASLAAMN 60

Query: 173 GMLLNSKIVFV 183
           G  +  K V V
Sbjct: 61  GRKIMGKEVKV 71

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

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           VY+ N   D  + +++++F  YG I     +    +  G+ F+ +E    AE A++  +G
Sbjct: 2   VYVGNLPGDIREREVEDLFYKYGPIVDID-LKLPPRPPGYAFIEFEDARDAEDAIRGRDG 60

Query: 266 KEVDGKILYV 275
            + DG+ L V
Sbjct: 61  YDFDGQRLRV 70

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

>gnl|CDD|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           V++ ++D+ +  + +   FS  G ++ C+V  D     + + F+ F  EE A  ++    
Sbjct: 5   VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLR-FAFIEFTDEEGARAALSLSG 63

Query: 173 GML 175
            ML
Sbjct: 64  TML 66

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 2/57 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
           +++    ED  +  L++ FE YG I    +M +   GK RGF FV ++  +  +K V
Sbjct: 3   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 59

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFG--SILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIE 169
           +++ NL     ++ +    +  G   + S K  + +  G SKG+ +V F +E AA    E
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 170 KVNGMLLNSK 179
           K+ G   N K
Sbjct: 61  KLEGREFNGK 70

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

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

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 16/73 (21%), Positives = 36/73 (49%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           N+FI NLD ++    +   F  +G I    + +  +G    Y F+ F+  + A+++   +
Sbjct: 10  NLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKRPARGQGGAYAFLKFQNLDMAHRAKVAM 69

Query: 172 NGMLLNSKIVFVG 184
           +G ++    + +G
Sbjct: 70  SGRVIGRNPIKIG 82

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

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

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 13/30 (43%), Positives = 19/30 (63%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           +++V +L   ID E LR  F PFG I+ A+
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDAR 30

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 16/74 (21%)

Query: 115 IKNLDKSIDNKAMYDTFSAFGS---------ILSCKVAQDE-------QGNSKGYGFVHF 158
           I+NL KS+D K + + F    S         I   K+ +D        +G SKGYGFV F
Sbjct: 5   IRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEF 64

Query: 159 ETEEAANKSIEKVN 172
              E A K++  +N
Sbjct: 65  TNHEHALKALRALN 78

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 120 KSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIE 169
           KS   + + + F  FG I    + +D+  G SKG+G+V F     A  ++E
Sbjct: 10  KSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 60

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

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

 Score = 35.6 bits (82), Expect = 0.004
 Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHF 158
           +F+  L      + +   FS +G ++ C + +D+  N S+G+GFV F
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKF 48

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

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 35.3 bits (81), Expect = 0.004
 Identities = 16/60 (26%), Positives = 30/60 (50%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +FI  L + +    +       G I   ++  D  GN++GY FV F  ++ A  +I+++N
Sbjct: 4   IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNNRGYAFVTFSNKQEAKNAIKQLN 63

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            +++  +        +   F  FG I    +   + G++  YGFV +     A ++IE  
Sbjct: 4   VIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGDN--YGFVTYRYACDAFRAIEHG 61

Query: 172 N 172
           N
Sbjct: 62  N 62

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	336
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
KOG0145|consensus	360		100.0
KOG0123|consensus	369		100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
KOG0117|consensus	506		100.0
KOG0127|consensus	678		100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
KOG0148|consensus	321		100.0
KOG0117|consensus	506		100.0
KOG0144|consensus	510		100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
KOG0145|consensus	360		100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
KOG0123|consensus	369		99.98
KOG0127|consensus	678		99.98
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.98
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.97
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.97
KOG0110|consensus	725		99.97
KOG0110|consensus	725		99.97
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.97
KOG0124|consensus	544		99.96
KOG0144|consensus	510		99.96
KOG0148|consensus	321		99.96
KOG0147|consensus	549		99.94
KOG0131|consensus	203		99.94
KOG4212|consensus	608		99.93
KOG0131|consensus	203		99.93
KOG1190|consensus	492		99.93
KOG0109|consensus	346		99.92
KOG4211|consensus	510		99.9
KOG0124|consensus	544		99.9
KOG0146|consensus	371		99.89
KOG0109|consensus	346		99.86
KOG0147|consensus	549		99.85
KOG0146|consensus	371		99.84
KOG4205|consensus	311		99.82
KOG0120|consensus	500		99.82
KOG1190|consensus	492		99.8
KOG4205|consensus	311		99.77
KOG0105|consensus	241		99.76
KOG4206|consensus	221		99.75
KOG1365|consensus	508		99.74
KOG1457|consensus	284		99.71
KOG1548|consensus	382		99.7
KOG1456|consensus	494		99.7
KOG4206|consensus	221		99.69
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.69
KOG0105|consensus	241		99.68
KOG1456|consensus	494		99.68
KOG4211|consensus	510		99.68
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.66
KOG4212|consensus	608		99.66
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.63
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.61
KOG0106|consensus	216		99.61
KOG1548|consensus	382		99.58
KOG4307|consensus	944		99.55
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.55
KOG0122|consensus	270		99.54
KOG0122|consensus	270		99.54
KOG1457|consensus	284		99.54
KOG0125|consensus	376		99.53
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.52
KOG0125|consensus	376		99.5
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.47
PLN03120	260	nucleic acid binding protein; Provisional	99.45
PLN03120	260	nucleic acid binding protein; Provisional	99.45
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.45
KOG0106|consensus	216		99.43
KOG0107|consensus	195		99.43
KOG0114|consensus	124		99.43
KOG0121|consensus	153		99.42
smart00362	72	RRM_2 RNA recognition motif.	99.42
KOG0114|consensus	124		99.41
KOG0149|consensus	247		99.41
smart00362	72	RRM_2 RNA recognition motif.	99.4
PLN03213	759	repressor of silencing 3; Provisional	99.4
PLN03213	759	repressor of silencing 3; Provisional	99.39
KOG0121|consensus	153		99.38
PLN03121	243	nucleic acid binding protein; Provisional	99.38
KOG0107|consensus	195		99.38
KOG4207|consensus	256		99.37
KOG4307|consensus	944		99.37
KOG0113|consensus	335		99.36
KOG0149|consensus	247		99.36
KOG0126|consensus	219		99.36
KOG1365|consensus	508		99.36
KOG0126|consensus	219		99.35
PLN03121	243	nucleic acid binding protein; Provisional	99.35
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.34
KOG0113|consensus	335		99.34
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.34
smart00360	71	RRM RNA recognition motif.	99.33
KOG0111|consensus	298		99.33
KOG4207|consensus	256		99.32
KOG0120|consensus	500		99.31
KOG0130|consensus	170		99.31
smart00360	71	RRM RNA recognition motif.	99.31
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.3
KOG0111|consensus	298		99.26
KOG4660|consensus	549		99.22
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.22
KOG0130|consensus	170		99.21
KOG0108|consensus	435		99.19
smart00361	70	RRM_1 RNA recognition motif.	99.18
KOG0108|consensus	435		99.18
smart00361	70	RRM_1 RNA recognition motif.	99.18
KOG0128|consensus	881		99.17
KOG0129|consensus	520		99.16
KOG0129|consensus	520		99.13
KOG4454|consensus	267		99.12
KOG0112|consensus	975		99.05
KOG4454|consensus	267		99.01
KOG0128|consensus	881		98.98
KOG4208|consensus	214		98.97
KOG0226|consensus	290		98.97
KOG0226|consensus	290		98.96
KOG0132|consensus	894		98.91
KOG0112|consensus	975		98.91
KOG0415|consensus	479		98.9
KOG0415|consensus	479		98.89
KOG4210|consensus	285		98.88
KOG0132|consensus	894		98.84
KOG4208|consensus	214		98.83
KOG4210|consensus	285		98.82
KOG0153|consensus	377		98.75
KOG4661|consensus	940		98.74
KOG0153|consensus	377		98.72
KOG0533|consensus	243		98.68
KOG4660|consensus	549		98.56
KOG4676|consensus	479		98.54
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.54
KOG0533|consensus	243		98.52
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.52
KOG4661|consensus	940		98.46
KOG0116|consensus	419		98.39
KOG0151|consensus	877		98.38
KOG0151|consensus	877		98.35
KOG2193|consensus	584		98.34
KOG0116|consensus	419		98.32
KOG4209|consensus	231		98.27
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.2
KOG2193|consensus	584		98.19
KOG4209|consensus	231		98.11
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.06
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.92
KOG4676|consensus	479		97.91
KOG0115|consensus	275		97.79
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.77
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.67
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.65
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.63
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.56
KOG0115|consensus	275		97.47
KOG2314|consensus	698		97.47
KOG1995|consensus	351		97.38
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.31
KOG2202|consensus	260		97.2
KOG2314|consensus	698		97.11
KOG1995|consensus	351		97.05
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.96
KOG3152|consensus	278		96.94
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.94
KOG1996|consensus	378		96.9
KOG2202|consensus	260		96.89
KOG3152|consensus	278		96.85
KOG1855|consensus	484		96.82
KOG1996|consensus	378		96.62
KOG4849|consensus	498		96.58
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.55
KOG4849|consensus	498		96.54
KOG1855|consensus	484		96.52
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.96
KOG2591|consensus	684		95.95
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.72
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.68
KOG2416|consensus	718		95.61
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.5
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.47
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.41
KOG2416|consensus	718		95.4
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.38
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.23
KOG2591|consensus	684		94.95
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.86
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	94.74
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.66
KOG0804|consensus	493		94.09
KOG2068|consensus	327		94.04
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.95
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	93.51
KOG4285|consensus	350		93.29
KOG0804|consensus	493		93.07
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	92.76
KOG2068|consensus	327		92.59
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	91.3
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	91.04
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	90.86
KOG2135|consensus	526		88.77
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	88.27
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	87.92
KOG2135|consensus	526		85.82
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	85.27
KOG4574|consensus	1007		84.35
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	82.81

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

Probab=100.00  E-value=1.2e-53  Score=408.55  Aligned_cols=310  Identities=56%  Similarity=0.883  Sum_probs=279.8

Q ss_pred             ceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEE
Q psy12549         19 HNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIM   97 (336)
Q Consensus        19 ~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~   97 (336)
                      .+|||+|||+++||++|+++| .+|.+.+|++.++.   .|++++|||||+|.+.  ++|++|++.+++..+.|++|+|.
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~---~t~~s~G~afV~F~~~--~~A~~Al~~ln~~~i~gk~i~i~   75 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDS---VTRRSLGYGYVNFQNP--ADAERALETMNFKRLGGKPIRIM   75 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC---CCCCcceEEEEEECCH--HHHHHHHHHhCCCEECCeeEEee
Confidence            379999999999999999999 77788999999988   4789999999999999  99999999999999999999999


Q ss_pred             eccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeC
Q psy12549         98 WSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLN  177 (336)
Q Consensus        98 ~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~  177 (336)
                      |+..++........+|||+|||.++++++|+++|+.||.|.+|++..+..|+++|||||+|.+.++|.+|++.++|..+.
T Consensus        76 ~s~~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~  155 (562)
T TIGR01628        76 WSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLN  155 (562)
T ss_pred             cccccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEec
Confidence            99888777777778999999999999999999999999999999999998999999999999999999999999999999


Q ss_pred             CeEEEEeeccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHH
Q psy12549        178 SKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFA  256 (336)
Q Consensus       178 ~~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a  256 (336)
                      |+.+.+....+.....   .......++|||+|||.++++++|+++|+.||.|.++.+.. .++.++|+|||+|.+.++|
T Consensus       156 ~~~i~v~~~~~~~~~~---~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A  232 (562)
T TIGR01628       156 DKEVYVGRFIKKHERE---AAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDA  232 (562)
T ss_pred             CceEEEeccccccccc---cccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHH
Confidence            9999998766554432   11233447899999999999999999999999999999987 6788899999999999999


Q ss_pred             HHHHHHhCCceec----CEEEEEeecccchhhHHHHHHHHHHHHHHhhcCCCCceEEEecCCCCCCHHHHHHhcCCCCCe
Q psy12549        257 EKAVQAWNGKEVD----GKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTI  332 (336)
Q Consensus       257 ~~a~~~l~g~~~~----g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~V  332 (336)
                      .+|++.++|..+.    |+.+.|.++..+.......................+++|||+||+..+++++|+++|++||.|
T Consensus       233 ~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i  312 (562)
T TIGR01628       233 AKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEI  312 (562)
T ss_pred             HHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCe
Confidence            9999999999999    999999999888777666666666555555566778899999999999999999999999999


Q ss_pred             eecC
Q psy12549        333 TSAK  336 (336)
Q Consensus       333 ~~vk  336 (336)
                      .+||
T Consensus       313 ~~~~  316 (562)
T TIGR01628       313 TSAK  316 (562)
T ss_pred             EEEE
Confidence            9875

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=5.5e-47  Score=343.64  Aligned_cols=261  Identities=22%  Similarity=0.381  Sum_probs=226.6

Q ss_pred             ccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeee
Q psy12549         16 IPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPI   94 (336)
Q Consensus        16 ~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i   94 (336)
                      .++++|||+|||++++|++|+++| .+|.+.++++++++   .+|+++|||||+|.+.  ++|.+|++.+||..+.|++|
T Consensus         1 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~---~~g~s~g~afV~f~~~--~~A~~Ai~~l~g~~l~g~~i   75 (352)
T TIGR01661         1 ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDK---VTGQSLGYGFVNYVRP--EDAEKAVNSLNGLRLQNKTI   75 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcC---CCCccceEEEEEECcH--HHHHHHHhhcccEEECCeeE
Confidence            367899999999999999999999 77888999999987   4689999999999999  99999999999999999999


Q ss_pred             EEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCC
Q psy12549         95 RIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNG  173 (336)
Q Consensus        95 ~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~  173 (336)
                      .|.++.+...  ....++|||+|||..+++++|+++|+.||.+..+.++.+. ++.++|||||+|.+.++|..|++.|||
T Consensus        76 ~v~~a~~~~~--~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g  153 (352)
T TIGR01661        76 KVSYARPSSD--SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNG  153 (352)
T ss_pred             EEEeeccccc--ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCC
Confidence            9999865432  2345789999999999999999999999999999999886 678999999999999999999999999


Q ss_pred             ceeCC--eEEEEeeccCchhhhHh---------------h----------------------------------------
Q psy12549        174 MLLNS--KIVFVGKFIPRKEREKE---------------L----------------------------------------  196 (336)
Q Consensus       174 ~~~~~--~~i~v~~~~~~~~~~~~---------------~----------------------------------------  196 (336)
                      ..+.|  .++.+.++.........               .                                        
T Consensus       154 ~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  233 (352)
T TIGR01661       154 TTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQH  233 (352)
T ss_pred             CccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhc
Confidence            98876  67788776533210000               0                                        


Q ss_pred             -----------h------------------ccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceE
Q psy12549        197 -----------G------------------EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGF  245 (336)
Q Consensus       197 -----------~------------------~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~  245 (336)
                                 .                  .......+|||+|||.++++++|+++|++||.|.+++++.  .+|.++||
T Consensus       234 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~  313 (352)
T TIGR01661       234 AVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGY  313 (352)
T ss_pred             ccccccccccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccce
Confidence                       0                  0001112599999999999999999999999999999987  48999999


Q ss_pred             EEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchh
Q psy12549        246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAE  283 (336)
Q Consensus       246 afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~  283 (336)
                      |||+|.+.++|.+|+..|||..+.|+.|+|.|+..+..
T Consensus       314 aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       314 GFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             EEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCCCC
Confidence            99999999999999999999999999999999987753

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

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

Probab=100.00  E-value=1.8e-45  Score=343.89  Aligned_cols=303  Identities=18%  Similarity=0.231  Sum_probs=238.7

Q ss_pred             cCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhc--CccccCCee
Q psy12549         17 PKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTM--NFDALKGRP   93 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~--~~~~~~g~~   93 (336)
                      |+++|+|+|||++++|++|+++| .+|.+.++.++++         +|||||+|.+.  ++|+.|++.+  ++..+.|++
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~---------k~~afVef~~~--e~A~~Ai~~~~~~~~~l~g~~   69 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG---------KRQALVEFEDE--ESAKACVNFATSVPIYIRGQP   69 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC---------CCEEEEEeCch--HHHHHHHHHhhcCCceEcCeE
Confidence            78899999999999999999999 7889999988864         47899999999  9999999864  678999999


Q ss_pred             eEEEeccCCCCcC----------CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHH
Q psy12549         94 IRIMWSQRDPSLR----------KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEA  163 (336)
Q Consensus        94 i~v~~~~~~~~~~----------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~  163 (336)
                      |+|.|+.......          .....+|+|+||+..+|+++|+++|+.||.|.+|.+.++.   .+++|||+|.+.++
T Consensus        70 l~v~~s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~---~~~~afVef~~~~~  146 (481)
T TIGR01649        70 AFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN---NVFQALVEFESVNS  146 (481)
T ss_pred             EEEEecCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC---CceEEEEEECCHHH
Confidence            9999986532111          1122479999999999999999999999999999998754   24689999999999


Q ss_pred             HHHHHHHhCCceeCC--eEEEEeeccCchhh--------------------h-----------Hh---------------
Q psy12549        164 ANKSIEKVNGMLLNS--KIVFVGKFIPRKER--------------------E-----------KE---------------  195 (336)
Q Consensus       164 a~~a~~~l~~~~~~~--~~i~v~~~~~~~~~--------------------~-----------~~---------------  195 (336)
                      |.+|++.|||..+.+  +.|.|.++.+..-.                    .           ..               
T Consensus       147 A~~A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  226 (481)
T TIGR01649       147 AQHAKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYS  226 (481)
T ss_pred             HHHHHHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccc
Confidence            999999999999854  57888776542100                    0           00               


Q ss_pred             --------------hh---------------------------ccccccceEEEcCCCC-CCcHHHHHHhhccCCceeEE
Q psy12549        196 --------------LG---------------------------EKAKLFTNVYIKNFGE-DFNDEKLKEMFEPYGTITSY  233 (336)
Q Consensus       196 --------------~~---------------------------~~~~~~~~l~V~nlp~-~~t~~~l~~~f~~~g~i~~~  233 (336)
                                    .+                           ....+.++|||+|||. .+++++|+++|+.||.|.++
T Consensus       227 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~v  306 (481)
T TIGR01649       227 SHGGPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERV  306 (481)
T ss_pred             cCCCCCCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEE
Confidence                          00                           0012346899999997 69999999999999999999


Q ss_pred             EEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchhhHHHH-------H--HHHHHHHHHh-----
Q psy12549        234 RVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQEL-------K--RRFEMLKIER-----  299 (336)
Q Consensus       234 ~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~~~~~~-------~--~~~~~~~~~~-----  299 (336)
                      +++..   .+|+|||+|.+.++|..|+..|||..+.|+.|+|.++..........       .  ..+......+     
T Consensus       307 ki~~~---~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~  383 (481)
T TIGR01649       307 KFMKN---KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPG  383 (481)
T ss_pred             EEEeC---CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcc
Confidence            99864   36899999999999999999999999999999999986542111000       0  0000000000     


Q ss_pred             -----hcCCCCceEEEecCCCCCCHHHHHHhcCCCCC--eeecC
Q psy12549        300 -----LNRYQGVNLYVKNLDDSIDDERLRKEFTPFGT--ITSAK  336 (336)
Q Consensus       300 -----~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~--V~~vk  336 (336)
                           ...+++.+|+|+|||..+++++|+++|++||.  |.+||
T Consensus       384 ~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik  427 (481)
T TIGR01649       384 SANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFK  427 (481)
T ss_pred             cccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEE
Confidence                 01245678999999999999999999999998  77664

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

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

Probab=100.00  E-value=5.1e-44  Score=331.73  Aligned_cols=294  Identities=17%  Similarity=0.230  Sum_probs=239.8

Q ss_pred             cCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccC-Ceee
Q psy12549         17 PKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALK-GRPI   94 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~-g~~i   94 (336)
                      ..++|||+|||++++|++|+++| .++.+.++++++|.    +|+++|||||+|.+.  ++|++|++.+|+..+. |+.+
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~----sG~sRGfaFV~F~~~--e~A~~Ai~~lng~~i~~Gr~l  130 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDF----SGQNRGYAFVTFCGK--EEAKEAVKLLNNYEIRPGRLL  130 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECC----CCCccceEEEEeCCH--HHHHHHHHHcCCCeecCCccc
Confidence            34789999999999999999999 77788899999984    689999999999999  9999999999998885 7887


Q ss_pred             EEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCC-eeEEEEeeCC--CCCcccEEEEEeCCHHHHHHHHHHh
Q psy12549         95 RIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGS-ILSCKVAQDE--QGNSKGYGFVHFETEEAANKSIEKV  171 (336)
Q Consensus        95 ~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~-v~~~~~~~~~--~~~~~g~afV~F~~~~~a~~a~~~l  171 (336)
                      .+.++..        .++|||+|||.++++++|.+.|++++. +..+.+....  .++++|||||+|.+.++|..|++.|
T Consensus       131 ~V~~S~~--------~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL  202 (578)
T TIGR01648       131 GVCISVD--------NCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKL  202 (578)
T ss_pred             ccccccc--------CceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHh
Confidence            7776532        478999999999999999999999974 4444444332  4678999999999999999999988


Q ss_pred             CC--ceeCCeEEEEeeccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccC--CceeEEEEeCCCCccceEEE
Q psy12549        172 NG--MLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPY--GTITSYRVMNNDGKSRGFGF  247 (336)
Q Consensus       172 ~~--~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~--g~i~~~~i~~~~~~~~g~af  247 (336)
                      +.  ..+.|+.|.|.|+.+.......   .....++|||+|||.++++++|+++|+.|  |.|.++.++      ++|||
T Consensus       203 ~~gki~l~Gr~I~VdwA~p~~~~d~~---~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~------rgfAF  273 (578)
T TIGR01648       203 MPGRIQLWGHVIAVDWAEPEEEVDED---VMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI------RDYAF  273 (578)
T ss_pred             hccceEecCceEEEEeeccccccccc---ccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee------cCeEE
Confidence            64  4688999999998876533221   12233689999999999999999999999  999999876      67999


Q ss_pred             EEeCCHHHHHHHHHHhCCceecCEEEEEeecccchhhHHH----------HHHHHHHHHHHhhcCCCCceEEEecCCCCC
Q psy12549        248 VAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQE----------LKRRFEMLKIERLNRYQGVNLYVKNLDDSI  317 (336)
Q Consensus       248 V~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~  317 (336)
                      |+|.+.++|.+|++.|||..|.|+.|+|.|+.+.......          ........+-.....+...++++.|+++..
T Consensus       274 VeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~~~~~~~~rg~gg~~~~~~~~~~~~g~~~sp~s~~~~~g~~~~~~  353 (578)
T TIGR01648       274 VHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYHP  353 (578)
T ss_pred             EEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCcccccccccccCCCcccccccccccCcccCccccccccccccccc
Confidence            9999999999999999999999999999999876433110          000000011111223456789999999999


Q ss_pred             CHHHHHHhcCCCCCee
Q psy12549        318 DDERLRKEFTPFGTIT  333 (336)
Q Consensus       318 t~~~l~~~F~~~G~V~  333 (336)
                      +++.+.++|..+|.|.
T Consensus       354 ~~~~~~~~f~~~g~~~  369 (578)
T TIGR01648       354 PYAPSLHFPRMPGPIR  369 (578)
T ss_pred             cccchhhccccCcccc
Confidence            9999999999999874

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.

>KOG0145|consensus

Probab=100.00  E-value=1.3e-43  Score=285.52  Aligned_cols=262  Identities=23%  Similarity=0.368  Sum_probs=230.2

Q ss_pred             CccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCC
Q psy12549         13 GIIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKG   91 (336)
Q Consensus        13 ~~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g   91 (336)
                      +....++||+|.-||..||++|+|++| +.|+++++++++|+   .+|+|.||+||.|-++  ++|++|+..+||..+..
T Consensus        36 ~t~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDK---itGqSLGYGFVNYv~p--~DAe~AintlNGLrLQ~  110 (360)
T KOG0145|consen   36 DTDESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDK---ITGQSLGYGFVNYVRP--KDAEKAINTLNGLRLQN  110 (360)
T ss_pred             CcCcccceeeeeecccccCHHHHHHHhhcccceeeeeeeecc---ccccccccceeeecCh--HHHHHHHhhhcceeecc
Confidence            357889999999999999999999999 77899999999999   6999999999999999  99999999999999999


Q ss_pred             eeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHH
Q psy12549         92 RPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK  170 (336)
Q Consensus        92 ~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~  170 (336)
                      +.|+|+++.+.  .......+|||.+||..+|..||.++|++||.|..-++..|. +|.++|.+||.|+...+|..|+..
T Consensus       111 KTIKVSyARPS--s~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~  188 (360)
T KOG0145|consen  111 KTIKVSYARPS--SDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKG  188 (360)
T ss_pred             ceEEEEeccCC--hhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHh
Confidence            99999997554  344566889999999999999999999999998888888887 899999999999999999999999


Q ss_pred             hCCceeCC--eEEEEeeccCchhhhHhh-----------------h----------------------------------
Q psy12549        171 VNGMLLNS--KIVFVGKFIPRKEREKEL-----------------G----------------------------------  197 (336)
Q Consensus       171 l~~~~~~~--~~i~v~~~~~~~~~~~~~-----------------~----------------------------------  197 (336)
                      |||..-.|  -+|.|.++..+.......                 .                                  
T Consensus       189 lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~  268 (360)
T KOG0145|consen  189 LNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAG  268 (360)
T ss_pred             ccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeee
Confidence            99987654  578887776443211000                 0                                  


Q ss_pred             ----ccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCE
Q psy12549        198 ----EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK  271 (336)
Q Consensus       198 ----~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~  271 (336)
                          ......-+|||.||..++++.-|+++|.+||.|..+++++  .+.+.+||+||.+.+.++|..|+..|||..++++
T Consensus       269 ~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~r  348 (360)
T KOG0145|consen  269 VNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDR  348 (360)
T ss_pred             eccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccce
Confidence                0001115799999999999999999999999999999999  6688899999999999999999999999999999


Q ss_pred             EEEEeecccc
Q psy12549        272 ILYVGRAQKK  281 (336)
Q Consensus       272 ~l~v~~~~~~  281 (336)
                      .|.|+|...+
T Consensus       349 vLQVsFKtnk  358 (360)
T KOG0145|consen  349 VLQVSFKTNK  358 (360)
T ss_pred             EEEEEEecCC
Confidence            9999997765

>KOG0123|consensus

Probab=100.00  E-value=3e-43  Score=313.16  Aligned_cols=298  Identities=59%  Similarity=0.883  Sum_probs=274.9

Q ss_pred             ceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEE
Q psy12549         19 HNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIM   97 (336)
Q Consensus        19 ~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~   97 (336)
                      ..||||   +++||..|.+.| ..+.+.++++.++.     + +.|||||.|.++  ++|++|++++|...+.|++|+|+
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-----t-slgy~yvnf~~~--~da~~A~~~~n~~~~~~~~~rim   70 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-----T-SLGYAYVNFQQP--ADAERALDTMNFDVLKGKPIRIM   70 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-----C-ccceEEEecCCH--HHHHHHHHHcCCcccCCcEEEee
Confidence            358888   999999999999 77788999999966     2 999999999999  99999999999999999999999


Q ss_pred             eccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeC
Q psy12549         98 WSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLN  177 (336)
Q Consensus        98 ~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~  177 (336)
                      |+..++..       +||.||+++++.++|...|+.||+|.+|++..+..| ++|| ||+|++++.|.+|+..+||..+.
T Consensus        71 ~s~rd~~~-------~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~  141 (369)
T KOG0123|consen   71 WSQRDPSL-------VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLN  141 (369)
T ss_pred             hhccCCce-------eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccC
Confidence            99988765       999999999999999999999999999999999988 9999 99999999999999999999999


Q ss_pred             CeEEEEeeccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHH
Q psy12549        178 SKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFA  256 (336)
Q Consensus       178 ~~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a  256 (336)
                      |++|.|....++..+.............+++.|++.+.+++.|.+.|+.+|+|..+.++. ..+.+++|+||.|.++++|
T Consensus       142 ~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a  221 (369)
T KOG0123|consen  142 GKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDA  221 (369)
T ss_pred             CCeeEEeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHH
Confidence            999999998888777655555555567899999999999999999999999999999998 7777899999999999999


Q ss_pred             HHHHHHhCCceecCEEEEEeecccchhhHHHHHHHHHHHHHHhhcCCCCceEEEecCCCCCCHHHHHHhcCCCCCeeecC
Q psy12549        257 EKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK  336 (336)
Q Consensus       257 ~~a~~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~V~~vk  336 (336)
                      ..|++.|++..+.|..+.|..+..+.+........+...........+..+|+|+|++..++.+.|++.|+.||+|.++|
T Consensus       222 ~~av~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~k  301 (369)
T KOG0123|consen  222 KKAVETLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAK  301 (369)
T ss_pred             HHHHHhccCCcCCccceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcccceeeEE
Confidence            99999999999999999999999988877777777777777777778889999999999999999999999999999864

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

Probab=100.00  E-value=4.3e-42  Score=328.97  Aligned_cols=272  Identities=32%  Similarity=0.479  Sum_probs=237.6

Q ss_pred             cCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeE
Q psy12549         17 PKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIR   95 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~   95 (336)
                      ..++|||+|||+++++++|+++| .+|.+.++++..+.    +|+++|||||+|.+.  ++|.+|++.+||..+.|+.|.
T Consensus        87 ~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~----~g~skg~afV~F~~~--e~A~~Ai~~lng~~~~~~~i~  160 (562)
T TIGR01628        87 GVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE----NGKSRGYGFVHFEKE--ESAKAAIQKVNGMLLNDKEVY  160 (562)
T ss_pred             CCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC----CCCcccEEEEEECCH--HHHHHHHHHhcccEecCceEE
Confidence            35689999999999999999999 77788999998876    478999999999999  999999999999999999999


Q ss_pred             EEeccCCCCc---CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhC
Q psy12549         96 IMWSQRDPSL---RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN  172 (336)
Q Consensus        96 v~~~~~~~~~---~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~  172 (336)
                      +.........   .....++|||+|||.++|+++|+++|+.||.|.++.+..+..|.++|||||.|.+.++|.+|++.++
T Consensus       161 v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~  240 (562)
T TIGR01628       161 VGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMN  240 (562)
T ss_pred             EeccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhC
Confidence            9765443222   2334578999999999999999999999999999999999889999999999999999999999999


Q ss_pred             CceeC----CeEEEEeeccCchhhhHhhh----------ccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-
Q psy12549        173 GMLLN----SKIVFVGKFIPRKEREKELG----------EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-  237 (336)
Q Consensus       173 ~~~~~----~~~i~v~~~~~~~~~~~~~~----------~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-  237 (336)
                      +..+.    |+.+.+.++..+..+.....          ......++|||+||+..+++++|+++|+.||.|.+++++. 
T Consensus       241 g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d  320 (562)
T TIGR01628       241 GKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD  320 (562)
T ss_pred             CcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC
Confidence            99999    99999988876654421111          1123346799999999999999999999999999999988 


Q ss_pred             CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchhhHHHHHHHHHH
Q psy12549        238 NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEM  294 (336)
Q Consensus       238 ~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~~~~  294 (336)
                      .+|.++|+|||+|.+.++|.+|+..|||..++|+.|.|.++..+..+.......+.+
T Consensus       321 ~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~~~~~~~~~~~q  377 (562)
T TIGR01628       321 EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQ  377 (562)
T ss_pred             CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHHHHHHHHHHHHH
Confidence            678899999999999999999999999999999999999999888776665555543

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

>KOG0117|consensus

Probab=100.00  E-value=2.2e-42  Score=297.82  Aligned_cols=247  Identities=21%  Similarity=0.330  Sum_probs=221.7

Q ss_pred             ceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccC-CeeeEE
Q psy12549         19 HNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALK-GRPIRI   96 (336)
Q Consensus        19 ~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~-g~~i~v   96 (336)
                      ..||||.||.++.|++|..+| +.+.+-++++++|+   .+|.+||||||.|.+.  ++|++|++.||+.+|. |+.|.|
T Consensus        84 ~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~---~sG~nRGYAFVtf~~K--e~Aq~Aik~lnn~Eir~GK~igv  158 (506)
T KOG0117|consen   84 CEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDP---FSGDNRGYAFVTFCTK--EEAQEAIKELNNYEIRPGKLLGV  158 (506)
T ss_pred             ceEEecCCCccccchhhHHHHHhccceeeEEEeecc---cCCCCcceEEEEeecH--HHHHHHHHHhhCccccCCCEeEE
Confidence            359999999999999999999 77799999999998   4799999999999999  9999999999999885 899999


Q ss_pred             EeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCC-eeEEEEeeCC--CCCcccEEEEEeCCHHHHHHHHHHhCC
Q psy12549         97 MWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGS-ILSCKVAQDE--QGNSKGYGFVHFETEEAANKSIEKVNG  173 (336)
Q Consensus        97 ~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~-v~~~~~~~~~--~~~~~g~afV~F~~~~~a~~a~~~l~~  173 (336)
                      +.+..+        ++|||+|||.+.++++|.+.+++.++ |..|.++.++  ..+++|||||+|.+...|..|...|-.
T Consensus       159 c~Svan--------~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~  230 (506)
T KOG0117|consen  159 CVSVAN--------CRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMP  230 (506)
T ss_pred             EEeeec--------ceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccC
Confidence            988654        67999999999999999999999986 7778888876  457899999999999999999988744


Q ss_pred             --ceeCCeEEEEeeccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeC
Q psy12549        174 --MLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYE  251 (336)
Q Consensus       174 --~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~  251 (336)
                        ..++|+.+.|.|+.+..........+.   ..|||+||+.++|+|.|+++|+.||.|++|+.+      +.||||+|.
T Consensus       231 g~~klwgn~~tVdWAep~~e~ded~ms~V---KvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~------rDYaFVHf~  301 (506)
T KOG0117|consen  231 GKIKLWGNAITVDWAEPEEEPDEDTMSKV---KVLYVRNLMESTTEETLKKLFNEFGKVERVKKP------RDYAFVHFA  301 (506)
T ss_pred             CceeecCCcceeeccCcccCCChhhhhhe---eeeeeeccchhhhHHHHHHHHHhccceEEeecc------cceeEEeec
Confidence              457999999999999877665533333   569999999999999999999999999999887      669999999


Q ss_pred             CHHHHHHHHHHhCCceecCEEEEEeecccchhhHHH
Q psy12549        252 SPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQE  287 (336)
Q Consensus       252 ~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~~~~~  287 (336)
                      ++++|.+|++.+||..++|..|.|.+|++..+....
T Consensus       302 eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k~~  337 (506)
T KOG0117|consen  302 EREDAVKAMKETNGKELDGSPIEVTLAKPVDKKKKE  337 (506)
T ss_pred             chHHHHHHHHHhcCceecCceEEEEecCChhhhccc
Confidence            999999999999999999999999999998766554

>KOG0127|consensus

Probab=100.00  E-value=7.1e-40  Score=288.54  Aligned_cols=304  Identities=21%  Similarity=0.324  Sum_probs=246.2

Q ss_pred             ceeeeecCchhhhhhhHHhhhccc-CCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEE
Q psy12549         19 HNVATRELSAKVVEGVSRSLSSLI-DGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIM   97 (336)
Q Consensus        19 ~~v~v~~lp~~~~e~~l~~~f~~~-~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~   97 (336)
                      .+|+|++||++++.++|.++|+.. ++...-++.+.+   ++.+|||+||.|.-.  ++++.|+....+..|.|+.|++.
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~g---s~~~RGfgfVtFam~--ED~qrA~~e~~~~kf~Gr~l~v~   80 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKG---SSEKRGFGFVTFAME--EDVQRALAETEQSKFEGRILNVD   80 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCC---cccccCccceeeehH--hHHHHHHHHhhcCcccceecccc
Confidence            689999999999999999999655 666778888775   578999999999999  99999999999999999999999


Q ss_pred             eccCCCCcC------------------------CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccE
Q psy12549         98 WSQRDPSLR------------------------KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGY  153 (336)
Q Consensus        98 ~~~~~~~~~------------------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~  153 (336)
                      ++....+..                        ......|+|+|||..+.+.+|+.+|+.||.|.++.|++.+.|...||
T Consensus        81 ~A~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGF  160 (678)
T KOG0127|consen   81 PAKKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGF  160 (678)
T ss_pred             cccccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccce
Confidence            877654422                        01145899999999999999999999999999999998888887899


Q ss_pred             EEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchhhhHhh-------------------------------------
Q psy12549        154 GFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKEL-------------------------------------  196 (336)
Q Consensus       154 afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~-------------------------------------  196 (336)
                      |||+|....+|..|++.+|+..++||+|.|.|+.++..-....                                     
T Consensus       161 aFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~e  240 (678)
T KOG0127|consen  161 AFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSE  240 (678)
T ss_pred             EEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhccccccc
Confidence            9999999999999999999999999999999987643211000                                     


Q ss_pred             ------h---------------------------------------ccccccceEEEcCCCCCCcHHHHHHhhccCCcee
Q psy12549        197 ------G---------------------------------------EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTIT  231 (336)
Q Consensus       197 ------~---------------------------------------~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~  231 (336)
                            +                                       .......+|||+|||+++|+++|.+.|++||+|.
T Consensus       241 deEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~  320 (678)
T KOG0127|consen  241 DEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVK  320 (678)
T ss_pred             ccccccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccce
Confidence                  0                                       0000016899999999999999999999999999


Q ss_pred             EEEEeC--CCCccceEEEEEeCCHHHHHHHHHHh-----CC-ceecCEEEEEeecccchhhHHHHHH-------------
Q psy12549        232 SYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW-----NG-KEVDGKILYVGRAQKKAERTQELKR-------------  290 (336)
Q Consensus       232 ~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l-----~g-~~~~g~~l~v~~~~~~~~~~~~~~~-------------  290 (336)
                      ++.++.  .++.+.|.|||.|.+..+|..||...     .| ..+.||.|.|..+..+.....-...             
T Consensus       321 ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~RkeA~dmeqkk~~Kk~~gkrNLy  400 (678)
T KOG0127|consen  321 YAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRKEAADMEQKKKRKKPKGKRNLY  400 (678)
T ss_pred             eEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccchHHHHHHHHHhhhhccCCcccee
Confidence            998887  89999999999999999999999876     23 6689999999999776543222110             


Q ss_pred             --------------------------HHHHHHHHhh----cCCCCceEEEecCCCCCCHHHHHHhcC
Q psy12549        291 --------------------------RFEMLKIERL----NRYQGVNLYVKNLDDSIDDERLRKEFT  327 (336)
Q Consensus       291 --------------------------~~~~~~~~~~----~~~~~~~l~v~nlp~~~t~~~l~~~F~  327 (336)
                                                .+........    -..+.+.|+|+|||..++...|..+..
T Consensus       401 La~EG~I~~gt~aAeglS~~Dm~kRer~~~~k~k~lknpnlhlSrtRL~i~Nlpramn~KqL~~Ll~  467 (678)
T KOG0127|consen  401 LAREGLIRDGTPAAEGLSATDMAKRERIAERKRKKLKNPNLHLSRTRLVIRNLPRAMNPKQLNRLLR  467 (678)
T ss_pred             eeccCccccCChhhcccchhhHHHHHHHHHHHHHhhcCCceeeehhhhhhhcCccccCHHHHHHHHH
Confidence                                      0111111111    112457799999999999999887654

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

Probab=100.00  E-value=1.9e-37  Score=290.43  Aligned_cols=260  Identities=22%  Similarity=0.268  Sum_probs=216.6

Q ss_pred             ccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCe
Q psy12549         14 IIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGR   92 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~   92 (336)
                      ...+.++|||+|||..+++++|+++| .+|.+..|+++.++   .+|.++|||||+|.+.  ++|.+|+. ++|..+.|+
T Consensus        85 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~---~~~~skg~afVeF~~~--e~A~~Al~-l~g~~~~g~  158 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDR---NSRRSKGVAYVEFYDV--ESVIKALA-LTGQMLLGR  158 (457)
T ss_pred             cccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecC---CCCCcceEEEEEECCH--HHHHHHHH-hCCCEECCe
Confidence            34567899999999999999999999 77788899999987   4789999999999999  99999998 999999999


Q ss_pred             eeEEEeccCCCC----------cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCH
Q psy12549         93 PIRIMWSQRDPS----------LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETE  161 (336)
Q Consensus        93 ~i~v~~~~~~~~----------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~  161 (336)
                      +|.|.++.....          ......++|||+|||..+++++|+++|+.||.|..|.++.++ +|.++|||||+|.+.
T Consensus       159 ~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~  238 (457)
T TIGR01622       159 PIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDA  238 (457)
T ss_pred             eeEEeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCH
Confidence            999987543211          111225789999999999999999999999999999999987 568999999999999


Q ss_pred             HHHHHHHHHhCCceeCCeEEEEeeccCchhhh----------------------------H-----h---------h---
Q psy12549        162 EAANKSIEKVNGMLLNSKIVFVGKFIPRKERE----------------------------K-----E---------L---  196 (336)
Q Consensus       162 ~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~----------------------------~-----~---------~---  196 (336)
                      ++|.+|+..|+|..+.|+.|.|.++.......                            .     .         .   
T Consensus       239 e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  318 (457)
T TIGR01622       239 EEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSK  318 (457)
T ss_pred             HHHHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccch
Confidence            99999999999999999999999954211000                            0     0         0   


Q ss_pred             -------------------------------------hccccccceEEEcCCCCCCc----------HHHHHHhhccCCc
Q psy12549        197 -------------------------------------GEKAKLFTNVYIKNFGEDFN----------DEKLKEMFEPYGT  229 (336)
Q Consensus       197 -------------------------------------~~~~~~~~~l~V~nlp~~~t----------~~~l~~~f~~~g~  229 (336)
                                                           ........+|+|.|+....+          .+||++.|++||.
T Consensus       319 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~  398 (457)
T TIGR01622       319 IALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGG  398 (457)
T ss_pred             hhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCC
Confidence                                                 00012235688888854433          3689999999999


Q ss_pred             eeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        230 ITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       230 i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      |..+.+..  ....|++||+|.++++|.+|+..|||..|+|+.|.+.|....
T Consensus       399 v~~v~v~~--~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~  448 (457)
T TIGR01622       399 VVHIYVDT--KNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVND  448 (457)
T ss_pred             eeEEEEeC--CCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHH
Confidence            99998874  235789999999999999999999999999999999998755

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.

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

Probab=100.00  E-value=4e-37  Score=292.20  Aligned_cols=261  Identities=15%  Similarity=0.181  Sum_probs=204.0

Q ss_pred             ccccCceeeeecCchhhhhhhHHhhhccc-CCce------EEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCc
Q psy12549         14 IIIPKHNVATRELSAKVVEGVSRSLSSLI-DGNT------VKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNF   86 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~~~e~~l~~~f~~~-~~~~------v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~   86 (336)
                      .....++|||+|||+.+|+++|+++|... ....      ...+.+   ...+.++|||||+|.+.  ++|..|+. |+|
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~---~~~~~~kg~afVeF~~~--e~A~~Al~-l~g  244 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSS---VNINKEKNFAFLEFRTV--EEATFAMA-LDS  244 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEE---EEECCCCCEEEEEeCCH--HHHhhhhc-CCC
Confidence            34567889999999999999999999431 1100      001110   01345779999999999  99999996 999


Q ss_pred             cccCCeeeEEEeccCCCC---------------------------cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeE
Q psy12549         87 DALKGRPIRIMWSQRDPS---------------------------LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILS  139 (336)
Q Consensus        87 ~~~~g~~i~v~~~~~~~~---------------------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~  139 (336)
                      ..+.|++|.|........                           ......++|||+|||..+++++|+++|+.||.|..
T Consensus       245 ~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~  324 (509)
T TIGR01642       245 IIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKA  324 (509)
T ss_pred             eEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeE
Confidence            999999999964322110                           01123468999999999999999999999999999


Q ss_pred             EEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchhhhHh---------------h-----hc
Q psy12549        140 CKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKE---------------L-----GE  198 (336)
Q Consensus       140 ~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~---------------~-----~~  198 (336)
                      +.++.+. +|.++|||||+|.+.++|..|+..|+|..+.|+.|.|.++.........               .     ..
T Consensus       325 ~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  404 (509)
T TIGR01642       325 FNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQI  404 (509)
T ss_pred             EEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhhccc
Confidence            9999986 7889999999999999999999999999999999999887532211000               0     00


Q ss_pred             cccccceEEEcCCCCC--C--------cHHHHHHhhccCCceeEEEEeCC-----CCccceEEEEEeCCHHHHHHHHHHh
Q psy12549        199 KAKLFTNVYIKNFGED--F--------NDEKLKEMFEPYGTITSYRVMNN-----DGKSRGFGFVAYESPEFAEKAVQAW  263 (336)
Q Consensus       199 ~~~~~~~l~V~nlp~~--~--------t~~~l~~~f~~~g~i~~~~i~~~-----~~~~~g~afV~F~~~~~a~~a~~~l  263 (336)
                      ...+...|++.|+...  +        ..++|++.|+.||.|..|.|++.     ++.+.|+|||+|.+.++|.+|+..|
T Consensus       405 ~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~l  484 (509)
T TIGR01642       405 GGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGM  484 (509)
T ss_pred             cCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHc
Confidence            1123467899998632  1        23689999999999999999863     2345789999999999999999999


Q ss_pred             CCceecCEEEEEeeccc
Q psy12549        264 NGKEVDGKILYVGRAQK  280 (336)
Q Consensus       264 ~g~~~~g~~l~v~~~~~  280 (336)
                      ||..|.|+.|.+.|...
T Consensus       485 nGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       485 NGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             CCCEECCeEEEEEEeCH
Confidence            99999999999999764

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

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

Probab=100.00  E-value=1.6e-36  Score=283.75  Aligned_cols=250  Identities=15%  Similarity=0.193  Sum_probs=206.5

Q ss_pred             ceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCC--eeeE
Q psy12549         19 HNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKG--RPIR   95 (336)
Q Consensus        19 ~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g--~~i~   95 (336)
                      .+|+|+||+.++|+++|+++| .+|.+..+.+.++.       ..|+|||+|.+.  ++|.+|++.|||..+.+  +.++
T Consensus        97 ~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~-------~~~~afVef~~~--~~A~~A~~~Lng~~i~~~~~~l~  167 (481)
T TIGR01649        97 LRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN-------NVFQALVEFESV--NSAQHAKAALNGADIYNGCCTLK  167 (481)
T ss_pred             EEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC-------CceEEEEEECCH--HHHHHHHHHhcCCcccCCceEEE
Confidence            479999999999999999999 77788899887755       247899999999  99999999999999865  4777


Q ss_pred             EEeccCCCC----------------c----------------C-------------------------------------
Q psy12549         96 IMWSQRDPS----------------L----------------R-------------------------------------  106 (336)
Q Consensus        96 v~~~~~~~~----------------~----------------~-------------------------------------  106 (336)
                      |.|+....-                .                .                                     
T Consensus       168 v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  247 (481)
T TIGR01649       168 IEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGP  247 (481)
T ss_pred             EEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCcccccccCCCcccC
Confidence            777543110                0                0                                     


Q ss_pred             ------------------------CCCCceEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCH
Q psy12549        107 ------------------------KSGVGNVFIKNLDK-SIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETE  161 (336)
Q Consensus       107 ------------------------~~~~~~l~v~nlp~-~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~  161 (336)
                                              ....++|||+|||+ .+|+++|+++|+.||.|.+|+++.++    +|+|||+|.+.
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~----~g~afV~f~~~  323 (481)
T TIGR01649       248 PSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK----KETALIEMADP  323 (481)
T ss_pred             CCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC----CCEEEEEECCH
Confidence                                    01235899999997 69999999999999999999999873    67999999999


Q ss_pred             HHHHHHHHHhCCceeCCeEEEEeeccCchhhhHh-------------h----------------hccccccceEEEcCCC
Q psy12549        162 EAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKE-------------L----------------GEKAKLFTNVYIKNFG  212 (336)
Q Consensus       162 ~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~-------------~----------------~~~~~~~~~l~V~nlp  212 (336)
                      ++|..|+..|||..+.|+.|.|.++.........             .                .....+..+|||.|||
T Consensus       324 ~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp  403 (481)
T TIGR01649       324 YQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIP  403 (481)
T ss_pred             HHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCC
Confidence            9999999999999999999999887543110000             0                0001234689999999


Q ss_pred             CCCcHHHHHHhhccCCc--eeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEE------EEEeecccc
Q psy12549        213 EDFNDEKLKEMFEPYGT--ITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKI------LYVGRAQKK  281 (336)
Q Consensus       213 ~~~t~~~l~~~f~~~g~--i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~------l~v~~~~~~  281 (336)
                      ..+++++|+++|+.||.  +..+++....+..+++|||+|.+.++|.+|+..|||..+.|+.      |+|.|++++
T Consensus       404 ~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       404 LSVSEEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             CCCCHHHHHHHHHhcCCccceEEEEecCCCCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence            99999999999999998  8888887644446899999999999999999999999999984      999998764

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).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=1.1e-36  Score=276.26  Aligned_cols=164  Identities=27%  Similarity=0.566  Sum_probs=149.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..+|||+|||..+++++|+++|+.||+|.+|+++.++ +|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.+
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            4789999999999999999999999999999999987 789999999999999999999999999999999999999876


Q ss_pred             chhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCc
Q psy12549        189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGK  266 (336)
Q Consensus       189 ~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~  266 (336)
                      ....        ...++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|+|||+|.+.++|.+|++.|||.
T Consensus        83 ~~~~--------~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~  154 (352)
T TIGR01661        83 SSDS--------IKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGT  154 (352)
T ss_pred             cccc--------cccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCC
Confidence            5421        1236799999999999999999999999999998876  46788999999999999999999999999


Q ss_pred             eecC--EEEEEeecccc
Q psy12549        267 EVDG--KILYVGRAQKK  281 (336)
Q Consensus       267 ~~~g--~~l~v~~~~~~  281 (336)
                      .+.|  ..|.|.++...
T Consensus       155 ~~~g~~~~i~v~~a~~~  171 (352)
T TIGR01661       155 TPSGCTEPITVKFANNP  171 (352)
T ss_pred             ccCCCceeEEEEECCCC
Confidence            9987  67899887544

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

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

Probab=100.00  E-value=3.9e-36  Score=279.50  Aligned_cols=168  Identities=21%  Similarity=0.385  Sum_probs=150.2

Q ss_pred             ccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeee
Q psy12549         16 IPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPI   94 (336)
Q Consensus        16 ~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i   94 (336)
                      ....+|||+|||++++|++|+++| .+|.+.++++++++   .+|+++|||||+|.+.  ++|+.|++.+||..+.|+.|
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~---~TgkskGfAFVeF~s~--e~A~~Ai~~lnG~~i~GR~I  179 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDP---ATGKHKGFAFVEYEVP--EAAQLALEQMNGQMLGGRNI  179 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecC---CCCCcCCeEEEEeCcH--HHHHHHHHhcCCeEEeccee
Confidence            345679999999999999999999 78899999999987   5799999999999999  99999999999999999999


Q ss_pred             EEEeccCCCCc---------CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHH
Q psy12549         95 RIMWSQRDPSL---------RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAA  164 (336)
Q Consensus        95 ~v~~~~~~~~~---------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a  164 (336)
                      +|.++...+..         .....++|||+|||+++++++|+++|+.||.|.++++.+++ +|.++|||||+|.+.++|
T Consensus       180 kV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A  259 (612)
T TIGR01645       180 KVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQ  259 (612)
T ss_pred             eecccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHH
Confidence            99865432211         11234689999999999999999999999999999999987 678999999999999999


Q ss_pred             HHHHHHhCCceeCCeEEEEeeccC
Q psy12549        165 NKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       165 ~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .+|+..||+..++|+.|.|.++.+
T Consensus       260 ~kAI~amNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       260 SEAIASMNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             HHHHHHhCCCeeCCeEEEEEecCC
Confidence            999999999999999999987663

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0148|consensus

Probab=100.00  E-value=2.1e-35  Score=239.42  Aligned_cols=223  Identities=25%  Similarity=0.475  Sum_probs=186.3

Q ss_pred             CceeeeecCchhhhhhhHHhhhccc-CCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEE
Q psy12549         18 KHNVATRELSAKVVEGVSRSLSSLI-DGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRI   96 (336)
Q Consensus        18 ~~~v~v~~lp~~~~e~~l~~~f~~~-~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v   96 (336)
                      -|+|||+||+.++||+.|..+|+.+ .+...+++.+.                                        +.|
T Consensus         6 prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e----------------------------------------~~v   45 (321)
T KOG0148|consen    6 PRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDE----------------------------------------LKV   45 (321)
T ss_pred             CceEEeeccChhhHHHHHHHHHHhccccccceeehhh----------------------------------------hcc
Confidence            4669999999999999999999554 66677776642                                        112


Q ss_pred             EeccCCCC---cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhC
Q psy12549         97 MWSQRDPS---LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVN  172 (336)
Q Consensus        97 ~~~~~~~~---~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~  172 (336)
                      .|+.....   .....--.+||+.|.+.++-++|++.|.+||+|.++++++|. ++++|||+||.|.+.++|+.|+..||
T Consensus        46 ~wa~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~Mn  125 (321)
T KOG0148|consen   46 NWATAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMN  125 (321)
T ss_pred             ccccCcccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhC
Confidence            22211110   111112469999999999999999999999999999999998 89999999999999999999999999


Q ss_pred             CceeCCeEEEEeeccCchhhh--------HhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccce
Q psy12549        173 GMLLNSKIVFVGKFIPRKERE--------KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRG  244 (336)
Q Consensus       173 ~~~~~~~~i~v~~~~~~~~~~--------~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g  244 (336)
                      |.=|++|.|+..|+..+....        .-........++||++|++..+++++|++.|++||+|.+|++.+.    +|
T Consensus       126 GqWlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~----qG  201 (321)
T KOG0148|consen  126 GQWLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD----QG  201 (321)
T ss_pred             CeeeccceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc----cc
Confidence            999999999999998776321        112233455689999999999999999999999999999999986    89


Q ss_pred             EEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchhh
Q psy12549        245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER  284 (336)
Q Consensus       245 ~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~~  284 (336)
                      ||||+|.+.|+|.+||..+||..+.|..+++.|.+.....
T Consensus       202 YaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~  241 (321)
T KOG0148|consen  202 YAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDG  241 (321)
T ss_pred             eEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCC
Confidence            9999999999999999999999999999999998766543

>KOG0117|consensus

Probab=100.00  E-value=2.5e-35  Score=254.40  Aligned_cols=242  Identities=23%  Similarity=0.317  Sum_probs=197.0

Q ss_pred             EEEeCCcchhhHHHHHhhcCccccC---CeeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEE
Q psy12549         66 LVQLGQPYMLDTERALDTMNFDALK---GRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKV  142 (336)
Q Consensus        66 fV~f~~~~~~~A~~A~~~~~~~~~~---g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~  142 (336)
                      .-...+.  ++|.+||.+..+..+.   |+.=.=-+++.-........+.|||++||.++.|++|.-+|++.|+|.++++
T Consensus        38 ~~~~~~~--eaal~al~E~tgy~l~ve~gqrk~ggPpP~weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRL  115 (506)
T KOG0117|consen   38 VAGVQSE--EAALKALLERTGYTLVVENGQRKYGGPPPGWEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRL  115 (506)
T ss_pred             ccccccH--HHHHHHHHHhcCceEEEeccccccCCCCCcccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEE
Confidence            3334457  8999999877765331   1100000000011112244678999999999999999999999999999999


Q ss_pred             eeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEeeccCchhhhHhhhccccccceEEEcCCCCCCcHHHH
Q psy12549        143 AQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLN-SKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKL  220 (336)
Q Consensus       143 ~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~-~~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l  220 (336)
                      ++|+ +|.++|||||.|.+.++|+.|++.||+.+|. |+.|.|..+...              +.|||+|+|..+++++|
T Consensus       116 MmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan--------------~RLFiG~IPK~k~keeI  181 (506)
T KOG0117|consen  116 MMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVAN--------------CRLFIGNIPKTKKKEEI  181 (506)
T ss_pred             eecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeec--------------ceeEeccCCccccHHHH
Confidence            9996 9999999999999999999999999999984 899988776544              88999999999999999


Q ss_pred             HHhhccCCc-eeEEEEeC---CCCccceEEEEEeCCHHHHHHHHHHhCCce--ecCEEEEEeecccchhhHHHHHHHHHH
Q psy12549        221 KEMFEPYGT-ITSYRVMN---NDGKSRGFGFVAYESPEFAEKAVQAWNGKE--VDGKILYVGRAQKKAERTQELKRRFEM  294 (336)
Q Consensus       221 ~~~f~~~g~-i~~~~i~~---~~~~~~g~afV~F~~~~~a~~a~~~l~g~~--~~g~~l~v~~~~~~~~~~~~~~~~~~~  294 (336)
                      .+.+++.++ |.+|.+..   +..++||||||+|.++..|..|.++|-...  +.|..+.|+||.++.........+.  
T Consensus       182 lee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~ms~V--  259 (506)
T KOG0117|consen  182 LEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKV--  259 (506)
T ss_pred             HHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCCChhhhhhe--
Confidence            999999886 77777766   667899999999999999999998885444  5899999999999977666533322  


Q ss_pred             HHHHhhcCCCCceEEEecCCCCCCHHHHHHhcCCCCCeeecC
Q psy12549        295 LKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK  336 (336)
Q Consensus       295 ~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~V~~vk  336 (336)
                                 ..|||+||+.++|+|.|+++|++||.|++||
T Consensus       260 -----------KvLYVRNL~~~tTeE~lk~~F~~~G~veRVk  290 (506)
T KOG0117|consen  260 -----------KVLYVRNLMESTTEETLKKLFNEFGKVERVK  290 (506)
T ss_pred             -----------eeeeeeccchhhhHHHHHHHHHhccceEEee
Confidence                       3699999999999999999999999999987

>KOG0144|consensus

Probab=100.00  E-value=8e-36  Score=256.26  Aligned_cols=264  Identities=22%  Similarity=0.363  Sum_probs=225.5

Q ss_pred             CCccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccc-c
Q psy12549         12 EGIIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDA-L   89 (336)
Q Consensus        12 ~~~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~-~   89 (336)
                      +..+...-.+||+.+|.+++|.|||++| .++.|.+|.+++|+   .||.++|||||.|++.  ++|.+|+..|++.. +
T Consensus        28 d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk---~t~~s~gcCFv~~~tr--k~a~~a~~Alhn~ktl  102 (510)
T KOG0144|consen   28 DNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDK---STGQSKGCCFVKYYTR--KEADEAINALHNQKTL  102 (510)
T ss_pred             CCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeeccc---ccCcccceEEEEeccH--HHHHHHHHHhhccccc
Confidence            3334445679999999999999999999 77788999999999   6899999999999999  99999999999864 4


Q ss_pred             C--CeeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHH
Q psy12549         90 K--GRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS  167 (336)
Q Consensus        90 ~--g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a  167 (336)
                      -  .++|.|+++..+... ..+.++|||+.|+..++|.+++++|++||.|++|.|.+++.+.++|||||+|.+.+.|..|
T Consensus       103 pG~~~pvqvk~Ad~E~er-~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~A  181 (510)
T KOG0144|consen  103 PGMHHPVQVKYADGERER-IVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAA  181 (510)
T ss_pred             CCCCcceeecccchhhhc-cccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHH
Confidence            3  388999998765432 2446889999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhCCce-eCC--eEEEEeeccCchhhhHhhhccc---------------ccc--------------------------
Q psy12549        168 IEKVNGML-LNS--KIVFVGKFIPRKEREKELGEKA---------------KLF--------------------------  203 (336)
Q Consensus       168 ~~~l~~~~-~~~--~~i~v~~~~~~~~~~~~~~~~~---------------~~~--------------------------  203 (336)
                      ++.|||.. +.|  .+|.|+|+++.+++........               ...                          
T Consensus       182 ika~ng~~tmeGcs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~  261 (510)
T KOG0144|consen  182 IKALNGTQTMEGCSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLG  261 (510)
T ss_pred             HHhhccceeeccCCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccc
Confidence            99999964 554  7889999887655422111000               000                          


Q ss_pred             --------------------------------------------------------------------------------
Q psy12549        204 --------------------------------------------------------------------------------  203 (336)
Q Consensus       204 --------------------------------------------------------------------------------  203 (336)
                                                                                                      
T Consensus       262 g~~~L~~l~a~~~qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t  341 (510)
T KOG0144|consen  262 GLPPLGPLNATQLQQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGT  341 (510)
T ss_pred             cccCCCCcchhHHHHHHHhhhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCC
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------------------------------
Q psy12549        204 --------------------------------------------------------------------------------  203 (336)
Q Consensus       204 --------------------------------------------------------------------------------  203 (336)
                                                                                                      
T Consensus       342 ~~~~n~~~~~a~a~~~sp~aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eG  421 (510)
T KOG0144|consen  342 PANYNLAGGMAGAGTTSPVAASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEG  421 (510)
T ss_pred             chhcccccccccccccCcccccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccC
Confidence                                                                                            


Q ss_pred             ---ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        204 ---TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       204 ---~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                         ..+||.+||.+.-+.+|...|..||.|...++..  .++-++-|+||.|++..+|..||..|||..+++++++|...
T Consensus       422 peGanlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk  501 (510)
T KOG0144|consen  422 PEGANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLK  501 (510)
T ss_pred             CCccceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEee
Confidence               5699999999999999999999999999776655  78888999999999999999999999999999999999886


Q ss_pred             ccc
Q psy12549        279 QKK  281 (336)
Q Consensus       279 ~~~  281 (336)
                      ..+
T Consensus       502 ~~~  504 (510)
T KOG0144|consen  502 RDR  504 (510)
T ss_pred             ecc
Confidence            655

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

Probab=100.00  E-value=1.4e-34  Score=268.91  Aligned_cols=235  Identities=21%  Similarity=0.309  Sum_probs=188.8

Q ss_pred             hhHHHHHhhcCccccCCeeeEEEeccCC---CCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcc
Q psy12549         75 LDTERALDTMNFDALKGRPIRIMWSQRD---PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSK  151 (336)
Q Consensus        75 ~~A~~A~~~~~~~~~~g~~i~v~~~~~~---~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~  151 (336)
                      ++|.+|+.++++..+........+..+.   ........++|||+|||.++++++|+++|++||.|.++++++|.+|.++
T Consensus        20 ~~a~~a~~~~~gy~~~~~~g~r~~g~Pp~~~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sR   99 (578)
T TIGR01648        20 EAALKALLERTGYTLVQENGQRKYGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNR   99 (578)
T ss_pred             HHHHHHHHHhhCccccccCCcccCCCCCCcccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCcc
Confidence            7889999989887664433322222111   1112234589999999999999999999999999999999999999999


Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEeeccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCc-
Q psy12549        152 GYGFVHFETEEAANKSIEKVNGMLLN-SKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGT-  229 (336)
Q Consensus       152 g~afV~F~~~~~a~~a~~~l~~~~~~-~~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~-  229 (336)
                      |||||+|.+.++|++|++.||+..+. ++.+.+..+..              .++|||+|||.++++++|.+.|++++. 
T Consensus       100 GfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~~--------------~~rLFVgNLP~~~TeeeL~eeFskv~eg  165 (578)
T TIGR01648       100 GYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISVD--------------NCRLFVGGIPKNKKREEILEEFSKVTEG  165 (578)
T ss_pred             ceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccccc--------------CceeEeecCCcchhhHHHHHHhhcccCC
Confidence            99999999999999999999999885 77777755432              278999999999999999999999864 


Q ss_pred             eeEEEEeC---CCCccceEEEEEeCCHHHHHHHHHHhCC--ceecCEEEEEeecccchhhHHHHHHHHHHHHHHhhcCCC
Q psy12549        230 ITSYRVMN---NDGKSRGFGFVAYESPEFAEKAVQAWNG--KEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQ  304 (336)
Q Consensus       230 i~~~~i~~---~~~~~~g~afV~F~~~~~a~~a~~~l~g--~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  304 (336)
                      +..+.+..   ..++++|||||+|.++++|.+|++.|+.  ..+.|+.|.|.|+.++......             ....
T Consensus       166 vv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~~-------------~~~~  232 (578)
T TIGR01648       166 VVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDED-------------VMAK  232 (578)
T ss_pred             ceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeeccccccccc-------------cccc
Confidence            44444433   4567899999999999999999998864  3578999999999876432211             1112


Q ss_pred             CceEEEecCCCCCCHHHHHHhcCCC--CCeeecC
Q psy12549        305 GVNLYVKNLDDSIDDERLRKEFTPF--GTITSAK  336 (336)
Q Consensus       305 ~~~l~v~nlp~~~t~~~l~~~F~~~--G~V~~vk  336 (336)
                      ..+|||+|||..+++++|+++|++|  |+|.+|+
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~  266 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVK  266 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEE
Confidence            3689999999999999999999999  9999874

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.

>KOG0145|consensus

Probab=100.00  E-value=5.5e-34  Score=229.89  Aligned_cols=221  Identities=29%  Similarity=0.560  Sum_probs=184.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|.|.-||.++|++|++.+|.+.|+|++|++++|+ +|.+-||+||.|.+++||.+|+..|||..+..+.|+|.++
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyA  118 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYA  118 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEec
Confidence            344689999999999999999999999999999999999 8999999999999999999999999999999999999999


Q ss_pred             cCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhC
Q psy12549        187 IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWN  264 (336)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~  264 (336)
                      .|..+....        ..|||.+||...|..+|.++|++||.|..-+|+.  .+|.++|.+||+|+...+|+.|+..||
T Consensus       119 RPSs~~Ik~--------aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lN  190 (360)
T KOG0145|consen  119 RPSSDSIKD--------ANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLN  190 (360)
T ss_pred             cCChhhhcc--------cceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhcc
Confidence            987654432        5699999999999999999999999987666555  778999999999999999999999999


Q ss_pred             CceecC--EEEEEeecccchhhHHHHH-H-------------------HH---------------HHHHHHhhc------
Q psy12549        265 GKEVDG--KILYVGRAQKKAERTQELK-R-------------------RF---------------EMLKIERLN------  301 (336)
Q Consensus       265 g~~~~g--~~l~v~~~~~~~~~~~~~~-~-------------------~~---------------~~~~~~~~~------  301 (336)
                      |..-.|  .+|.|.|+....+...... .                   ++               .++..+...      
T Consensus       191 G~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~  270 (360)
T KOG0145|consen  191 GQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVN  270 (360)
T ss_pred             CCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeec
Confidence            999877  5699999865432211110 0                   00               000000000      


Q ss_pred             ----CCCCceEEEecCCCCCCHHHHHHhcCCCCCeeecC
Q psy12549        302 ----RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK  336 (336)
Q Consensus       302 ----~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~V~~vk  336 (336)
                          ...+.+|||.||.++++|.-|+++|.+||.|.+||
T Consensus       271 lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVK  309 (360)
T KOG0145|consen  271 LPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVK  309 (360)
T ss_pred             cCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEE
Confidence                01246899999999999999999999999999987

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=2e-31  Score=236.35  Aligned_cols=170  Identities=28%  Similarity=0.512  Sum_probs=153.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       106 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      .....++|||+|||.++|+++|+++|+.||.|.+|+++.+. ++.++|||||+|.++++|.+|++.|++..+.+++|.|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            33456899999999999999999999999999999999986 78999999999999999999999999999999999999


Q ss_pred             eccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHH
Q psy12549        185 KFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQA  262 (336)
Q Consensus       185 ~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~  262 (336)
                      ++.+....        ...++|||.|||..+++++|+++|++||.|..+.++.  .+++++++|||+|.+.++|++|++.
T Consensus       183 ~a~p~~~~--------~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~  254 (346)
T TIGR01659       183 YARPGGES--------IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISA  254 (346)
T ss_pred             cccccccc--------cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHH
Confidence            87654321        1236799999999999999999999999999999887  5788899999999999999999999


Q ss_pred             hCCceecC--EEEEEeecccchh
Q psy12549        263 WNGKEVDG--KILYVGRAQKKAE  283 (336)
Q Consensus       263 l~g~~~~g--~~l~v~~~~~~~~  283 (336)
                      ||+..+.|  +.|+|.++.....
T Consensus       255 lng~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       255 LNNVIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             hCCCccCCCceeEEEEECCcccc
Confidence            99999876  7899999886643

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).

>KOG0123|consensus

Probab=99.98  E-value=1.6e-31  Score=238.03  Aligned_cols=259  Identities=36%  Similarity=0.565  Sum_probs=227.8

Q ss_pred             eeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEEec
Q psy12549         21 VATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWS   99 (336)
Q Consensus        21 v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~~~   99 (336)
                      |+|.||+++++-.+|.++| .+|.+.++++..+.+    | ++|| ||+|.++  +.|.+|++.+||..+.|++|.+-..
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~----g-~kg~-FV~f~~e--~~a~~ai~~~ng~ll~~kki~vg~~  150 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN----G-SKGY-FVQFESE--ESAKKAIEKLNGMLLNGKKIYVGLF  150 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC----C-ceee-EEEeCCH--HHHHHHHHHhcCcccCCCeeEEeec
Confidence            9999999999999999999 888999999999885    4 9999 9999999  9999999999999999999999765


Q ss_pred             cCCCCcC------CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCC
Q psy12549        100 QRDPSLR------KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG  173 (336)
Q Consensus       100 ~~~~~~~------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~  173 (336)
                      .......      ....+.+++.+++.+.++..|...|+.+|.+..+.++.+..|.+++|+||.|.++++|..|+..+++
T Consensus       151 ~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~  230 (369)
T KOG0123|consen  151 ERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNG  230 (369)
T ss_pred             cchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccC
Confidence            5533211      1224579999999999999999999999999999999999888999999999999999999999999


Q ss_pred             ceeCCeEEEEeeccCchhhhHhhhc----------cccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCcc
Q psy12549        174 MLLNSKIVFVGKFIPRKEREKELGE----------KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKS  242 (336)
Q Consensus       174 ~~~~~~~i~v~~~~~~~~~~~~~~~----------~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~  242 (336)
                      ..+.+..+.|..+....+.......          .......|+|.|++..++.+.|++.|+.||.|.++.++. ..|.+
T Consensus       231 ~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~GeI~s~kv~~~~~g~s  310 (369)
T KOG0123|consen  231 KIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSFGEITSAKVMVDENGKS  310 (369)
T ss_pred             CcCCccceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcccceeeEEEEeccCCCc
Confidence            9999999999888775443322221          123346799999999999999999999999999999988 88999


Q ss_pred             ceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchhhHHH
Q psy12549        243 RGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQE  287 (336)
Q Consensus       243 ~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~~~~~  287 (336)
                      +|++||.|.+.++|.+|+..+||..+.|+.+.|.++..+..+..+
T Consensus       311 kG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~~r~~~  355 (369)
T KOG0123|consen  311 KGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKEDRRAR  355 (369)
T ss_pred             cceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhccchhh
Confidence            999999999999999999999999999999999998855444443

>KOG0127|consensus

Probab=99.98  E-value=1.6e-31  Score=235.94  Aligned_cols=227  Identities=25%  Similarity=0.411  Sum_probs=184.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..||||++||++++.++|.++|+.+|+|..+.++.++ ++.++||+||.|+-.+|++.|++..++..+.|+.|.|..+..
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~   84 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKK   84 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccc
Confidence            3799999999999999999999999999999999998 678999999999999999999999999999999999988776


Q ss_pred             chhhhH-----------hhhc-------cccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEE
Q psy12549        189 RKEREK-----------ELGE-------KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVA  249 (336)
Q Consensus       189 ~~~~~~-----------~~~~-------~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~  249 (336)
                      +.....           ....       ...+...|.|+|||+.+...+|+.+|+.||.|..+.|++ ..|+-.|||||.
T Consensus        85 R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~  164 (678)
T KOG0127|consen   85 RARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQ  164 (678)
T ss_pred             cccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEE
Confidence            543220           0000       011235799999999999999999999999999999998 566666999999


Q ss_pred             eCCHHHHHHHHHHhCCceecCEEEEEeecccchhhHHHH-------HHHHHHHH-----------------------H--
Q psy12549        250 YESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQEL-------KRRFEMLK-----------------------I--  297 (336)
Q Consensus       250 F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~~~~~~-------~~~~~~~~-----------------------~--  297 (336)
                      |.+..+|..|++.+||..|.||++-|.||.++.......       ........                       .  
T Consensus       165 fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe  244 (678)
T KOG0127|consen  165 FKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEE  244 (678)
T ss_pred             EeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhccccccccccc
Confidence            999999999999999999999999999997765322111       00000000                       0  


Q ss_pred             -H---------------------------------------hhcCCCCceEEEecCCCCCCHHHHHHhcCCCCCeeecC
Q psy12549        298 -E---------------------------------------RLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK  336 (336)
Q Consensus       298 -~---------------------------------------~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~V~~vk  336 (336)
                       +                                       +.+...+.+|||+|||+++++++|.++|++||+|.+++
T Consensus       245 ~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~  323 (678)
T KOG0127|consen  245 TDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAI  323 (678)
T ss_pred             ccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEE
Confidence             0                                       00001236899999999999999999999999998863

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

Probab=99.98  E-value=8.7e-31  Score=245.53  Aligned_cols=170  Identities=27%  Similarity=0.519  Sum_probs=149.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+|||..+++++|+++|+.||.|..|.++.++ +|.++|||||+|.+.++|.+|+. |+|..+.|++|.|..+.
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~  166 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQ  166 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecc
Confidence            35789999999999999999999999999999999987 78899999999999999999998 89999999999998765


Q ss_pred             CchhhhHh----hhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHH
Q psy12549        188 PRKEREKE----LGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQ  261 (336)
Q Consensus       188 ~~~~~~~~----~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~  261 (336)
                      ........    ........++|||+|||..+++++|+++|+.||.|..+.+..  .+|.++|||||+|.+.++|.+|+.
T Consensus       167 ~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~  246 (457)
T TIGR01622       167 AEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALE  246 (457)
T ss_pred             hhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHH
Confidence            43322211    001112247899999999999999999999999999999887  556889999999999999999999


Q ss_pred             HhCCceecCEEEEEeecc
Q psy12549        262 AWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       262 ~l~g~~~~g~~l~v~~~~  279 (336)
                      .|+|..+.|+.|.|.|+.
T Consensus       247 ~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       247 VMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             hcCCcEECCEEEEEEEcc
Confidence            999999999999999965

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.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.97  E-value=9.9e-31  Score=231.98  Aligned_cols=170  Identities=18%  Similarity=0.303  Sum_probs=152.8

Q ss_pred             ccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCe
Q psy12549         14 IIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGR   92 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~   92 (336)
                      .....++|||+|||+++||++|+++| .++.+.+++++++.   .+++++|||||+|.++  ++|++|++.|++..+.++
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~---~tg~srGyaFVeF~~~--e~A~~Ai~~LnG~~l~gr  177 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDY---KTGYSFGYAFVDFGSE--ADSQRAIKNLNGITVRNK  177 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecC---CCCccCcEEEEEEccH--HHHHHHHHHcCCCccCCc
Confidence            34578899999999999999999999 67789999999987   4789999999999999  999999999999999999


Q ss_pred             eeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHh
Q psy12549         93 PIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV  171 (336)
Q Consensus        93 ~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l  171 (336)
                      +|+|.++.....  ....++|||+|||.++|+++|+++|++||.|..+.+++++ ++.++++|||+|.+.++|++|++.|
T Consensus       178 ~i~V~~a~p~~~--~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~l  255 (346)
T TIGR01659       178 RLKVSYARPGGE--SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISAL  255 (346)
T ss_pred             eeeeeccccccc--ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHh
Confidence            999998765332  2345789999999999999999999999999999999987 8889999999999999999999999


Q ss_pred             CCceeCC--eEEEEeeccCch
Q psy12549        172 NGMLLNS--KIVFVGKFIPRK  190 (336)
Q Consensus       172 ~~~~~~~--~~i~v~~~~~~~  190 (336)
                      |+..+.+  ++|.|.++....
T Consensus       256 ng~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       256 NNVIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             CCCccCCCceeEEEEECCccc
Confidence            9998865  789998877654

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

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

Probab=99.97  E-value=4.3e-30  Score=239.27  Aligned_cols=173  Identities=25%  Similarity=0.508  Sum_probs=151.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+|||.++++++|+++|+.||.|.+|.++.++ +|+++|||||+|.+.++|.+|++.|||..+.|+.|.|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            35789999999999999999999999999999999997 88999999999999999999999999999999999998654


Q ss_pred             CchhhhH---hhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHH
Q psy12549        188 PRKEREK---ELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQA  262 (336)
Q Consensus       188 ~~~~~~~---~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~  262 (336)
                      .......   .........++|||+|||.++++++|+++|+.||.|.++++.+  .++.++|||||+|.+.++|.+|+..
T Consensus       186 ~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~a  265 (612)
T TIGR01645       186 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  265 (612)
T ss_pred             cccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHH
Confidence            3221111   0111122347899999999999999999999999999999987  4677899999999999999999999


Q ss_pred             hCCceecCEEEEEeecccc
Q psy12549        263 WNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       263 l~g~~~~g~~l~v~~~~~~  281 (336)
                      |||..++|+.|+|.++...
T Consensus       266 mNg~elgGr~LrV~kAi~p  284 (612)
T TIGR01645       266 MNLFDLGGQYLRVGKCVTP  284 (612)
T ss_pred             hCCCeeCCeEEEEEecCCC
Confidence            9999999999999998753

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.

>KOG0110|consensus

Probab=99.97  E-value=4.9e-30  Score=233.57  Aligned_cols=257  Identities=21%  Similarity=0.371  Sum_probs=213.8

Q ss_pred             ccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeee
Q psy12549         16 IPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPI   94 (336)
Q Consensus        16 ~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i   94 (336)
                      +.++-+.++|||..+..+++...| .++++..+.+++..    +    + |+|+|.++  .+|.+|+..+.+..+...++
T Consensus       383 rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~G----~----~-aiv~fl~p--~eAr~Afrklaysr~k~~pl  451 (725)
T KOG0110|consen  383 RSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPGG----T----G-AIVEFLNP--LEARKAFRKLAYSRFKSAPL  451 (725)
T ss_pred             hhcceeeeccCccccccHHHHHHhhcccccceeecCccc----c----e-eeeeecCc--cchHHHHHHhchhhhccCcc
Confidence            445778999999999999999988 78888888665322    1    2 99999999  99999999999999998888


Q ss_pred             EEEeccCCCCc------------------------------------------------CCCCCceEEEcCCCCCCCHHH
Q psy12549         95 RIMWSQRDPSL------------------------------------------------RKSGVGNVFIKNLDKSIDNKA  126 (336)
Q Consensus        95 ~v~~~~~~~~~------------------------------------------------~~~~~~~l~v~nlp~~~t~~~  126 (336)
                      .+.|++.+...                                                .....++||++||+.+++.++
T Consensus       452 yle~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~  531 (725)
T KOG0110|consen  452 YLEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLED  531 (725)
T ss_pred             ccccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhH
Confidence            88875442110                                                001123499999999999999


Q ss_pred             HHHHhhccCCeeEEEEeeCCCC----CcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchhhhH-hhhcccc
Q psy12549        127 MYDTFSAFGSILSCKVAQDEQG----NSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK-ELGEKAK  201 (336)
Q Consensus       127 l~~~f~~~G~v~~~~~~~~~~~----~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~-~~~~~~~  201 (336)
                      +..+|...|.|.++.|...+.+    .|.|||||+|.++++|++|++.|+|..++|+.|.+.++........ .......
T Consensus       532 l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk  611 (725)
T KOG0110|consen  532 LEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKK  611 (725)
T ss_pred             HHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCcccccccccccccc
Confidence            9999999999999988887644    2569999999999999999999999999999999999872222111 1111122


Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ..+.|.|+|+|+..+..+++++|..||.+.+++++.  ..+.++|||||.|.++.+|.+|+.+|.+..+.||+|.++|+.
T Consensus       612 ~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~  691 (725)
T KOG0110|consen  612 KGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAK  691 (725)
T ss_pred             ccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhc
Confidence            246899999999999999999999999999999998  455679999999999999999999999999999999999998


Q ss_pred             cchh
Q psy12549        280 KKAE  283 (336)
Q Consensus       280 ~~~~  283 (336)
                      ....
T Consensus       692 ~d~~  695 (725)
T KOG0110|consen  692 SDNT  695 (725)
T ss_pred             cchH
Confidence            7765

>KOG0110|consensus

Probab=99.97  E-value=4.5e-30  Score=233.80  Aligned_cols=283  Identities=23%  Similarity=0.323  Sum_probs=223.0

Q ss_pred             CccccCceeeeecCchhhhhhhHHhhhcccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCe
Q psy12549         13 GIIIPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGR   92 (336)
Q Consensus        13 ~~~~p~~~v~v~~lp~~~~e~~l~~~f~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~   92 (336)
                      ..+..+-.|||+|||++.+|+|++.+|                         |||.|--+  ++|.+|...+++..+.|+
T Consensus       222 e~i~etgrlf~RNLpyt~~eed~~~lf-------------------------a~v~~~~~--~~avka~~~~D~k~fqgr  274 (725)
T KOG0110|consen  222 EDISETGRLFVRNLPYTSTEEDLLKLF-------------------------AFVTFMFP--EHAVKAYSELDGKVFQGR  274 (725)
T ss_pred             hHHHhhhhhhhccCCccccHHHHHHhh-------------------------HHHhhhhh--HHHHhhhhhccccccccc
Confidence            345666679999999999999999998                         79999999  999999999999999999


Q ss_pred             eeEEEeccCCCC--------------------------------------------------------------------
Q psy12549         93 PIRIMWSQRDPS--------------------------------------------------------------------  104 (336)
Q Consensus        93 ~i~v~~~~~~~~--------------------------------------------------------------------  104 (336)
                      -+.|.+......                                                                    
T Consensus       275 mlhvlp~~~k~~~~~~~~~~~~~~k~~ke~~rk~~~~~~~~wn~l~~~~~ava~~~a~k~~v~k~~i~d~~~~gsavr~a  354 (725)
T KOG0110|consen  275 MLHVLPSKEKSTAKEDASELGSDYKKEKELKRKAASASFHSWNTLFMGANAVAGILAQKLGVEKSRILDGSLSGSAVRLA  354 (725)
T ss_pred             eeeecCcchhhhhhhhHhhcCCcHHHHHHhccccchhcceecccccccccHHHHHHHHHhCCeeeeeechhhcchHHHHH
Confidence            999866433211                                                                    


Q ss_pred             -------------------------cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeC
Q psy12549        105 -------------------------LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFE  159 (336)
Q Consensus       105 -------------------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~  159 (336)
                                               ......+.++++|||..+..++|..+|..||.|..+.++  +.|   -.|+|+|.
T Consensus       355 l~etr~~~e~~~~~ee~gV~l~~F~~~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp--~~G---~~aiv~fl  429 (725)
T KOG0110|consen  355 LGETRVVQEVRRFFEENGVKLDAFSQAERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP--PGG---TGAIVEFL  429 (725)
T ss_pred             HHHhhhchhhhhhHHhhCcccccchhhhhhcceeeeccCccccccHHHHHHhhcccccceeecC--ccc---ceeeeeec
Confidence                                     011123578999999999999999999999999999655  322   24999999


Q ss_pred             CHHHHHHHHHHhCCceeCCeEEEEeeccCchhh-------------hH--------------hh---------------h
Q psy12549        160 TEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER-------------EK--------------EL---------------G  197 (336)
Q Consensus       160 ~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~-------------~~--------------~~---------------~  197 (336)
                      ++.+|..|+..|....+...++.+.|+......             ..              ..               .
T Consensus       430 ~p~eAr~Afrklaysr~k~~plyle~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a  509 (725)
T KOG0110|consen  430 NPLEARKAFRKLAYSRFKSAPLYLEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVA  509 (725)
T ss_pred             CccchHHHHHHhchhhhccCccccccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhh
Confidence            999999999999998888888877654311100             00              00               0


Q ss_pred             ccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCc----cceEEEEEeCCHHHHHHHHHHhCCceecCEE
Q psy12549        198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGK----SRGFGFVAYESPEFAEKAVQAWNGKEVDGKI  272 (336)
Q Consensus       198 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~----~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~  272 (336)
                      ......++|||.||+++++.++|...|...|.|..+.|.. ..+.    +.|||||+|.++++|..|++.|+|..++|+.
T Consensus       510 ~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~  589 (725)
T KOG0110|consen  510 EDEETETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHK  589 (725)
T ss_pred             hccccchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCce
Confidence            0001114499999999999999999999999999998876 3332    4699999999999999999999999999999


Q ss_pred             EEEeecccchhhHHHHHHHHHHHHHHhhcCCCCceEEEecCCCCCCHHHHHHhcCCCCCeeecC
Q psy12549        273 LYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK  336 (336)
Q Consensus       273 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~V~~vk  336 (336)
                      |.|.++..+....-.         ........++.|.|+|||++++-.+|+++|+.||.|.+|+
T Consensus       590 l~lk~S~~k~~~~~g---------K~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvR  644 (725)
T KOG0110|consen  590 LELKISENKPASTVG---------KKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVR  644 (725)
T ss_pred             EEEEeccCccccccc---------cccccccccceeeeeccchHHHHHHHHHHHhcccceeeec
Confidence            999999833211111         1222233468899999999999999999999999999885

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

Probab=99.97  E-value=2.5e-29  Score=238.89  Aligned_cols=223  Identities=18%  Similarity=0.328  Sum_probs=166.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhcc------------CCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCce
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAF------------GSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGML  175 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~------------G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~  175 (336)
                      ...++|||+|||..+|+++|.++|+.+            +.|..+.+.     ..+|||||+|.+.++|..|+. |+|..
T Consensus       173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~-----~~kg~afVeF~~~e~A~~Al~-l~g~~  246 (509)
T TIGR01642       173 RQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNIN-----KEKNFAFLEFRTVEEATFAMA-LDSII  246 (509)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEEC-----CCCCEEEEEeCCHHHHhhhhc-CCCeE
Confidence            345799999999999999999999975            234444443     357899999999999999996 99999


Q ss_pred             eCCeEEEEeeccCchhhh---------------H------hhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEE
Q psy12549        176 LNSKIVFVGKFIPRKERE---------------K------ELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYR  234 (336)
Q Consensus       176 ~~~~~i~v~~~~~~~~~~---------------~------~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~  234 (336)
                      +.|+.|.|..........               .      .........++|||+|||..+++++|+++|+.||.|..+.
T Consensus       247 ~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~  326 (509)
T TIGR01642       247 YSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFN  326 (509)
T ss_pred             eeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE
Confidence            999999997654322100               0      0000112347899999999999999999999999999999


Q ss_pred             EeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchhhHHHHHH--------HHH--HHHHHhhcC
Q psy12549        235 VMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKR--------RFE--MLKIERLNR  302 (336)
Q Consensus       235 i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~--------~~~--~~~~~~~~~  302 (336)
                      ++.  .+|.++|||||+|.+.++|..|+..|+|..+.|+.|.|.++............        ...  .........
T Consensus       327 ~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  406 (509)
T TIGR01642       327 LIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGG  406 (509)
T ss_pred             EEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhhccccC
Confidence            887  57889999999999999999999999999999999999998543221100000        000  000001122


Q ss_pred             CCCceEEEecCCCCC----------CHHHHHHhcCCCCCeeecC
Q psy12549        303 YQGVNLYVKNLDDSI----------DDERLRKEFTPFGTITSAK  336 (336)
Q Consensus       303 ~~~~~l~v~nlp~~~----------t~~~l~~~F~~~G~V~~vk  336 (336)
                      .+..+|+|.||...-          ..++|+++|++||.|.+|+
T Consensus       407 ~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~  450 (509)
T TIGR01642       407 KPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIV  450 (509)
T ss_pred             CCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEE
Confidence            356789999996421          2368999999999999874

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

>KOG0124|consensus

Probab=99.96  E-value=4.3e-28  Score=204.67  Aligned_cols=252  Identities=20%  Similarity=0.362  Sum_probs=206.3

Q ss_pred             eeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEEe
Q psy12549         20 NVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMW   98 (336)
Q Consensus        20 ~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~~   98 (336)
                      .||||.+.....|+-||.-| .+|++.++.+.||+   .|++++|||||+|+-+  |.|+.|++.+||..++||.|.|..
T Consensus       115 RvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp---~T~kHKgFAFVEYEvP--EaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  115 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDP---ATGKHKGFAFVEYEVP--EAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             heeeeeeEEEechHHHHhhccCCCCcceeeccccc---ccccccceEEEEEeCc--HHHHHHHHHhccccccCccccccC
Confidence            49999999999999999999 99999999999999   6899999999999999  999999999999999999999976


Q ss_pred             ccCCCC---------cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCC-CCcccEEEEEeCCHHHHHHHH
Q psy12549         99 SQRDPS---------LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSI  168 (336)
Q Consensus        99 ~~~~~~---------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~-~~~~g~afV~F~~~~~a~~a~  168 (336)
                      ....+.         .+.....+|||..+.++.+++||+..|+.||+|..|.+-+.++ +.++||+|++|.+..+-..|+
T Consensus       190 PsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAi  269 (544)
T KOG0124|consen  190 PSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAI  269 (544)
T ss_pred             CCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHh
Confidence            444332         1112346899999999999999999999999999999999984 569999999999999999999


Q ss_pred             HHhCCceeCCeEEEEeeccCchhhhHh----------------------------hhcc---------------------
Q psy12549        169 EKVNGMLLNSKIVFVGKFIPRKEREKE----------------------------LGEK---------------------  199 (336)
Q Consensus       169 ~~l~~~~~~~~~i~v~~~~~~~~~~~~----------------------------~~~~---------------------  199 (336)
                      ..+|-+.++|..++|..+......-..                            .+..                     
T Consensus       270 asMNlFDLGGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vSpA~~aa~p~  349 (544)
T KOG0124|consen  270 ASMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQPL  349 (544)
T ss_pred             hhcchhhcccceEecccccCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccCccccccCCC
Confidence            999999999999999776533221000                            0000                     


Q ss_pred             --------------------------------------------------------------------------------
Q psy12549        200 --------------------------------------------------------------------------------  199 (336)
Q Consensus       200 --------------------------------------------------------------------------------  199 (336)
                                                                                                      
T Consensus       350 ~~l~qa~~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~G  429 (544)
T KOG0124|consen  350 GTLPQAVMAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLSEQEHMSISG  429 (544)
T ss_pred             CCccccchhccCCceeccCCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhhhhhCccccC
Confidence                                                                                            


Q ss_pred             -------------ccccceEEEcCC--CCCCcH---HHHHHhhccCCceeEEEEeC-CCCcc-----ceEEEEEeCCHHH
Q psy12549        200 -------------AKLFTNVYIKNF--GEDFND---EKLKEMFEPYGTITSYRVMN-NDGKS-----RGFGFVAYESPEF  255 (336)
Q Consensus       200 -------------~~~~~~l~V~nl--p~~~t~---~~l~~~f~~~g~i~~~~i~~-~~~~~-----~g~afV~F~~~~~  255 (336)
                                   ...++.+.++|+  |.++++   .+|.+.+++||.|.++.|.. ..+..     ---.||+|....+
T Consensus       430 ~sARhlvMqkLmR~~~S~VivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~e~edaeiiVKIFVefS~~~e  509 (544)
T KOG0124|consen  430 SSARHLVMQKLMRKQESTVIVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAEIIVKIFVEFSIASE  509 (544)
T ss_pred             ccHHHHHHHHHhccccCcEEEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccccccchhhhheeeeeechhhH
Confidence                         000045667786  555554   68999999999999998887 22211     1236999999999


Q ss_pred             HHHHHHHhCCceecCEEEEEe
Q psy12549        256 AEKAVQAWNGKEVDGKILYVG  276 (336)
Q Consensus       256 a~~a~~~l~g~~~~g~~l~v~  276 (336)
                      +.+|.+.|+|+.|+|+++..+
T Consensus       510 ~~rak~ALdGRfFgGr~VvAE  530 (544)
T KOG0124|consen  510 THRAKQALDGRFFGGRKVVAE  530 (544)
T ss_pred             HHHHHHhhccceecCceeehh
Confidence            999999999999999998764

>KOG0144|consensus

Probab=99.96  E-value=2.6e-28  Score=210.13  Aligned_cols=193  Identities=22%  Similarity=0.387  Sum_probs=161.3

Q ss_pred             CCeeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHH
Q psy12549         90 KGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSI  168 (336)
Q Consensus        90 ~g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~  168 (336)
                      .|..++...+...+.....+..++||+-+|..++|+||+++|++||.|.+|.+++|+ ++.++|||||.|.+.++|.+|+
T Consensus        14 ~gs~~~~~~~~~~~d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~   93 (510)
T KOG0144|consen   14 GGSSLADNGSLDHTDNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAI   93 (510)
T ss_pred             CCcchhhcCCCCCCCCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHH
Confidence            344444444333333444556789999999999999999999999999999999998 8899999999999999999999


Q ss_pred             HHhCCce-eC--CeEEEEeeccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccce
Q psy12549        169 EKVNGML-LN--SKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRG  244 (336)
Q Consensus       169 ~~l~~~~-~~--~~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g  244 (336)
                      .+|++.. +.  .++|.|.++.....+.       ...++|||+-|++.++|.+++++|++||.|++|.|++ ..+.+||
T Consensus        94 ~Alhn~ktlpG~~~pvqvk~Ad~E~er~-------~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRG  166 (510)
T KOG0144|consen   94 NALHNQKTLPGMHHPVQVKYADGERERI-------VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRG  166 (510)
T ss_pred             HHhhcccccCCCCcceeecccchhhhcc-------ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccc
Confidence            9998864 43  4788888876655442       1227799999999999999999999999999999999 8899999


Q ss_pred             EEEEEeCCHHHHHHHHHHhCCce-ecC--EEEEEeecccchhhHHHHH
Q psy12549        245 FGFVAYESPEFAEKAVQAWNGKE-VDG--KILYVGRAQKKAERTQELK  289 (336)
Q Consensus       245 ~afV~F~~~~~a~~a~~~l~g~~-~~g--~~l~v~~~~~~~~~~~~~~  289 (336)
                      +|||+|.+.+.|..|++.|||.. ++|  .+|.|+||..+.++.....
T Consensus       167 caFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~~~l  214 (510)
T KOG0144|consen  167 CAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDGKRL  214 (510)
T ss_pred             eeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCchHHHH
Confidence            99999999999999999999976 666  5799999987766555444

>KOG0148|consensus

Probab=99.96  E-value=8.2e-28  Score=195.41  Aligned_cols=170  Identities=26%  Similarity=0.342  Sum_probs=155.2

Q ss_pred             ccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCe
Q psy12549         14 IIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGR   92 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~   92 (336)
                      ..+.+-.|+|+-|.+.++-++||+-| .++.+.+.++++|.+   |++|+||+||.|.+.  ++|+.|+..|||.=+++|
T Consensus        58 t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~---T~KsKGYgFVSf~~k--~dAEnAI~~MnGqWlG~R  132 (321)
T KOG0148|consen   58 TSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMN---TGKSKGYGFVSFPNK--EDAENAIQQMNGQWLGRR  132 (321)
T ss_pred             ccccceeEEehhcchhcchHHHHHHhccccccccceEeeccc---CCcccceeEEeccch--HHHHHHHHHhCCeeeccc
Confidence            33446679999999999999999999 999999999999984   899999999999999  999999999999999999


Q ss_pred             eeEEEeccCCCC--------------cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEe
Q psy12549         93 PIRIMWSQRDPS--------------LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHF  158 (336)
Q Consensus        93 ~i~v~~~~~~~~--------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F  158 (336)
                      .||-.|+.+++.              ......++||++|++..+++++|++.|+.||.|.+|++.++     +|||||.|
T Consensus       133 ~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-----qGYaFVrF  207 (321)
T KOG0148|consen  133 TIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-----QGYAFVRF  207 (321)
T ss_pred             eeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-----cceEEEEe
Confidence            999999998874              22235689999999999999999999999999999999987     68999999


Q ss_pred             CCHHHHHHHHHHhCCceeCCeEEEEeeccCchhhh
Q psy12549        159 ETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKERE  193 (336)
Q Consensus       159 ~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~  193 (336)
                      ++.|.|.+|+-.+|+..+.|+.++|.|-+......
T Consensus       208 ~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~~  242 (321)
T KOG0148|consen  208 ETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDGI  242 (321)
T ss_pred             cchhhHHHHHHHhcCceeCceEEEEeccccCCCCC
Confidence            99999999999999999999999999987665543

>KOG0147|consensus

Probab=99.94  E-value=8.2e-27  Score=207.26  Aligned_cols=255  Identities=21%  Similarity=0.304  Sum_probs=203.5

Q ss_pred             cCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeE
Q psy12549         17 PKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIR   95 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~   95 (336)
                      -.++|+.-.|+...++.+|.+|| ..+.+..|.++.|++   +++++|.|||+|.+.  +....|+. |.|..+.|-+|.
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~---s~rskgi~Yvef~D~--~sVp~aia-LsGqrllg~pv~  251 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRN---SRRSKGIAYVEFCDE--QSVPLAIA-LSGQRLLGVPVI  251 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeecccc---chhhcceeEEEEecc--cchhhHhh-hcCCcccCceeE
Confidence            35789999999999999999999 667888999999994   688999999999999  99999997 999999999999


Q ss_pred             EEeccCCCC--------cC----CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHH
Q psy12549         96 IMWSQRDPS--------LR----KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEE  162 (336)
Q Consensus        96 v~~~~~~~~--------~~----~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~  162 (336)
                      |..+.....        ..    ...-..|||+||..++++++|+..|+.||.|..|.+.++. +|.++||+|++|.+.+
T Consensus       252 vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~  331 (549)
T KOG0147|consen  252 VQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKE  331 (549)
T ss_pred             ecccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHH
Confidence            987543211        11    0011239999999999999999999999999999999997 9999999999999999


Q ss_pred             HHHHHHHHhCCceeCCeEEEEeeccCchhhhH------------------------h-----------------------
Q psy12549        163 AANKSIEKVNGMLLNSKIVFVGKFIPRKEREK------------------------E-----------------------  195 (336)
Q Consensus       163 ~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~------------------------~-----------------------  195 (336)
                      +|.+|+..|||..+.|+.|.|...........                        .                       
T Consensus       332 ~ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~  411 (549)
T KOG0147|consen  332 DARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLL  411 (549)
T ss_pred             HHHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHh
Confidence            99999999999999999999854321110000                        0                       


Q ss_pred             ---------hh--------ccc-------cccceEEEcCCC--CCCc--------HHHHHHhhccCCceeEEEEeCCCCc
Q psy12549        196 ---------LG--------EKA-------KLFTNVYIKNFG--EDFN--------DEKLKEMFEPYGTITSYRVMNNDGK  241 (336)
Q Consensus       196 ---------~~--------~~~-------~~~~~l~V~nlp--~~~t--------~~~l~~~f~~~g~i~~~~i~~~~~~  241 (336)
                               .+        ...       .+..++.+.|+=  ...|        .+++.+.+++||.|..|.+.+.   
T Consensus       412 ~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n---  488 (549)
T KOG0147|consen  412 LAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN---  488 (549)
T ss_pred             ccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC---
Confidence                     00        000       111234445542  1112        2688899999999999988653   


Q ss_pred             cceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       242 ~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      +-|+.||.|.+.++|..|+.+|||.||.|+.|...|...
T Consensus       489 s~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~~  527 (549)
T KOG0147|consen  489 SAGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLPL  527 (549)
T ss_pred             CCceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEeeh
Confidence            248999999999999999999999999999999998653

>KOG0131|consensus

Probab=99.94  E-value=3.9e-26  Score=175.31  Aligned_cols=172  Identities=28%  Similarity=0.409  Sum_probs=152.7

Q ss_pred             cccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCee
Q psy12549         15 IIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRP   93 (336)
Q Consensus        15 ~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~   93 (336)
                      .....+|||+||+..++++.|-++| ..++++++++.+++   .+....||||++|.++  |+|.-|++.+|...+.|++
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDr---v~~~~qGygF~Ef~~e--edadYAikiln~VkLYgrp   80 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDR---VTQKHQGYGFAEFRTE--EDADYAIKILNMVKLYGRP   80 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhh---hcccccceeEEEEech--hhhHHHHHHHHHHHhcCce
Confidence            3567889999999999999999999 78899999999998   5678999999999999  9999999999999999999


Q ss_pred             eEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeE-EEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHh
Q psy12549         94 IRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILS-CKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV  171 (336)
Q Consensus        94 i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~-~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l  171 (336)
                      |++..+..... ...-.+++||+||.+.+++..|...|+.||.+.. ..+++++ +|.++|+||+.|++.+.+.+|+..+
T Consensus        81 Irv~kas~~~~-nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~  159 (203)
T KOG0131|consen   81 IRVNKASAHQK-NLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSM  159 (203)
T ss_pred             eEEEecccccc-cccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHh
Confidence            99998873322 2333489999999999999999999999998665 5777777 6889999999999999999999999


Q ss_pred             CCceeCCeEEEEeeccCchhh
Q psy12549        172 NGMLLNSKIVFVGKFIPRKER  192 (336)
Q Consensus       172 ~~~~~~~~~i~v~~~~~~~~~  192 (336)
                      +|..+.++++.|.++..+...
T Consensus       160 ngq~l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  160 NGQYLCNRPITVSYAFKKDTK  180 (203)
T ss_pred             ccchhcCCceEEEEEEecCCC
Confidence            999999999999988765543

>KOG4212|consensus

Probab=99.93  E-value=5e-24  Score=184.04  Aligned_cols=164  Identities=19%  Similarity=0.304  Sum_probs=138.7

Q ss_pred             ccccCceeeeecCchhhhhhhHHhhh--cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCC
Q psy12549         14 IIIPKHNVATRELSAKVVEGVSRSLS--SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKG   91 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~~~e~~l~~~f--~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g   91 (336)
                      .-...|.+||.|||+++.=++|++++  .-+.++-|.+..|.    .|+++|+|.|+|+++  |.+++|++.||...+.|
T Consensus        40 ~~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~----~GK~rGcavVEFk~~--E~~qKa~E~lnk~~~~G  113 (608)
T KOG4212|consen   40 VAARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE----SGKARGCAVVEFKDP--ENVQKALEKLNKYEVNG  113 (608)
T ss_pred             cccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc----CCCcCCceEEEeeCH--HHHHHHHHHhhhccccC
Confidence            34456679999999999999999999  55688888888877    599999999999999  99999999999999999


Q ss_pred             eeeEEEeccCCCC-------------------------------------------------------------------
Q psy12549         92 RPIRIMWSQRDPS-------------------------------------------------------------------  104 (336)
Q Consensus        92 ~~i~v~~~~~~~~-------------------------------------------------------------------  104 (336)
                      |+|.+.-....+.                                                                   
T Consensus       114 R~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~  193 (608)
T KOG4212|consen  114 RELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSN  193 (608)
T ss_pred             ceEEEeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchh
Confidence            9999975333111                                                                   


Q ss_pred             ----------------cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHH
Q psy12549        105 ----------------LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSI  168 (336)
Q Consensus       105 ----------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~  168 (336)
                                      .......++||.||...+..+.|++.|.-.|.+..+.+--++.|.++|+|.++|..+-+|..|+
T Consensus       194 ~~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaI  273 (608)
T KOG4212|consen  194 YNLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAI  273 (608)
T ss_pred             hhcccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHH
Confidence                            0112234799999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhCCceeCCeEEEE
Q psy12549        169 EKVNGMLLNSKIVFV  183 (336)
Q Consensus       169 ~~l~~~~~~~~~i~v  183 (336)
                      ..|++.-+..++..+
T Consensus       274 sml~~~g~~~~~~~~  288 (608)
T KOG4212|consen  274 SMLDRQGLFDRRMTV  288 (608)
T ss_pred             HhhccCCCcccccee
Confidence            999875554554444

>KOG0131|consensus

Probab=99.93  E-value=2.3e-25  Score=171.09  Aligned_cols=171  Identities=25%  Similarity=0.515  Sum_probs=150.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      .+...+|||+||+..++++-|.++|-+.|+|..+.+++++ ++..+||||++|.++++|+-|++-||...+.|++|+|..
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~k   85 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNK   85 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEe
Confidence            4556899999999999999999999999999999999998 777999999999999999999999999999999999988


Q ss_pred             ccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEE-EEeC--CCCccceEEEEEeCCHHHHHHHHHH
Q psy12549        186 FIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSY-RVMN--NDGKSRGFGFVAYESPEFAEKAVQA  262 (336)
Q Consensus       186 ~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~-~i~~--~~~~~~g~afV~F~~~~~a~~a~~~  262 (336)
                      +....       ........+||+||.+.+++..|.+.|+.||.+..- ++++  .+|+++|+|||.|.+.+.+.+|+..
T Consensus        86 as~~~-------~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s  158 (203)
T KOG0131|consen   86 ASAHQ-------KNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGS  158 (203)
T ss_pred             ccccc-------ccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHH
Confidence            76221       222233679999999999999999999999987653 4555  6688999999999999999999999


Q ss_pred             hCCceecCEEEEEeecccchhh
Q psy12549        263 WNGKEVDGKILYVGRAQKKAER  284 (336)
Q Consensus       263 l~g~~~~g~~l~v~~~~~~~~~  284 (336)
                      ++|+.+..++++|+++..+...
T Consensus       159 ~ngq~l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  159 MNGQYLCNRPITVSYAFKKDTK  180 (203)
T ss_pred             hccchhcCCceEEEEEEecCCC
Confidence            9999999999999999766443

>KOG1190|consensus

Probab=99.93  E-value=1.5e-24  Score=185.87  Aligned_cols=305  Identities=17%  Similarity=0.202  Sum_probs=219.5

Q ss_pred             CccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCcc--cc
Q psy12549         13 GIIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFD--AL   89 (336)
Q Consensus        13 ~~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~--~~   89 (336)
                      ++-.|++.|.++|||.+++|+||.+++ .+|.++.+.+.+..+         .||++|.++  +.|..-+......  .+
T Consensus        23 ~~~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGkn---------QAflem~d~--~sAvtmv~~y~~~~p~l   91 (492)
T KOG1190|consen   23 SMAEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKN---------QAFLEMADE--ESAVTMVNYYTSVTPVL   91 (492)
T ss_pred             cccCCcceeEeccCCccccHHHHHHhcccccceeeeeeeccch---------hhhhhhcch--hhhhheeecccccCccc
Confidence            455689999999999999999999999 888999998887553         499999999  8876633322221  55


Q ss_pred             CCeeeEEEeccCCCC-----------------------------c---------CCCCCceEEEcCCCCCCCHHHHHHHh
Q psy12549         90 KGRPIRIMWSQRDPS-----------------------------L---------RKSGVGNVFIKNLDKSIDNKAMYDTF  131 (336)
Q Consensus        90 ~g~~i~v~~~~~~~~-----------------------------~---------~~~~~~~l~v~nlp~~~t~~~l~~~f  131 (336)
                      .|++|.|.++.....                             .         ..+.--.++|.|+-..++-+-|.++|
T Consensus        92 r~~~~yiq~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvF  171 (492)
T KOG1190|consen   92 RGQPIYIQYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVF  171 (492)
T ss_pred             cCcceeehhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHH
Confidence            678888776433110                             0         00011257789999999999999999


Q ss_pred             hccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEeeccCch------------------h
Q psy12549        132 SAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNS--KIVFVGKFIPRK------------------E  191 (336)
Q Consensus       132 ~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~--~~i~v~~~~~~~------------------~  191 (336)
                      ++||.|..+.-....   ..-.|+|+|.+.+.|+.|...|+|..+.+  +.+++.+++-..                  .
T Consensus       172 S~fG~VlKIiTF~Kn---n~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP  248 (492)
T KOG1190|consen  172 SKFGFVLKIITFTKN---NGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLP  248 (492)
T ss_pred             hhcceeEEEEEEecc---cchhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCC
Confidence            999999876555432   22359999999999999999999988754  445554443100                  0


Q ss_pred             hh---------------------------------H--hhhcccc--ccceEEEcCCC-CCCcHHHHHHhhccCCceeEE
Q psy12549        192 RE---------------------------------K--ELGEKAK--LFTNVYIKNFG-EDFNDEKLKEMFEPYGTITSY  233 (336)
Q Consensus       192 ~~---------------------------------~--~~~~~~~--~~~~l~V~nlp-~~~t~~~l~~~f~~~g~i~~~  233 (336)
                      ..                                 .  ..+....  ....|.|.||. +.+|.+-|-.+|+.||+|.++
T Consensus       249 ~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvYGdVqRV  328 (492)
T KOG1190|consen  249 VGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRV  328 (492)
T ss_pred             CCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhhcceEEE
Confidence            00                                 0  0000001  13568888886 558999999999999999999


Q ss_pred             EEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchhhH-------HHHHHHHHHHHHHh-------
Q psy12549        234 RVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERT-------QELKRRFEMLKIER-------  299 (336)
Q Consensus       234 ~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~~~-------~~~~~~~~~~~~~~-------  299 (336)
                      +|+...+   .-|.|+|.+...|+.|+..|+|..+.|+.|+|.+++...-..       ....+.+....-.+       
T Consensus       329 kil~nkk---d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~egq~d~glT~dy~~spLhrfkkpgsK  405 (492)
T KOG1190|consen  329 KILYNKK---DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSK  405 (492)
T ss_pred             EeeecCC---cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccccCCCCCCccccccccCCCCchhhccCcccc
Confidence            9997544   349999999999999999999999999999999986543211       11111111111111       


Q ss_pred             --hcC-CCCceEEEecCCCCCCHHHHHHhcCCCCCeee
Q psy12549        300 --LNR-YQGVNLYVKNLDDSIDDERLRKEFTPFGTITS  334 (336)
Q Consensus       300 --~~~-~~~~~l~v~nlp~~~t~~~l~~~F~~~G~V~~  334 (336)
                        .+. ++..++.+.|+|..++||+++++|..-|-..+
T Consensus       406 N~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vk  443 (492)
T KOG1190|consen  406 NYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVK  443 (492)
T ss_pred             cccccCCchhheeeccCCcccchhHHHHhhhcCCceEE
Confidence              111 45678999999999999999999999887654

>KOG0109|consensus

Probab=99.92  E-value=7.2e-25  Score=180.07  Aligned_cols=151  Identities=25%  Similarity=0.501  Sum_probs=140.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCch
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRK  190 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~  190 (336)
                      -+|||+|||..+++.+|+.+|++||+|.+|.|+++       ||||+.++...|..|+..|++-.++|..|.|+.++.+.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN-------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN-------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc-------cceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            35999999999999999999999999999999976       99999999999999999999999999999998877662


Q ss_pred             hhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecC
Q psy12549        191 EREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG  270 (336)
Q Consensus       191 ~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g  270 (336)
                                ...++++|+|+...++.++|+..|++||+|..|+|+      ++|+||.|...++|..|+..|+|..|.|
T Consensus        76 ----------k~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv------kdy~fvh~d~~eda~~air~l~~~~~~g  139 (346)
T KOG0109|consen   76 ----------KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV------KDYAFVHFDRAEDAVEAIRGLDNTEFQG  139 (346)
T ss_pred             ----------CCccccccCCCCccccCHHHhhhhcccCCceeeeee------cceeEEEEeeccchHHHHhccccccccc
Confidence                      233789999999999999999999999999999998      8899999999999999999999999999


Q ss_pred             EEEEEeecccchhh
Q psy12549        271 KILYVGRAQKKAER  284 (336)
Q Consensus       271 ~~l~v~~~~~~~~~  284 (336)
                      ++++|..+.++...
T Consensus       140 k~m~vq~stsrlrt  153 (346)
T KOG0109|consen  140 KRMHVQLSTSRLRT  153 (346)
T ss_pred             ceeeeeeecccccc
Confidence            99999998877543

>KOG4211|consensus

Probab=99.90  E-value=1.3e-22  Score=178.43  Aligned_cols=247  Identities=17%  Similarity=0.208  Sum_probs=192.0

Q ss_pred             CceeeeecCchhhhhhhHHhhhcccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEE
Q psy12549         18 KHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIM   97 (336)
Q Consensus        18 ~~~v~v~~lp~~~~e~~l~~~f~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~   97 (336)
                      .--|.+++||+++|++||++||+...|.++.+.+.     +|+..|-|||+|.++  +++++|++ .+...+..+-|.|-
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~I~~~~~~r~-----~Gr~sGeA~Ve~~se--edv~~Alk-kdR~~mg~RYIEVf   81 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCGIENLEIPRR-----NGRPSGEAYVEFTSE--EDVEKALK-KDRESMGHRYIEVF   81 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCceeEEEEecc-----CCCcCcceEEEeech--HHHHHHHH-hhHHHhCCceEEEE
Confidence            34588899999999999999999999999888874     378999999999999  99999999 78888888888886


Q ss_pred             eccCCCC-------cCC--CCCceEEEcCCCCCCCHHHHHHHhhccCCeeE-EEEeeCCCCCcccEEEEEeCCHHHHHHH
Q psy12549         98 WSQRDPS-------LRK--SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILS-CKVAQDEQGNSKGYGFVHFETEEAANKS  167 (336)
Q Consensus        98 ~~~~~~~-------~~~--~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~-~~~~~~~~~~~~g~afV~F~~~~~a~~a  167 (336)
                      .+...+.       ...  .....|.+++||.+||++||.++|+..-.+.. +.++.++.+++.|-|||+|++.+.|+.|
T Consensus        82 ~~~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~A  161 (510)
T KOG4211|consen   82 TAGGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIA  161 (510)
T ss_pred             ccCCccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHH
Confidence            6533322       111  23457999999999999999999998876665 6678888888999999999999999999


Q ss_pred             HHHhCCceeCCeEEEEeeccCchhhhHh-------------------hh-------------------------------
Q psy12549        168 IEKVNGMLLNSKIVFVGKFIPRKEREKE-------------------LG-------------------------------  197 (336)
Q Consensus       168 ~~~l~~~~~~~~~i~v~~~~~~~~~~~~-------------------~~-------------------------------  197 (336)
                      +.. |...+..+-|.|-.+.........                   ..                               
T Consensus       162 l~r-hre~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~  240 (510)
T KOG4211|consen  162 LGR-HRENIGHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYP  240 (510)
T ss_pred             HHH-HHHhhccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCc
Confidence            984 666677777766433210000000                   00                               


Q ss_pred             --------------------c---------------cccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCc
Q psy12549        198 --------------------E---------------KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGK  241 (336)
Q Consensus       198 --------------------~---------------~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~  241 (336)
                                          .               .......+++++||+..++.++.++|+..-++ .+++-. ++|+
T Consensus       241 ~~~d~~~~gs~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~dGr  319 (510)
T KOG4211|consen  241 SLQDYGNFGSYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGPDGR  319 (510)
T ss_pred             cccccccccccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCCCCc
Confidence                                0               00000458899999999999999999987665 566655 8999


Q ss_pred             cceEEEEEeCCHHHHHHHHHHhCCceecCEEEEE
Q psy12549        242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV  275 (336)
Q Consensus       242 ~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v  275 (336)
                      .+|.|+|+|.+.++|..|+.. ++..+..+-+.+
T Consensus       320 ~TGEAdveF~t~edav~Amsk-d~anm~hrYVEl  352 (510)
T KOG4211|consen  320 ATGEADVEFATGEDAVGAMGK-DGANMGHRYVEL  352 (510)
T ss_pred             cCCcceeecccchhhHhhhcc-CCcccCcceeee
Confidence            999999999999999999986 677776666555

>KOG0124|consensus

Probab=99.90  E-value=2.3e-23  Score=176.21  Aligned_cols=169  Identities=25%  Similarity=0.529  Sum_probs=150.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      ++|||+.+.....|+.|+..|..||+|.++.+.+|+ +++++|||||+|+-++.|+.|++.+||..++||.|+|.+...-
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm  193 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM  193 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC
Confidence            579999999999999999999999999999999998 9999999999999999999999999999999999999875543


Q ss_pred             hhhh---HhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhC
Q psy12549        190 KERE---KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWN  264 (336)
Q Consensus       190 ~~~~---~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~  264 (336)
                      ....   ..........+.|||..+..+.+++||+..|+.||+|..|.+-+  ..+.++||+|++|.+..+...|+..||
T Consensus       194 pQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMN  273 (544)
T KOG0124|consen  194 PQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN  273 (544)
T ss_pred             cccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcc
Confidence            3221   22233334457899999999999999999999999999999988  556679999999999999999999999


Q ss_pred             CceecCEEEEEeecc
Q psy12549        265 GKEVDGKILYVGRAQ  279 (336)
Q Consensus       265 g~~~~g~~l~v~~~~  279 (336)
                      -..++|..|+|..+.
T Consensus       274 lFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  274 LFDLGGQYLRVGKCV  288 (544)
T ss_pred             hhhcccceEeccccc
Confidence            999999999998763

>KOG0146|consensus

Probab=99.89  E-value=8.3e-23  Score=166.02  Aligned_cols=190  Identities=29%  Similarity=0.463  Sum_probs=160.4

Q ss_pred             CeeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHH
Q psy12549         91 GRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK  170 (336)
Q Consensus        91 g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~  170 (336)
                      .|+|.|.++..+.+.  .+.++|||+.|...-.|+|++.+|..||.+.+|.+.+.++|.+||+|||.|.+..+|+.|+..
T Consensus         2 nrpiqvkpadsesrg--~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~a   79 (371)
T KOG0146|consen    2 NRPIQVKPADSESRG--GDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINA   79 (371)
T ss_pred             CCCccccccccccCC--ccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHH
Confidence            577888887665543  356899999999999999999999999999999999999999999999999999999999999


Q ss_pred             hCCce-eC--CeEEEEeeccCchhhhHhhhccc-----------------------------------------------
Q psy12549        171 VNGML-LN--SKIVFVGKFIPRKEREKELGEKA-----------------------------------------------  200 (336)
Q Consensus       171 l~~~~-~~--~~~i~v~~~~~~~~~~~~~~~~~-----------------------------------------------  200 (336)
                      |+|.. +.  ...+-|++++..+++.-......                                               
T Consensus        80 LHgSqTmpGASSSLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~  159 (371)
T KOG0146|consen   80 LHGSQTMPGASSSLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFA  159 (371)
T ss_pred             hcccccCCCCccceEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhH
Confidence            99964 43  46777888776655421100000                                               


Q ss_pred             --------------------------------------------------------------------------------
Q psy12549        201 --------------------------------------------------------------------------------  200 (336)
Q Consensus       201 --------------------------------------------------------------------------------  200 (336)
                                                                                                      
T Consensus       160 ~~~mQ~~aA~~angl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~v  239 (371)
T KOG0146|consen  160 AAQMQQMAALNANGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTV  239 (371)
T ss_pred             HHHHHHHHHHhhcccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccc
Confidence                                                                                            


Q ss_pred             -------------------------------------------cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC
Q psy12549        201 -------------------------------------------KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN  237 (336)
Q Consensus       201 -------------------------------------------~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~  237 (336)
                                                                 +..|.|||.-||.+..+.+|.++|-+||.|.+.++..
T Consensus       240 a~~lq~a~~g~~~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFv  319 (371)
T KOG0146|consen  240 ADPLQQAYAGVQQYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFV  319 (371)
T ss_pred             cchhhhhhhhHHHHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeee
Confidence                                                       0008899999999999999999999999999887765


Q ss_pred             --CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        238 --NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       238 --~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                        .++.++-|+||.|+++.+|+.||..|||..|+-++|+|....++.
T Consensus       320 DRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkd  366 (371)
T KOG0146|consen  320 DRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKD  366 (371)
T ss_pred             hhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcCccc
Confidence              677889999999999999999999999999999999998887774

>KOG0109|consensus

Probab=99.86  E-value=1.2e-21  Score=161.22  Aligned_cols=153  Identities=19%  Similarity=0.288  Sum_probs=138.6

Q ss_pred             eeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEEe
Q psy12549         20 NVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMW   98 (336)
Q Consensus        20 ~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~~   98 (336)
                      .|||||||..+++.+|+++| .++.+.++-++++           ||||..++.  ..|+.|+..|++..++|..|.|..
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN-----------YgFVHiEdk--taaedairNLhgYtLhg~nInVea   70 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVKN-----------YGFVHIEDK--TAAEDAIRNLHGYTLHGVNINVEA   70 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeecc-----------cceEEeecc--cccHHHHhhcccceecceEEEEEe
Confidence            58999999999999999999 7789999999873           389999999  999999999999999999999998


Q ss_pred             ccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCC
Q psy12549         99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNS  178 (336)
Q Consensus        99 ~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~  178 (336)
                      ++.+.    ...++|+|+||.+.++..||+..|++||+|.+|.++++       |+||+|...++|..|++.|++.++.|
T Consensus        71 SksKs----k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd-------y~fvh~d~~eda~~air~l~~~~~~g  139 (346)
T KOG0109|consen   71 SKSKS----KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD-------YAFVHFDRAEDAVEAIRGLDNTEFQG  139 (346)
T ss_pred             ccccC----CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc-------eeEEEEeeccchHHHHhccccccccc
Confidence            87763    23578999999999999999999999999999999976       99999999999999999999999999


Q ss_pred             eEEEEeeccCchhhhHhh
Q psy12549        179 KIVFVGKFIPRKEREKEL  196 (336)
Q Consensus       179 ~~i~v~~~~~~~~~~~~~  196 (336)
                      +.++|+.+..+....+..
T Consensus       140 k~m~vq~stsrlrtapgm  157 (346)
T KOG0109|consen  140 KRMHVQLSTSRLRTAPGM  157 (346)
T ss_pred             ceeeeeeeccccccCCCC
Confidence            999999987765544433

>KOG0147|consensus

Probab=99.85  E-value=3.3e-21  Score=171.80  Aligned_cols=173  Identities=25%  Similarity=0.455  Sum_probs=150.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..+++|+.-|+...++.+|.++|+.+|.|..|.++.++ ++.++|.|||+|.+.+....|+. |.|..+.|.+|.|....
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~sE  256 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLSE  256 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecccH
Confidence            45689999999999999999999999999999999998 88999999999999999999997 99999999999997755


Q ss_pred             CchhhhHhhhcc------ccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHH
Q psy12549        188 PRKEREKELGEK------AKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKA  259 (336)
Q Consensus       188 ~~~~~~~~~~~~------~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a  259 (336)
                      ............      ..+...|||+||.+.+++++|+..|++||.|..+.+..  .+|.++||+||+|.+.++|.+|
T Consensus       257 aeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a  336 (549)
T KOG0147|consen  257 AEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKA  336 (549)
T ss_pred             HHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHH
Confidence            443332222211      22234499999999999999999999999999999988  4999999999999999999999


Q ss_pred             HHHhCCceecCEEEEEeecccch
Q psy12549        260 VQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       260 ~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      +..|||..+-|+.|+|.....+.
T Consensus       337 ~e~lngfelAGr~ikV~~v~~r~  359 (549)
T KOG0147|consen  337 LEQLNGFELAGRLIKVSVVTERV  359 (549)
T ss_pred             HHHhccceecCceEEEEEeeeec
Confidence            99999999999999997765443

>KOG0146|consensus

Probab=99.84  E-value=1.2e-20  Score=153.60  Aligned_cols=169  Identities=20%  Similarity=0.302  Sum_probs=150.0

Q ss_pred             cCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccC-C--e
Q psy12549         17 PKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALK-G--R   92 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~-g--~   92 (336)
                      .++.||||-|.+.-.|+|+|.+| .+|.++++.+.+..+    |.++|+|||.|.+.  .+|+.|+..|+|..-. |  .
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d----g~sKGCAFVKf~s~--~eAqaAI~aLHgSqTmpGASS   91 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD----GNSKGCAFVKFSSH--AEAQAAINALHGSQTMPGASS   91 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC----CCCCCceEEEeccc--hHHHHHHHHhcccccCCCCcc
Confidence            67899999999999999999999 888999999999874    89999999999999  9999999999997443 3  5


Q ss_pred             eeEEEeccCCCC--------------------------------------------------------------------
Q psy12549         93 PIRIMWSQRDPS--------------------------------------------------------------------  104 (336)
Q Consensus        93 ~i~v~~~~~~~~--------------------------------------------------------------------  104 (336)
                      .+-|.++..+..                                                                    
T Consensus        92 SLVVK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~a  171 (371)
T KOG0146|consen   92 SLVVKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNA  171 (371)
T ss_pred             ceEEEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhh
Confidence            677777655422                                                                    


Q ss_pred             --------------------------------------------------------------------------------
Q psy12549        105 --------------------------------------------------------------------------------  104 (336)
Q Consensus       105 --------------------------------------------------------------------------------  104 (336)
                                                                                                      
T Consensus       172 ngl~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~  251 (371)
T KOG0146|consen  172 NGLAAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQ  251 (371)
T ss_pred             cccccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHH
Confidence                                                                                            


Q ss_pred             ----------------------------cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEE
Q psy12549        105 ----------------------------LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGF  155 (336)
Q Consensus       105 ----------------------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~af  155 (336)
                                                  ....+.|+|||..||......||.+.|-.||.|.+.++..|+ ++.+|+|+|
T Consensus       252 ~Y~Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGF  331 (371)
T KOG0146|consen  252 QYAAAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGF  331 (371)
T ss_pred             HHhhhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceee
Confidence                                        333567999999999999999999999999999999999998 888999999


Q ss_pred             EEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchh
Q psy12549        156 VHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKE  191 (336)
Q Consensus       156 V~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~  191 (336)
                      |.|+++.+|+.|+..+||..|+=++++|....+++.
T Consensus       332 VSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkda  367 (371)
T KOG0146|consen  332 VSFDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDA  367 (371)
T ss_pred             EecCCchhHHHHHHHhcchhhhhhhhhhhhcCcccc
Confidence            999999999999999999999999999987766643

>KOG4205|consensus

Probab=99.82  E-value=2.6e-20  Score=160.57  Aligned_cols=173  Identities=26%  Similarity=0.486  Sum_probs=152.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      +.++|||++|+..++++.|++.|.+||.|.+|.+++++ +++++||+||+|++++...+++. ...+.++|+.|....+.
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            56889999999999999999999999999999999998 89999999999999999999988 47788999999999998


Q ss_pred             CchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCC
Q psy12549        188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNG  265 (336)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g  265 (336)
                      ++..........  ....+||++||.+++++++++.|.+||.|..+.++.  .+..+++|+||.|.+++++++++. ..-
T Consensus        84 ~r~~~~~~~~~~--~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f  160 (311)
T KOG4205|consen   84 SREDQTKVGRHL--RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKF  160 (311)
T ss_pred             Cccccccccccc--ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cce
Confidence            887654333222  346899999999999999999999999988887776  677789999999999999999997 488


Q ss_pred             ceecCEEEEEeecccchhhH
Q psy12549        266 KEVDGKILYVGRAQKKAERT  285 (336)
Q Consensus       266 ~~~~g~~l~v~~~~~~~~~~  285 (336)
                      ..|.|+.+.|..|.++....
T Consensus       161 ~~~~gk~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  161 HDFNGKKVEVKRAIPKEVMQ  180 (311)
T ss_pred             eeecCceeeEeeccchhhcc
Confidence            99999999999999886543

>KOG0120|consensus

Probab=99.82  E-value=3.2e-19  Score=161.18  Aligned_cols=254  Identities=15%  Similarity=0.241  Sum_probs=191.9

Q ss_pred             ccccCceeeeecCchhhhhhhHHhhhccc-C------------CceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHH
Q psy12549         14 IIIPKHNVATRELSAKVVEGVSRSLSSLI-D------------GNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERA   80 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~~~e~~l~~~f~~~-~------------~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A   80 (336)
                      .....+.++|+++|+.+.|+.+..+|... -            +..+.+         ...+.|||++|.+.  ++|..|
T Consensus       171 ~t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~---------n~~~nfa~ie~~s~--~~at~~  239 (500)
T KOG0120|consen  171 ATRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQL---------NLEKNFAFIEFRSI--SEATEA  239 (500)
T ss_pred             hhhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeee---------cccccceeEEecCC--Cchhhh
Confidence            44566779999999999999999988222 1            122222         34567899999999  999888


Q ss_pred             HhhcCccccCCeeeEEEeccCCCC---------------------cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeE
Q psy12549         81 LDTMNFDALKGRPIRIMWSQRDPS---------------------LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILS  139 (336)
Q Consensus        81 ~~~~~~~~~~g~~i~v~~~~~~~~---------------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~  139 (336)
                      +. +++..+.|.++.+........                     ........++|++||...++.++.++...||.+..
T Consensus       240 ~~-~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~  318 (500)
T KOG0120|consen  240 MA-LDGIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKA  318 (500)
T ss_pred             hc-ccchhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchh
Confidence            88 899999998888753221110                     11123458999999999999999999999999999


Q ss_pred             EEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchhhhHhhhc----------------cccc
Q psy12549        140 CKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGE----------------KAKL  202 (336)
Q Consensus       140 ~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~----------------~~~~  202 (336)
                      ..++.+. +|.++||||.+|.++.....|++.|||+.++++.+.++.+-...........                ...+
T Consensus       319 f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~  398 (500)
T KOG0120|consen  319 FRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIP  398 (500)
T ss_pred             heeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCccccccccchhhhcccCCCc
Confidence            9999987 6899999999999999999999999999999999999876544322111111                0011


Q ss_pred             cceEEEcCC--CCCC--------cHHHHHHhhccCCceeEEEEeCC-----CCccceEEEEEeCCHHHHHHHHHHhCCce
Q psy12549        203 FTNVYIKNF--GEDF--------NDEKLKEMFEPYGTITSYRVMNN-----DGKSRGFGFVAYESPEFAEKAVQAWNGKE  267 (336)
Q Consensus       203 ~~~l~V~nl--p~~~--------t~~~l~~~f~~~g~i~~~~i~~~-----~~~~~g~afV~F~~~~~a~~a~~~l~g~~  267 (336)
                      ...|...|+  |.+.        -.|+++..+++||.|..|.+.++     ..-..|-.||+|.+.+++++|++.|+|..
T Consensus       399 t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrK  478 (500)
T KOG0120|consen  399 TEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRK  478 (500)
T ss_pred             chhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCce
Confidence            122233332  1111        11567888999999999999873     22246779999999999999999999999


Q ss_pred             ecCEEEEEeecc
Q psy12549        268 VDGKILYVGRAQ  279 (336)
Q Consensus       268 ~~g~~l~v~~~~  279 (336)
                      |.||.+...|-.
T Consensus       479 F~nRtVvtsYyd  490 (500)
T KOG0120|consen  479 FANRTVVASYYD  490 (500)
T ss_pred             eCCcEEEEEecC
Confidence            999999988854

>KOG1190|consensus

Probab=99.80  E-value=3.9e-18  Score=146.73  Aligned_cols=245  Identities=16%  Similarity=0.193  Sum_probs=185.6

Q ss_pred             eeeeecCchhhhhhhHHhhh-cccCCceE-EEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCC--eeeE
Q psy12549         20 NVATRELSAKVVEGVSRSLS-SLIDGNTV-KYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKG--RPIR   95 (336)
Q Consensus        20 ~v~v~~lp~~~~e~~l~~~f-~~~~~~~v-~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g--~~i~   95 (336)
                      .++|+|+-..++-+-|.+.| .+|.+..+ .+.++.+        =.|.|+|.+.  +.|+.|...|+|..+..  +.++
T Consensus       152 r~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~Knn~--------FQALvQy~d~--~sAq~AK~aLdGqnIyngcCtLr  221 (492)
T KOG1190|consen  152 RTIIENMFYPVSLDVLHQVFSKFGFVLKIITFTKNNG--------FQALVQYTDA--VSAQAAKLALDGQNIYNGCCTLR  221 (492)
T ss_pred             EEEeccceeeeEHHHHHHHHhhcceeEEEEEEecccc--------hhhhhhccch--hhHHHHHHhccCCcccCceeEEE
Confidence            46679999999999999999 45544333 3333332        2399999999  99999999999987764  5566


Q ss_pred             EEeccCCC----------C---------c------------------------------------------CCCCCceEE
Q psy12549         96 IMWSQRDP----------S---------L------------------------------------------RKSGVGNVF  114 (336)
Q Consensus        96 v~~~~~~~----------~---------~------------------------------------------~~~~~~~l~  114 (336)
                      |.++....          +         .                                          .......|.
T Consensus       222 Id~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vll  301 (492)
T KOG1190|consen  222 IDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLL  301 (492)
T ss_pred             eehhhcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEE
Confidence            65432210          0         0                                          000135677


Q ss_pred             EcCCC-CCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchhhh
Q psy12549        115 IKNLD-KSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKERE  193 (336)
Q Consensus       115 v~nlp-~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~  193 (336)
                      |.||. ..+|.+.|..+|.-||.|.+|+|...+    +-.|+|++.+...|+.|++.|+|..+.|++|+|.+++-..-..
T Consensus       302 vsnln~~~VT~d~LftlFgvYGdVqRVkil~nk----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vql  377 (492)
T KOG1190|consen  302 VSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQL  377 (492)
T ss_pred             EecCchhccchhHHHHHHhhhcceEEEEeeecC----CcceeeeecchhHHHHHHHHhhcceecCceEEEeeccCccccC
Confidence            88885 468999999999999999999999875    2469999999999999999999999999999998876321110


Q ss_pred             ---------------------------HhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeE-EEEeCCCCccceE
Q psy12549        194 ---------------------------KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS-YRVMNNDGKSRGF  245 (336)
Q Consensus       194 ---------------------------~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~-~~i~~~~~~~~g~  245 (336)
                                                 ++.....++..+++..|+|.++++|++++.|..-|.... .+..   ++.+.+
T Consensus       378 p~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff---~kd~km  454 (492)
T KOG1190|consen  378 PREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF---QKDRKM  454 (492)
T ss_pred             CCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeec---CCCcce
Confidence                                       011111244468999999999999999999987776533 3333   345778


Q ss_pred             EEEEeCCHHHHHHHHHHhCCceecCE-EEEEeecccc
Q psy12549        246 GFVAYESPEFAEKAVQAWNGKEVDGK-ILYVGRAQKK  281 (336)
Q Consensus       246 afV~F~~~~~a~~a~~~l~g~~~~g~-~l~v~~~~~~  281 (336)
                      |++.+.+.+.|..|+-.+++..+++. .++|+|++..
T Consensus       455 al~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks~  491 (492)
T KOG1190|consen  455 ALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKST  491 (492)
T ss_pred             eecccCChhHhhhhccccccccCCCCceEEEEeeccc
Confidence            99999999999999999999998764 8999998753

>KOG4205|consensus

Probab=99.77  E-value=1.5e-18  Score=149.79  Aligned_cols=239  Identities=19%  Similarity=0.234  Sum_probs=177.8

Q ss_pred             cCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeE
Q psy12549         17 PKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIR   95 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~   95 (336)
                      ....++|++|+++++++.|+.+| .++.+.++.+.+++   ++++++||+||+|.++  +...+++. .....+-|+.|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~---~t~rsrgFgfv~f~~~--~~v~~vl~-~~~h~~dgr~ve   78 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDP---STGRSRGFGFVTFATP--EGVDAVLN-ARTHKLDGRSVE   78 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccC---CCCCcccccceecCCC--cchheeec-ccccccCCcccc
Confidence            45679999999999999999999 77899999999998   5799999999999999  88877777 455678888888


Q ss_pred             EEeccCCCCcCCCC----CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHH
Q psy12549         96 IMWSQRDPSLRKSG----VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK  170 (336)
Q Consensus        96 v~~~~~~~~~~~~~----~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~  170 (336)
                      +..+.+........    ..+|||++||.+++++++++.|++||.|..+.++.|. +...+||+||.|.+++.+.+++. 
T Consensus        79 ~k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-  157 (311)
T KOG4205|consen   79 PKRAVSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-  157 (311)
T ss_pred             ceeccCcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-
Confidence            87766654333322    4589999999999999999999999999999999887 78899999999999999999998 


Q ss_pred             hCCceeCCeEEEEeeccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEe------C-CCCccc
Q psy12549        171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM------N-NDGKSR  243 (336)
Q Consensus       171 l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~------~-~~~~~~  243 (336)
                      ..-+.+.++.+.|..+.++...........   ......|+....+.-.|..+|..|++......-      . ....+.
T Consensus       158 ~~f~~~~gk~vevkrA~pk~~~~~~~~~~~---~~~~~~~~g~~~~~~~l~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~  234 (311)
T KOG4205|consen  158 QKFHDFNGKKVEVKRAIPKEVMQSTKSSVS---TRGKGNNLGNGRTGFFLKKYFKGYGPVGMSDYGGRPVGRRYGPLFNG  234 (311)
T ss_pred             cceeeecCceeeEeeccchhhccccccccc---cccccccccccccccccchhccccCccccccccccccccccccccCC
Confidence            688999999999999988765443211000   111112344444444455666666655311100      1 111346


Q ss_pred             eEEEEEeCCHHHHHHHHHHhCC
Q psy12549        244 GFGFVAYESPEFAEKAVQAWNG  265 (336)
Q Consensus       244 g~afV~F~~~~~a~~a~~~l~g  265 (336)
                      +.+|..|.+......+...+++
T Consensus       235 g~g~~~~~~~~~~~~~~~~~~~  256 (311)
T KOG4205|consen  235 GSGYPEFGNSGLGFGYGNKLNR  256 (311)
T ss_pred             CccccccCccccccccccccCC
Confidence            7788888877666555544443

>KOG0105|consensus

Probab=99.76  E-value=1.7e-17  Score=128.12  Aligned_cols=154  Identities=19%  Similarity=0.232  Sum_probs=129.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..++|||+|||.++.+.+|..+|.+||.|..+.+...+ + ..+||||+|+++.+|+.|+..-+|-.++|..|.|+++..
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~-g-~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprg   82 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP-G-PPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRG   82 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC-C-CCCeeEEEecCccchhhhhhcccccccCcceEEEEeccC
Confidence            45789999999999999999999999999998876543 2 356999999999999999999999999999999998775


Q ss_pred             chhhhH------------------hhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEe
Q psy12549        189 RKEREK------------------ELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAY  250 (336)
Q Consensus       189 ~~~~~~------------------~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F  250 (336)
                      ......                  ...+.......|.|.+||.+-+.+||++...+.|.|....+.+     -|++.|+|
T Consensus        83 gr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~r-----Dg~GvV~~  157 (241)
T KOG0105|consen   83 GRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQR-----DGVGVVEY  157 (241)
T ss_pred             CCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeec-----ccceeeee
Confidence            432111                  0111222336799999999999999999999999999988876     45789999


Q ss_pred             CCHHHHHHHHHHhCCceec
Q psy12549        251 ESPEFAEKAVQAWNGKEVD  269 (336)
Q Consensus       251 ~~~~~a~~a~~~l~g~~~~  269 (336)
                      .+.++.+-|+..|+...+.
T Consensus       158 ~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  158 LRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             eehhhHHHHHHhhcccccc
Confidence            9999999999999988874

>KOG4206|consensus

Probab=99.75  E-value=5.1e-17  Score=130.34  Aligned_cols=164  Identities=23%  Similarity=0.371  Sum_probs=138.2

Q ss_pred             ceEEEcCCCCCCCHHHHHH----HhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        111 GNVFIKNLDKSIDNKAMYD----TFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~----~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      .||||.||+..+..++|+.    +|++||.|..|....  +.+.+|.|||.|.+.+.|..|+..|+|..+.|+.+.+.++
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k--t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA   87 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK--TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYA   87 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC--CCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecc
Confidence            4899999999999999887    999999999877665  4567899999999999999999999999999999999998


Q ss_pred             cCchhhhHhh------------------------------------------hccccccceEEEcCCCCCCcHHHHHHhh
Q psy12549        187 IPRKEREKEL------------------------------------------GEKAKLFTNVYIKNFGEDFNDEKLKEMF  224 (336)
Q Consensus       187 ~~~~~~~~~~------------------------------------------~~~~~~~~~l~V~nlp~~~t~~~l~~~f  224 (336)
                      ....+.....                                          .....+...+++.|+|..++.+.+..+|
T Consensus        88 ~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~lf  167 (221)
T KOG4206|consen   88 KSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSDLF  167 (221)
T ss_pred             cCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHHHH
Confidence            7654321110                                          1113344679999999999999999999


Q ss_pred             ccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceec-CEEEEEeecc
Q psy12549        225 EPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD-GKILYVGRAQ  279 (336)
Q Consensus       225 ~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~-g~~l~v~~~~  279 (336)
                      ..|.....++++..   -.+.|||+|.+...|..|...++|..+. ...+.+.++.
T Consensus       168 ~qf~g~keir~i~~---~~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  168 EQFPGFKEIRLIPP---RSGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             hhCcccceeEeccC---CCceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            99999999988862   2667999999999999999999999987 7888887764

>KOG1365|consensus

Probab=99.74  E-value=1.2e-17  Score=142.48  Aligned_cols=262  Identities=15%  Similarity=0.130  Sum_probs=186.5

Q ss_pred             CCccccCceeeeecCchhhhhhhHHhhhcccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCC
Q psy12549         12 EGIIIPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKG   91 (336)
Q Consensus        12 ~~~~~p~~~v~v~~lp~~~~e~~l~~~f~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g   91 (336)
                      .+.+.-+.-|..++||+..+..++..+|....+..--..-.-  ...|+..|.|.|.|.++  |.-..|++ .+...+.+
T Consensus        54 ~~~~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG--~~qgrRnge~lvrf~d~--e~Rdlalk-Rhkhh~g~  128 (508)
T KOG1365|consen   54 NHSADDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCL--NAQGRRNGEALVRFVDP--EGRDLALK-RHKHHMGT  128 (508)
T ss_pred             ccccCcceEEEecCCCCCcccCCHHHHHhhhhccccceeeee--hhhhccccceEEEecCc--hhhhhhhH-hhhhhccC
Confidence            455556666778999999999999999965554422111111  13577889999999999  99999999 67777777


Q ss_pred             eeeEEEeccCCCC--------------cCCCCCceEEEcCCCCCCCHHHHHHHhhc---c-CCeeEEEEeeCCCCCcccE
Q psy12549         92 RPIRIMWSQRDPS--------------LRKSGVGNVFIKNLDKSIDNKAMYDTFSA---F-GSILSCKVAQDEQGNSKGY  153 (336)
Q Consensus        92 ~~i~v~~~~~~~~--------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~---~-G~v~~~~~~~~~~~~~~g~  153 (336)
                      +.|.+-.+....-              ......--|.++|||.++++.++.++|..   . |....+.++..++|+..|-
T Consensus       129 ryievYka~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGd  208 (508)
T KOG1365|consen  129 RYIEVYKATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGD  208 (508)
T ss_pred             CceeeeccCchhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccc
Confidence            8777744333211              11122335778999999999999999953   2 2456677787778999999


Q ss_pred             EEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC----------------------chh-hhHhhhccccccceEEEcC
Q psy12549        154 GFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP----------------------RKE-REKELGEKAKLFTNVYIKN  210 (336)
Q Consensus       154 afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~----------------------~~~-~~~~~~~~~~~~~~l~V~n  210 (336)
                      |||.|..+++|+.|+.. |...++-|.|.+-++..                      ... .............+|.+++
T Consensus       209 AFvlfa~ee~aq~aL~k-hrq~iGqRYIElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRG  287 (508)
T KOG1365|consen  209 AFVLFACEEDAQFALRK-HRQNIGQRYIELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRG  287 (508)
T ss_pred             eEEEecCHHHHHHHHHH-HHHHHhHHHHHHHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecC
Confidence            99999999999999985 44344433333211110                      000 0001111122346899999


Q ss_pred             CCCCCcHHHHHHhhccCCc-eeE--EEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        211 FGEDFNDEKLKEMFEPYGT-ITS--YRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       211 lp~~~t~~~l~~~f~~~g~-i~~--~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ||+..+.++|.++|..|.. |..  +++.. ..|+..|.|||+|.+.++|..|....+.....+|.|.|--+.
T Consensus       288 LPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S  360 (508)
T KOG1365|consen  288 LPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCS  360 (508)
T ss_pred             CChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeecc
Confidence            9999999999999998865 333  55554 788999999999999999999999888888888999985554

>KOG1457|consensus

Probab=99.71  E-value=1.7e-16  Score=126.27  Aligned_cols=159  Identities=18%  Similarity=0.374  Sum_probs=124.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC--CCCcccEEEEEeCCHHHHHHHHHHhCCceeC---CeEEE
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE--QGNSKGYGFVHFETEEAANKSIEKVNGMLLN---SKIVF  182 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~--~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~---~~~i~  182 (336)
                      ...+||||.|||.++...+|+.+|..|-.-+.+.+....  ...++.+||+.|.+.++|..|++.|||..++   +..++
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            446899999999999999999999999766666555543  3457789999999999999999999999885   67788


Q ss_pred             EeeccCchhhhHhhhcc---------------------------------------------------------------
Q psy12549        183 VGKFIPRKEREKELGEK---------------------------------------------------------------  199 (336)
Q Consensus       183 v~~~~~~~~~~~~~~~~---------------------------------------------------------------  199 (336)
                      ++.++.........+..                                                               
T Consensus       112 iElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P  191 (284)
T KOG1457|consen  112 IELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAP  191 (284)
T ss_pred             eeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCC
Confidence            77765332211100000                                                               


Q ss_pred             ---------------ccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhC
Q psy12549        200 ---------------AKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN  264 (336)
Q Consensus       200 ---------------~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~  264 (336)
                                     .....+|||.||..++++++|+.+|+.|.....+++....|.  ..||++|.+.+.|..|+..|+
T Consensus       192 ~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~--~vaf~~~~~~~~at~am~~lq  269 (284)
T KOG1457|consen  192 SANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGM--PVAFADFEEIEQATDAMNHLQ  269 (284)
T ss_pred             cccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCc--ceEeecHHHHHHHHHHHHHhh
Confidence                           000057999999999999999999999988877777654343  469999999999999999999


Q ss_pred             Ccee
Q psy12549        265 GKEV  268 (336)
Q Consensus       265 g~~~  268 (336)
                      |..+
T Consensus       270 g~~~  273 (284)
T KOG1457|consen  270 GNLL  273 (284)
T ss_pred             ccee
Confidence            8776

>KOG1548|consensus

Probab=99.70  E-value=7.5e-16  Score=130.23  Aligned_cols=170  Identities=24%  Similarity=0.296  Sum_probs=138.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCee--------EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSIL--------SCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIV  181 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~--------~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i  181 (336)
                      .+.|||.|||.++|.+++.++|+++|.|.        .|+++++..|.-+|-|++.|-..++...|+..|++..+.|+.|
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~  213 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRGKKL  213 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccCcEE
Confidence            46799999999999999999999999765        4899999999999999999999999999999999999999999


Q ss_pred             EEeeccCchhh-----------------hH-------------hhhccccccceEEEcCCCC----CCc-------HHHH
Q psy12549        182 FVGKFIPRKER-----------------EK-------------ELGEKAKLFTNVYIKNFGE----DFN-------DEKL  220 (336)
Q Consensus       182 ~v~~~~~~~~~-----------------~~-------------~~~~~~~~~~~l~V~nlp~----~~t-------~~~l  220 (336)
                      +|..+.-....                 ..             .........++|.+.|+=.    ..+       .++|
T Consensus       214 rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl  293 (382)
T KOG1548|consen  214 RVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDL  293 (382)
T ss_pred             EEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHH
Confidence            99876521100                 00             0011122337888888732    122       3677


Q ss_pred             HHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        221 KEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       221 ~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ++-+++||.|.++.+..  ..+.|.+-|.|.+.++|..+++.|+|++|+||.|..+....+
T Consensus       294 ~eec~K~G~v~~vvv~d--~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  294 TEECEKFGQVRKVVVYD--RHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHhCCcceEEEec--cCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            88899999999999874  234788999999999999999999999999999999876554

>KOG1456|consensus

Probab=99.70  E-value=7.3e-15  Score=125.34  Aligned_cols=298  Identities=15%  Similarity=0.127  Sum_probs=210.9

Q ss_pred             cccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhh--cCccccCC
Q psy12549         15 IIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDT--MNFDALKG   91 (336)
Q Consensus        15 ~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~--~~~~~~~g   91 (336)
                      ..|+-.|.|++|-..++|.+|.+-. .++.+.-+..+..+         +.|.|+|++.  +-|..++.-  -+...+.|
T Consensus        28 ~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~---------r~alvefedi--~~akn~Vnfaa~n~i~i~g   96 (494)
T KOG1456|consen   28 PNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHK---------RQALVEFEDI--EGAKNCVNFAADNQIYIAG   96 (494)
T ss_pred             CCCCceEEEeccccccchhHHHHHHhcCCceEEEEecccc---------ceeeeeeccc--cchhhheehhccCcccccC
Confidence            3566679999999999999999977 55555555555433         5599999999  999988762  23356677


Q ss_pred             eeeEEEeccCCC----CcCCCCCc-eEEE--cCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHH
Q psy12549         92 RPIRIMWSQRDP----SLRKSGVG-NVFI--KNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAA  164 (336)
Q Consensus        92 ~~i~v~~~~~~~----~~~~~~~~-~l~v--~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a  164 (336)
                      +.-.+.++..+.    ..+..... .|.+  -|--+.+|.+-|..+....|.|.++.|.+. +|   -.|.|+|++.+.|
T Consensus        97 q~Al~NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-ng---VQAmVEFdsv~~A  172 (494)
T KOG1456|consen   97 QQALFNYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-NG---VQAMVEFDSVEVA  172 (494)
T ss_pred             chhhcccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-cc---eeeEEeechhHHH
Confidence            776666653321    11111222 3333  344457899999999999999999998875 22   3699999999999


Q ss_pred             HHHHHHhCCceeC--CeEEEEeeccCchhhhH----------------------h---h--------------h------
Q psy12549        165 NKSIEKVNGMLLN--SKIVFVGKFIPRKEREK----------------------E---L--------------G------  197 (336)
Q Consensus       165 ~~a~~~l~~~~~~--~~~i~v~~~~~~~~~~~----------------------~---~--------------~------  197 (336)
                      ++|.+.|||..|.  =..|++++++|..-.-.                      .   .              +      
T Consensus       173 qrAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y  252 (494)
T KOG1456|consen  173 QRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGY  252 (494)
T ss_pred             HHHHhhcccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCC
Confidence            9999999997763  36778887775321100                      0   0              0      


Q ss_pred             -----------------------------ccccccceEEEcCCCCC-CcHHHHHHhhccCCceeEEEEeCCCCccceEEE
Q psy12549        198 -----------------------------EKAKLFTNVYIKNFGED-FNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGF  247 (336)
Q Consensus       198 -----------------------------~~~~~~~~l~V~nlp~~-~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~af  247 (336)
                                                   ....+.+.++|.+|... .+-+.|-++|..||.|.++++++.   ..|.|+
T Consensus       253 ~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkT---k~gtam  329 (494)
T KOG1456|consen  253 YSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKT---KPGTAM  329 (494)
T ss_pred             cccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeec---ccceeE
Confidence                                         00011256899999854 677899999999999999999972   256799


Q ss_pred             EEeCCHHHHHHHHHHhCCceecCEEEEEeecccchhh----------HHHHHHHHHH----------HHHHhhcCCCCce
Q psy12549        248 VAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER----------TQELKRRFEM----------LKIERLNRYQGVN  307 (336)
Q Consensus       248 V~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~~----------~~~~~~~~~~----------~~~~~~~~~~~~~  307 (336)
                      |++.+..+.++|+..||+..+.|.+|.+-.++...-.          .... +.+..          ......-.+++++
T Consensus       330 Vemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSf-Kdys~SkNnRFssp~qAsKNrIq~Ps~v  408 (494)
T KOG1456|consen  330 VEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNFVSPVQPFLLPDGSPSF-KDYSGSKNNRFSSPEQASKNRIQPPSNV  408 (494)
T ss_pred             EEcCcHHHHHHHHHHhccCccccceEEEeeccccccccCCceecCCCCcch-hhcccccccccCChhHhhcccccCCcce
Confidence            9999999999999999999999999999776533210          0000 11111          1111122357789


Q ss_pred             EEEecCCCCCCHHHHHHhcCCCCC
Q psy12549        308 LYVKNLDDSIDDERLRKEFTPFGT  331 (336)
Q Consensus       308 l~v~nlp~~~t~~~l~~~F~~~G~  331 (336)
                      |..-|.|..+||+.|.++|..-+.
T Consensus       409 LHffNaP~~vtEe~l~~i~nek~v  432 (494)
T KOG1456|consen  409 LHFFNAPLGVTEEQLIGICNEKDV  432 (494)
T ss_pred             eEEecCCCccCHHHHHHHhhhcCC
Confidence            999999999999999999977653

>KOG4206|consensus

Probab=99.69  E-value=7.2e-16  Score=123.79  Aligned_cols=160  Identities=15%  Similarity=0.242  Sum_probs=135.9

Q ss_pred             cccCceeeeecCchhhhhhhHHh----hh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCcccc
Q psy12549         15 IIPKHNVATRELSAKVVEGVSRS----LS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDAL   89 (336)
Q Consensus        15 ~~p~~~v~v~~lp~~~~e~~l~~----~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~   89 (336)
                      +.|+.+|||.||...+..++|+.    +| .+|.+.+|...+      |.+.+|.|||.|.+.  +.|-.|+..++|..|
T Consensus         6 ~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k------t~KmRGQA~VvFk~~--~~As~A~r~l~gfpF   77 (221)
T KOG4206|consen    6 VNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK------TPKMRGQAFVVFKET--EAASAALRALQGFPF   77 (221)
T ss_pred             cCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC------CCCccCceEEEecCh--hHHHHHHHHhcCCcc
Confidence            46777999999999999999999    88 566788887776      457899999999999  999999999999999


Q ss_pred             CCeeeEEEeccCCCCc------------------------------------------------CCCCCceEEEcCCCCC
Q psy12549         90 KGRPIRIMWSQRDPSL------------------------------------------------RKSGVGNVFIKNLDKS  121 (336)
Q Consensus        90 ~g~~i~v~~~~~~~~~------------------------------------------------~~~~~~~l~v~nlp~~  121 (336)
                      .|++++|.++..+...                                                .......+++.|||..
T Consensus        78 ygK~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~e  157 (221)
T KOG4206|consen   78 YGKPMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSE  157 (221)
T ss_pred             cCchhheecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcc
Confidence            9999999987654220                                                0112347999999999


Q ss_pred             CCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEeec
Q psy12549        122 IDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLN-SKIVFVGKF  186 (336)
Q Consensus       122 ~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~-~~~i~v~~~  186 (336)
                      ++.+.+..+|++|..-.+++++...    ++.|||+|.+...|..|...+.+..+. ...+.+.++
T Consensus       158 s~~e~l~~lf~qf~g~keir~i~~~----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a  219 (221)
T KOG4206|consen  158 SESEMLSDLFEQFPGFKEIRLIPPR----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFA  219 (221)
T ss_pred             hhHHHHHHHHhhCcccceeEeccCC----CceeEEecchhhhhHHHhhhhccceeccCceEEeccc
Confidence            9999999999999999999998864    458999999999999999999998876 777776554

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

Probab=99.69  E-value=3.4e-16  Score=122.06  Aligned_cols=83  Identities=33%  Similarity=0.550  Sum_probs=77.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||..+++++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|+.|++.|++..+.|+.|.|.++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            345789999999999999999999999999999999987 7889999999999999999999999999999999999998


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .++.
T Consensus       112 ~~~~  115 (144)
T PLN03134        112 NDRP  115 (144)
T ss_pred             CcCC
Confidence            7654

>KOG0105|consensus

Probab=99.68  E-value=1.1e-15  Score=118.20  Aligned_cols=147  Identities=16%  Similarity=0.173  Sum_probs=125.2

Q ss_pred             ccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeee
Q psy12549         16 IPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPI   94 (336)
Q Consensus        16 ~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i   94 (336)
                      +.+..|||+|||.++-|.++.++| .++.+..+.+...+      ...+||||+|+++  .+|+.|+...+|..+.|+.+
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~------g~ppfafVeFEd~--RDAeDAiygRdGYdydg~rL   75 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP------GPPPFAFVEFEDP--RDAEDAIYGRDGYDYDGCRL   75 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC------CCCCeeEEEecCc--cchhhhhhcccccccCcceE
Confidence            456789999999999999999999 88888888776544      2568999999999  99999999999999999999


Q ss_pred             EEEeccCCCC------------------------cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCc
Q psy12549         95 RIMWSQRDPS------------------------LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS  150 (336)
Q Consensus        95 ~v~~~~~~~~------------------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~  150 (336)
                      +|.++.....                        +..-....|.|.+||++.+..||+.+..+.|.|-...+.+|     
T Consensus        76 RVEfprggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-----  150 (241)
T KOG0105|consen   76 RVEFPRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-----  150 (241)
T ss_pred             EEEeccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-----
Confidence            9998654311                        11122347999999999999999999999999998888876     


Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCcee
Q psy12549        151 KGYGFVHFETEEAANKSIEKVNGMLL  176 (336)
Q Consensus       151 ~g~afV~F~~~~~a~~a~~~l~~~~~  176 (336)
                       |++.|+|...++-.-|+..|+...+
T Consensus       151 -g~GvV~~~r~eDMkYAvr~ld~~~~  175 (241)
T KOG0105|consen  151 -GVGVVEYLRKEDMKYAVRKLDDQKF  175 (241)
T ss_pred             -cceeeeeeehhhHHHHHHhhccccc
Confidence             4889999999999999999887655

>KOG1456|consensus

Probab=99.68  E-value=4.1e-14  Score=120.83  Aligned_cols=252  Identities=13%  Similarity=0.130  Sum_probs=191.0

Q ss_pred             cceeccCCCCccccCceeee--ecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHH
Q psy12549          4 AQTVQLSEEGIIIPKHNVAT--RELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERA   80 (336)
Q Consensus         4 ~~~~~~~~~~~~~p~~~v~v--~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A   80 (336)
                      |+-++-+-...-.|+.-|.+  -|--+.+|-+.|.+.. ..+.+..+.+.+..+        -.|.|+|.+.  +.|++|
T Consensus       106 sq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkng--------VQAmVEFdsv--~~AqrA  175 (494)
T KOG1456|consen  106 SQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNG--------VQAMVEFDSV--EVAQRA  175 (494)
T ss_pred             hhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccc--------eeeEEeechh--HHHHHH
Confidence            55555555555566666544  5666789999999988 888888877776543        3499999999  999999


Q ss_pred             HhhcCccccCC--eeeEEEeccCCCC------------------------------------------------------
Q psy12549         81 LDTMNFDALKG--RPIRIMWSQRDPS------------------------------------------------------  104 (336)
Q Consensus        81 ~~~~~~~~~~g--~~i~v~~~~~~~~------------------------------------------------------  104 (336)
                      ...|||..+..  +.++|.++.+...                                                      
T Consensus       176 k~alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg  255 (494)
T KOG1456|consen  176 KAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSG  255 (494)
T ss_pred             HhhcccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCccc
Confidence            99999987753  5677766555211                                                      


Q ss_pred             -----------------c---------CCCCCceEEEcCCCCC-CCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEE
Q psy12549        105 -----------------L---------RKSGVGNVFIKNLDKS-IDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVH  157 (336)
Q Consensus       105 -----------------~---------~~~~~~~l~v~nlp~~-~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~  157 (336)
                                       .         .....+.++|.+|... +..+.|.++|..||+|..+++++.+.|    .|.|+
T Consensus       256 ~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~g----tamVe  331 (494)
T KOG1456|consen  256 DRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPG----TAMVE  331 (494)
T ss_pred             ccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccc----eeEEE
Confidence                             0         0012457899999874 688899999999999999999998654    89999


Q ss_pred             eCCHHHHHHHHHHhCCceeCCeEEEEeeccCchhh-----------------------------hHhhhccccccceEEE
Q psy12549        158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER-----------------------------EKELGEKAKLFTNVYI  208 (336)
Q Consensus       158 F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~-----------------------------~~~~~~~~~~~~~l~V  208 (336)
                      +.+..+.++|+..||+..+-|.+|.+..++..--.                             .........+++.|+.
T Consensus       332 mgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHf  411 (494)
T KOG1456|consen  332 MGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHF  411 (494)
T ss_pred             cCcHHHHHHHHHHhccCccccceEEEeeccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEE
Confidence            99999999999999999999999988665522100                             0111112345578999


Q ss_pred             cCCCCCCcHHHHHHhhccCCc-eeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecC
Q psy12549        209 KNFGEDFNDEKLKEMFEPYGT-ITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG  270 (336)
Q Consensus       209 ~nlp~~~t~~~l~~~f~~~g~-i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g  270 (336)
                      -|.|..+||+.|.++|...+. -.++++.. .+.+ ...+.++|++.++|..|+..+|...+.+
T Consensus       412 fNaP~~vtEe~l~~i~nek~v~~~svkvFp~kser-SssGllEfe~~s~Aveal~~~NH~pi~~  474 (494)
T KOG1456|consen  412 FNAPLGVTEEQLIGICNEKDVPPTSVKVFPLKSER-SSSGLLEFENKSDAVEALMKLNHYPIEG  474 (494)
T ss_pred             ecCCCccCHHHHHHHhhhcCCCcceEEeecccccc-cccceeeeehHHHHHHHHHHhccccccC
Confidence            999999999999999986553 45666766 3333 4458999999999999999999999876

>KOG4211|consensus

Probab=99.68  E-value=1.2e-15  Score=134.90  Aligned_cols=166  Identities=20%  Similarity=0.253  Sum_probs=130.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      ..-|.+++||.++|++||.++|+..+ |+.+.+.+. +|+..|-|||+|.+++++.+|++ .+...+..+.|.|-.+...
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~-~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR-NGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc-CCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEccCCc
Confidence            35688999999999999999999886 676555543 67888999999999999999999 5888999999999666444


Q ss_pred             hhhhHh--hh-ccccccceEEEcCCCCCCcHHHHHHhhccCCceeE-EEEeC-CCCccceEEEEEeCCHHHHHHHHHHhC
Q psy12549        190 KEREKE--LG-EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS-YRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWN  264 (336)
Q Consensus       190 ~~~~~~--~~-~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~-~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~  264 (336)
                      ......  .+ ........|.+++||+.++++||.++|+..-.+.. +-++. ..++++|.|||+|++.+.|++|+.. |
T Consensus        87 e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-h  165 (510)
T KOG4211|consen   87 EADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-H  165 (510)
T ss_pred             cccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-H
Confidence            322111  11 11123467999999999999999999998765555 22222 6777899999999999999999986 7


Q ss_pred             CceecCEEEEEeecc
Q psy12549        265 GKEVDGKILYVGRAQ  279 (336)
Q Consensus       265 g~~~~g~~l~v~~~~  279 (336)
                      ...|.-|-|.|-.+.
T Consensus       166 re~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  166 RENIGHRYIEVFRSS  180 (510)
T ss_pred             HHhhccceEEeehhH
Confidence            777887888886554

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

Probab=99.66  E-value=6.6e-16  Score=120.46  Aligned_cols=83  Identities=28%  Similarity=0.574  Sum_probs=76.5

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|++||.|.++.++.  .++.+++||||+|.+.++|+.|++.|++..+.|+.|+|.++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            3447899999999999999999999999999999986  57889999999999999999999999999999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus       112 ~~~~~  116 (144)
T PLN03134        112 NDRPS  116 (144)
T ss_pred             CcCCC
Confidence            76643

>KOG4212|consensus

Probab=99.66  E-value=3.8e-15  Score=129.45  Aligned_cols=168  Identities=23%  Similarity=0.344  Sum_probs=140.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhc-cCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSA-FGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~-~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .+.+||.|||++....+|+.+|.. .|+|+.|.+..|..|+++|+|.|+|.++|.+++|++.||.+.+.|++|.|.--..
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            356999999999999999999965 6899999999999999999999999999999999999999999999999954332


Q ss_pred             chhhh---------------------------------------------------------------------------
Q psy12549        189 RKERE---------------------------------------------------------------------------  193 (336)
Q Consensus       189 ~~~~~---------------------------------------------------------------------------  193 (336)
                      .....                                                                           
T Consensus       124 ~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~F  203 (608)
T KOG4212|consen  124 EQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASF  203 (608)
T ss_pred             hhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhhh
Confidence            11000                                                                           


Q ss_pred             --HhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecC
Q psy12549        194 --KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG  270 (336)
Q Consensus       194 --~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g  270 (336)
                        ....-..+...++||.||.+.+....|++.|.-.|.++.+.+-. ..|.++|+|.++|.++-.|-.|+..+++.-+..
T Consensus       204 lr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g~~~  283 (608)
T KOG4212|consen  204 LRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQGLFD  283 (608)
T ss_pred             hhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCCCcc
Confidence              00000112236799999999999999999999999999998765 677889999999999999999999998877777


Q ss_pred             EEEEEee
Q psy12549        271 KILYVGR  277 (336)
Q Consensus       271 ~~l~v~~  277 (336)
                      ++..++.
T Consensus       284 ~~~~~Rl  290 (608)
T KOG4212|consen  284 RRMTVRL  290 (608)
T ss_pred             ccceeec
Confidence            7776665

>PF00076 RRM_1: RNA recognition motif

Probab=99.63  E-value=2.4e-15  Score=103.00  Aligned_cols=70  Identities=40%  Similarity=0.707  Sum_probs=67.3

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q psy12549        113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF  182 (336)
Q Consensus       113 l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~  182 (336)
                      |||+|||.++++++|+++|+.||.+..+.+..+..+..+++|||+|.+.++|..|++.++|..+.|+.|+
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            7999999999999999999999999999999987888999999999999999999999999999999875

(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=99.61  E-value=5.6e-15  Score=101.17  Aligned_cols=69  Identities=41%  Similarity=0.796  Sum_probs=66.4

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEE
Q psy12549        206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILY  274 (336)
Q Consensus       206 l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~  274 (336)
                      |||+|||.++++++|+++|+.||.+..+.+.. .++..+++|||+|.+.++|++|++.++|..+.|+.|+
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            79999999999999999999999999999988 7888999999999999999999999999999999986

(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 ....

>KOG0106|consensus

Probab=99.61  E-value=1.5e-15  Score=123.28  Aligned_cols=155  Identities=22%  Similarity=0.443  Sum_probs=129.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchh
Q psy12549        112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKE  191 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~  191 (336)
                      .+||++||+.+.+++|..+|..||.+..+.+..       ||+||.|.+..+|..|+..+|+..+.+-.+.+.++.....
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~-------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~   75 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMKN-------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRR   75 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceeec-------ccceeccCchhhhhcccchhcCceecceeeeeeccccccc
Confidence            589999999999999999999999999888763       5999999999999999999999999988888888774211


Q ss_pred             hh------------HhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHH
Q psy12549        192 RE------------KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKA  259 (336)
Q Consensus       192 ~~------------~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a  259 (336)
                      ..            ..........+.+.+.|++..+...+|.+.|.++|.+.....      ..+++||+|...++|.+|
T Consensus        76 ~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~------~~~~~~v~Fs~~~da~ra  149 (216)
T KOG0106|consen   76 GRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA------RRNFAFVEFSEQEDAKRA  149 (216)
T ss_pred             ccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh------hccccceeehhhhhhhhc
Confidence            11            011111233467899999999999999999999999855444      378899999999999999


Q ss_pred             HHHhCCceecCEEEEEeecc
Q psy12549        260 VQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       260 ~~~l~g~~~~g~~l~v~~~~  279 (336)
                      +..++|..+.|+.|.+....
T Consensus       150 ~~~l~~~~~~~~~l~~~~~~  169 (216)
T KOG0106|consen  150 LEKLDGKKLNGRRISVEKNS  169 (216)
T ss_pred             chhccchhhcCceeeecccC
Confidence            99999999999999995443

>KOG1548|consensus

Probab=99.58  E-value=6.6e-14  Score=118.62  Aligned_cols=165  Identities=16%  Similarity=0.192  Sum_probs=132.5

Q ss_pred             ccCceeeeecCchhhhhhhHHhhhcccCCc---------eEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCc
Q psy12549         16 IPKHNVATRELSAKVVEGVSRSLSSLIDGN---------TVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNF   86 (336)
Q Consensus        16 ~p~~~v~v~~lp~~~~e~~l~~~f~~~~~~---------~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~   86 (336)
                      .-+++|||.|||.++|-+++.++|+..++.         .+++.++..    |+-+|=|.+.|-..  ++...|++.|++
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~----G~lKGDaLc~y~K~--ESVeLA~~ilDe  205 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ----GKLKGDALCCYIKR--ESVELAIKILDE  205 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC----CCccCceEEEeecc--cHHHHHHHHhCc
Confidence            446779999999999999999999433322         577888773    88999999999999  999999999999


Q ss_pred             cccCCeeeEEEeccCCCC------------------------------------cCCCCCceEEEcCCCC----CCC---
Q psy12549         87 DALKGRPIRIMWSQRDPS------------------------------------LRKSGVGNVFIKNLDK----SID---  123 (336)
Q Consensus        87 ~~~~g~~i~v~~~~~~~~------------------------------------~~~~~~~~l~v~nlp~----~~t---  123 (336)
                      ..+.|+.|+|..+.-...                                    ......++|.++|+=.    ..+   
T Consensus       206 ~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l  285 (382)
T KOG1548|consen  206 DELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDL  285 (382)
T ss_pred             ccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHH
Confidence            999999999986543211                                    1122356899999821    222   


Q ss_pred             ----HHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        124 ----NKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       124 ----~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                          +++|.+-.++||.|..|.+.-.   +..|.+-|.|.+.++|..|++.|+|..++||.|....+...
T Consensus       286 ~~dlkedl~eec~K~G~v~~vvv~d~---hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  286 LNDLKEDLTEECEKFGQVRKVVVYDR---HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHHHHHHHhCCcceEEEecc---CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence                3567788999999999988854   24578999999999999999999999999999998776543

>KOG4307|consensus

Probab=99.55  E-value=8.5e-14  Score=127.51  Aligned_cols=165  Identities=10%  Similarity=0.014  Sum_probs=129.7

Q ss_pred             cCceeeeecCchhhhhhhHHhhhcccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEE
Q psy12549         17 PKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRI   96 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~l~~~f~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v   96 (336)
                      -+--+.+.+.+.+..+.|+|+||.-..+..+.+..+..   .+...|-++|+|...  ..+++|+. .|...+-.|.+.+
T Consensus       310 d~~y~~~~gm~fn~~~nd~rkfF~g~~~~~~~l~~~~v---~~~~tG~~~v~f~~~--~~~q~A~~-rn~~~~~~R~~q~  383 (944)
T KOG4307|consen  310 DKYYNNYKGMEFNNDFNDGRKFFPGRNAQSTDLSENRV---APPQTGRKTVMFTPQ--APFQNAFT-RNPSDDVNRPFQT  383 (944)
T ss_pred             hhheeeecccccccccchhhhhcCcccccccchhhhhc---CCCcCCceEEEecCc--chHHHHHh-cCchhhhhcceee
Confidence            33446679999999999999999777777777666552   233468899999999  99999998 7888777888877


Q ss_pred             EeccCCCC-------------------------------------cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeE
Q psy12549         97 MWSQRDPS-------------------------------------LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILS  139 (336)
Q Consensus        97 ~~~~~~~~-------------------------------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~  139 (336)
                      .++.....                                     ........|||.+||..+++.++.++|...-.|+.
T Consensus       384 ~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved  463 (944)
T KOG4307|consen  384 GPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVED  463 (944)
T ss_pred             cCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhh
Confidence            65332110                                     11122458999999999999999999998887777


Q ss_pred             -EEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        140 -CKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       140 -~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                       +.+.+.+++...+.|||.|..++++..|...-+.++++.+.|.|....
T Consensus       464 ~I~lt~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~  512 (944)
T KOG4307|consen  464 FIELTRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIA  512 (944)
T ss_pred             eeEeccCCcccccchhhheeccccccchhhhcccccccCceEEEeechh
Confidence             777777788889999999999999999988667778888888886544

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.55  E-value=4.7e-14  Score=96.59  Aligned_cols=70  Identities=30%  Similarity=0.623  Sum_probs=64.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q psy12549        113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF  182 (336)
Q Consensus       113 l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~  182 (336)
                      |+|+|||+++++++|+++|+.+|.|..+.+..++.+.++++|||+|.++++|..|+..+++..++|+.|.
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            7999999999999999999999999999999998788999999999999999999999999999999874

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 ....

>KOG0122|consensus

Probab=99.54  E-value=2.6e-14  Score=115.56  Aligned_cols=81  Identities=33%  Similarity=0.559  Sum_probs=77.0

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|.|.||+.++++++|.++|.+||.|.++.+.+  .+|.++|||||+|.+.++|.+||+.|||.-++.-.|+|+|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            3457899999999999999999999999999999887  89999999999999999999999999999999999999999


Q ss_pred             ccc
Q psy12549        279 QKK  281 (336)
Q Consensus       279 ~~~  281 (336)
                      +|+
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            886

>KOG0122|consensus

Probab=99.54  E-value=3.7e-14  Score=114.66  Aligned_cols=82  Identities=29%  Similarity=0.490  Sum_probs=78.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      .+.++|.|.||+.++++.+|.++|.+||.|.++.+.+++ +|.++|||||.|.+.++|++|++.|||.-+++--|.|.|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            356789999999999999999999999999999999998 9999999999999999999999999999999999999999


Q ss_pred             cCc
Q psy12549        187 IPR  189 (336)
Q Consensus       187 ~~~  189 (336)
                      .|.
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            875

>KOG1457|consensus

Probab=99.54  E-value=6.7e-14  Score=111.56  Aligned_cols=151  Identities=17%  Similarity=0.213  Sum_probs=115.4

Q ss_pred             cCceeeeecCchhhhhhhHHhhh-cccCCc--eEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccC---
Q psy12549         17 PKHNVATRELSAKVVEGVSRSLS-SLIDGN--TVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALK---   90 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~--~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~---   90 (336)
                      .-|+|||.+||.++.-.||..+| .+.+-+  -+++....+    ...+.+||+.|.+.  +.|+.|+..|||..|.   
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~----~~~~pvaFatF~s~--q~A~aamnaLNGvrFDpE~  106 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGD----QVCKPVAFATFTSH--QFALAAMNALNGVRFDPET  106 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCC----ccccceEEEEecch--HHHHHHHHHhcCeeecccc
Confidence            46899999999999999999999 333333  333332221    22458999999999  9999999999999884   


Q ss_pred             CeeeEEEeccCCCC------------------------------------------------------------------
Q psy12549         91 GRPIRIMWSQRDPS------------------------------------------------------------------  104 (336)
Q Consensus        91 g~~i~v~~~~~~~~------------------------------------------------------------------  104 (336)
                      +..++|..+..+..                                                                  
T Consensus       107 ~stLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~  186 (284)
T KOG1457|consen  107 GSTLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAP  186 (284)
T ss_pred             CceeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhh
Confidence            68888887665432                                                                  


Q ss_pred             -------------c-----CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHH
Q psy12549        105 -------------L-----RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANK  166 (336)
Q Consensus       105 -------------~-----~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~  166 (336)
                                   .     ....-.+|||.||..+++|++|+.+|+.|.....+++.. +.|  ...||+.|++.+.|-.
T Consensus       187 ~~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~-~~g--~~vaf~~~~~~~~at~  263 (284)
T KOG1457|consen  187 DSKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA-RGG--MPVAFADFEEIEQATD  263 (284)
T ss_pred             hhcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec-CCC--cceEeecHHHHHHHHH
Confidence                         0     000012899999999999999999999997766555543 233  4589999999999999


Q ss_pred             HHHHhCCcee
Q psy12549        167 SIEKVNGMLL  176 (336)
Q Consensus       167 a~~~l~~~~~  176 (336)
                      |+..|.|..+
T Consensus       264 am~~lqg~~~  273 (284)
T KOG1457|consen  264 AMNHLQGNLL  273 (284)
T ss_pred             HHHHhhccee
Confidence            9999988765

>KOG0125|consensus

Probab=99.53  E-value=1.4e-14  Score=121.78  Aligned_cols=79  Identities=30%  Similarity=0.569  Sum_probs=74.8

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      +.|+|.|+|+...+-||+.+|.+||.|.+|.|+.....++||+||+|++.+||++|-++|||..+.||+|.|..+..+.
T Consensus        97 kRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATarV  175 (376)
T KOG0125|consen   97 KRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATARV  175 (376)
T ss_pred             ceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchhh
Confidence            7899999999999999999999999999999998666779999999999999999999999999999999999987664

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.52  E-value=1.4e-13  Score=94.14  Aligned_cols=69  Identities=41%  Similarity=0.770  Sum_probs=62.9

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEE
Q psy12549        206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILY  274 (336)
Q Consensus       206 l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~  274 (336)
                      |+|+|||..+++++|+++|+.||.|..+.+.. ..+.++++|||+|.++++|.+|+..++|..++|+.|+
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            78999999999999999999999999999987 4578899999999999999999999999999999885

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0125|consensus

Probab=99.50  E-value=7.6e-14  Score=117.41  Aligned_cols=99  Identities=23%  Similarity=0.450  Sum_probs=83.7

Q ss_pred             ccCCeeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHH
Q psy12549         88 ALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS  167 (336)
Q Consensus        88 ~~~g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a  167 (336)
                      ...|.++....+...  ......++|+|.|||....+-||+.+|++||.|.+|.|+.+..| ||||+||+|++++||++|
T Consensus        76 ~t~g~~~~~~~st~s--~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRA  152 (376)
T KOG0125|consen   76 PTDGQPIQTQPSTNS--SSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRA  152 (376)
T ss_pred             CCCCCccccCCCCcC--CCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHH
Confidence            334444444433222  23345678999999999999999999999999999999999877 899999999999999999


Q ss_pred             HHHhCCceeCCeEEEEeeccCc
Q psy12549        168 IEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       168 ~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      .+.|||..+.||+|.|..+..+
T Consensus       153 Ra~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  153 RAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             HHHhhcceeeceEEEEeccchh
Confidence            9999999999999999988766

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

Probab=99.47  E-value=6.3e-13  Score=116.47  Aligned_cols=128  Identities=28%  Similarity=0.490  Sum_probs=108.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..+|||+|||..+++++|.++|..||.+..+.+..++ +|.++|+|||.|.++++|..|+..+++..+.|+.+.|.+..+
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            5899999999999999999999999999999999996 899999999999999999999999999999999999999542


Q ss_pred             ----chhhhH------------hhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC
Q psy12549        189 ----RKEREK------------ELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN  237 (336)
Q Consensus       189 ----~~~~~~------------~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~  237 (336)
                          ......            ...........+++.+++..++..++...|..+|.+....+..
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  259 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPP  259 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccC
Confidence                222210            0011122336789999999999999999999999996666655

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.45  E-value=3.8e-13  Score=112.26  Aligned_cols=76  Identities=18%  Similarity=0.324  Sum_probs=69.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ++|||+|||+.+++++|+++|+.||.|.++.++... .++|||||+|.++++|+.|+. |+|..+.|+.|+|.++...
T Consensus         5 rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~-~~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          5 RTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN-ERSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC-CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCC
Confidence            789999999999999999999999999999998743 357999999999999999996 9999999999999998643

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.45  E-value=6.5e-13  Score=110.91  Aligned_cols=78  Identities=15%  Similarity=0.251  Sum_probs=71.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      .++|||+|||+.+++++|+++|+.||.|.++.++.++.  ++|||||+|.++++|..|+. |+|..+.|+.|.|.++...
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccCC
Confidence            47899999999999999999999999999999998753  46899999999999999996 9999999999999997654


Q ss_pred             h
Q psy12549        190 K  190 (336)
Q Consensus       190 ~  190 (336)
                      .
T Consensus        81 ~   81 (260)
T PLN03120         81 Q   81 (260)
T ss_pred             C
Confidence            3

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

Probab=99.45  E-value=5.2e-13  Score=117.01  Aligned_cols=133  Identities=35%  Similarity=0.536  Sum_probs=105.8

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ..+|||+|||.++++++|+++|..||.+..+.+..  .++.++|+|||+|.+.++|..|+..++|..|.|+.|.|.++..
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            48999999999999999999999999999998887  4799999999999999999999999999999999999999653


Q ss_pred             ----chhhHHH--HHHHHHHHHHHhhcCCCCceEEEecCCCCCCHHHHHHhcCCCCCeeec
Q psy12549        281 ----KAERTQE--LKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSA  335 (336)
Q Consensus       281 ----~~~~~~~--~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~V~~v  335 (336)
                          +......  .................+..+++.|++...+..++...|..+|.+...
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  255 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRA  255 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceee
Confidence                2111110  000000011112223456789999999999999999999999988543

>KOG0106|consensus

Probab=99.43  E-value=2.1e-13  Score=110.82  Aligned_cols=147  Identities=19%  Similarity=0.279  Sum_probs=123.7

Q ss_pred             eeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEEe
Q psy12549         20 NVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMW   98 (336)
Q Consensus        20 ~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~~   98 (336)
                      .|||++||+.+.+.+|..|| .++.+..+.+..           ||+||+|.+.  .+|..|+..+++..+.|-.+.+.|
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~-----------gf~fv~fed~--rda~Dav~~l~~~~l~~e~~vve~   69 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMKN-----------GFGFVEFEDP--RDADDAVHDLDGKELCGERLVVEH   69 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceeec-----------ccceeccCch--hhhhcccchhcCceecceeeeeec
Confidence            58999999999999999999 777777766654           7789999999  999999999999999987788888


Q ss_pred             ccCC------CC------------cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCC
Q psy12549         99 SQRD------PS------------LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFET  160 (336)
Q Consensus        99 ~~~~------~~------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~  160 (336)
                      +...      +.            ......+.+.+.+++..+.+.+|...|+.+|.+....+.       .+++||+|.+
T Consensus        70 ~r~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~-------~~~~~v~Fs~  142 (216)
T KOG0106|consen   70 ARGKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDAR-------RNFAFVEFSE  142 (216)
T ss_pred             ccccccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhhh-------ccccceeehh
Confidence            6631      11            112234689999999999999999999999998655442       4589999999


Q ss_pred             HHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        161 EEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       161 ~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      .++|.+|+..|++..+.++.|.+...
T Consensus       143 ~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  143 QEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             hhhhhhcchhccchhhcCceeeeccc
Confidence            99999999999999999999999443

>KOG0107|consensus

Probab=99.43  E-value=6.1e-13  Score=102.35  Aligned_cols=78  Identities=24%  Similarity=0.417  Sum_probs=71.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..++|||+||+..+++.||...|..||++..|+|-..+    .|||||+|+++.||..|+..|+|..+.|..|.|+.+.-
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            45889999999999999999999999999999999875    45999999999999999999999999999999988765


Q ss_pred             ch
Q psy12549        189 RK  190 (336)
Q Consensus       189 ~~  190 (336)
                      ..
T Consensus        85 ~~   86 (195)
T KOG0107|consen   85 RP   86 (195)
T ss_pred             Cc
Confidence            44

>KOG0114|consensus

Probab=99.43  E-value=2e-12  Score=90.55  Aligned_cols=78  Identities=33%  Similarity=0.471  Sum_probs=70.8

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      +-|||+|||+++|.++..++|.+||+|..+++-...+ .+|.|||.|++..+|.+|+++|+|..+.++.|.|-+..+..
T Consensus        19 riLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~-TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~~   96 (124)
T KOG0114|consen   19 RILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE-TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPED   96 (124)
T ss_pred             eeEEEecCCccccHHHHHHHhhcccceEEEEecCccC-cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHHH
Confidence            6699999999999999999999999999998865333 38899999999999999999999999999999999987654

>KOG0121|consensus

Probab=99.42  E-value=4.8e-13  Score=97.41  Aligned_cols=79  Identities=19%  Similarity=0.348  Sum_probs=73.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      +++|||+||+..++|++|.++|+..|+|..|.+-.++ .....|||||+|-+.++|..|++.+++..++.++|.+.|-..
T Consensus        36 S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~G  115 (153)
T KOG0121|consen   36 SCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDAG  115 (153)
T ss_pred             cceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecccc
Confidence            5889999999999999999999999999999888887 566789999999999999999999999999999999987543

>smart00362 RRM_2 RNA recognition motif

Probab=99.42  E-value=2.2e-12  Score=88.20  Aligned_cols=71  Identities=41%  Similarity=0.705  Sum_probs=66.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      +|+|+|||..++.++|+++|+.||.+..+.+..++ +.++++|||+|.+.++|..|+..+++..+.|+.+.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEee
Confidence            48999999999999999999999999999999877 678899999999999999999999999999999876

>KOG0114|consensus

Probab=99.41  E-value=2.3e-12  Score=90.24  Aligned_cols=89  Identities=22%  Similarity=0.416  Sum_probs=77.5

Q ss_pred             CCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q psy12549        103 PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF  182 (336)
Q Consensus       103 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~  182 (336)
                      .+..+...+-|||+|||.++|.++..++|.+||+|.++++-..+  ..+|-|||.|++..+|.+|+..|+|..+.++.+.
T Consensus        11 ~rlppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k--~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~   88 (124)
T KOG0114|consen   11 IRLPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK--ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLV   88 (124)
T ss_pred             CCCChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc--CcCceEEEEehHhhhHHHHHHHhcccccCCceEE
Confidence            33444556789999999999999999999999999999887654  3578999999999999999999999999999999


Q ss_pred             EeeccCchhhh
Q psy12549        183 VGKFIPRKERE  193 (336)
Q Consensus       183 v~~~~~~~~~~  193 (336)
                      |.++.+.....
T Consensus        89 vlyyq~~~~~~   99 (124)
T KOG0114|consen   89 VLYYQPEDAFK   99 (124)
T ss_pred             EEecCHHHHHH
Confidence            99988765543

>KOG0149|consensus

Probab=99.41  E-value=6e-13  Score=107.35  Aligned_cols=77  Identities=26%  Similarity=0.463  Sum_probs=69.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ++|||+||+..+..++|++.|++||+|.+..++.|+ +|+||||+||+|.+.++|.+|++. -+-.|+||+.-|+.+.-
T Consensus        13 TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   13 TKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhhh
Confidence            689999999999999999999999999999999998 899999999999999999999994 34568899888877654

>smart00362 RRM_2 RNA recognition motif

Probab=99.40  E-value=2.6e-12  Score=87.86  Aligned_cols=72  Identities=42%  Similarity=0.743  Sum_probs=66.9

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEe
Q psy12549        205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG  276 (336)
Q Consensus       205 ~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~  276 (336)
                      +|+|.|||..++.++|+++|+.||++..+.+....+.++++|||+|.+.++|.+|+..++|..+.|+.+.|+
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            489999999999999999999999999999887547788999999999999999999999999999999873

>PLN03213 repressor of silencing 3; Provisional

Probab=99.40  E-value=9.1e-13  Score=116.59  Aligned_cols=77  Identities=21%  Similarity=0.465  Sum_probs=72.4

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCH--HHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESP--EFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~--~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      .+|||+||++.+++++|+..|+.||.|.++.|++.+|  +|||||+|.+.  .++.+|+..|||..|.|+.|+|..|++.
T Consensus        11 MRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP~   88 (759)
T PLN03213         11 VRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKEH   88 (759)
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccHH
Confidence            6799999999999999999999999999999998777  99999999987  6899999999999999999999999776


Q ss_pred             h
Q psy12549        282 A  282 (336)
Q Consensus       282 ~  282 (336)
                      -
T Consensus        89 Y   89 (759)
T PLN03213         89 Y   89 (759)
T ss_pred             H
Confidence            4

>PLN03213 repressor of silencing 3; Provisional

Probab=99.39  E-value=1.5e-12  Score=115.28  Aligned_cols=80  Identities=15%  Similarity=0.326  Sum_probs=72.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCH--HHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETE--EAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~--~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...+|||+||++.+++++|..+|..||.|..|.|++. +|  +|||||+|.+.  .++.+|+..|||..|.|+.|+|..+
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA   85 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA   85 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence            3468999999999999999999999999999999943 56  89999999988  7899999999999999999999999


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      .+.-.
T Consensus        86 KP~YL   90 (759)
T PLN03213         86 KEHYL   90 (759)
T ss_pred             cHHHH
Confidence            87643

>KOG0121|consensus

Probab=99.38  E-value=1.1e-12  Score=95.61  Aligned_cols=83  Identities=24%  Similarity=0.313  Sum_probs=73.2

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ..+++|||+||+..++|++|.++|+.+|+|..|.+--  .+..+=|||||+|-+.++|..|+..++|..++.++|++.|-
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            3458999999999999999999999999999986643  45556799999999999999999999999999999999997


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      ..-.+
T Consensus       114 ~GF~e  118 (153)
T KOG0121|consen  114 AGFVE  118 (153)
T ss_pred             ccchh
Confidence            65543

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.38  E-value=3.5e-12  Score=104.81  Aligned_cols=78  Identities=19%  Similarity=0.289  Sum_probs=71.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ...+|+|+||++.+|+++|+++|+.||.|..|.++++.  .++++|||+|.++++|..|+. |+|..|.++.|.|..+..
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~--et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG--EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC--CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCcc
Confidence            34789999999999999999999999999999999883  456899999999999999997 999999999999988664


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      .
T Consensus        81 y   81 (243)
T PLN03121         81 Y   81 (243)
T ss_pred             c
Confidence            4

>KOG0107|consensus

Probab=99.38  E-value=1.2e-12  Score=100.74  Aligned_cols=78  Identities=32%  Similarity=0.553  Sum_probs=71.1

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      .++|||+||+..+++.||...|..||++..+-|-.   .+.|||||+|+++.+|+.|+..|+|..|.|..|+|+++....
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvAr---nPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~~   86 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVAR---NPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGRP   86 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEee---cCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCCc
Confidence            47899999999999999999999999998887754   358999999999999999999999999999999999987664


Q ss_pred             h
Q psy12549        283 E  283 (336)
Q Consensus       283 ~  283 (336)
                      .
T Consensus        87 r   87 (195)
T KOG0107|consen   87 R   87 (195)
T ss_pred             c
Confidence            3

>KOG4207|consensus

Probab=99.37  E-value=7.7e-13  Score=104.36  Aligned_cols=80  Identities=29%  Similarity=0.468  Sum_probs=74.7

Q ss_pred             ccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEee
Q psy12549        200 AKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR  277 (336)
Q Consensus       200 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~  277 (336)
                      .....+|.|.||-+-++.++|+.+|++||.|-+|.|..  .++.++|||||.|....+|+.|+++|+|..++|+.|+|.+
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            34457899999999999999999999999999999988  7888999999999999999999999999999999999988


Q ss_pred             cc
Q psy12549        278 AQ  279 (336)
Q Consensus       278 ~~  279 (336)
                      |.
T Consensus        90 ar   91 (256)
T KOG4207|consen   90 AR   91 (256)
T ss_pred             hh
Confidence            74

>KOG4307|consensus

Probab=99.37  E-value=6e-12  Score=115.59  Aligned_cols=172  Identities=12%  Similarity=0.008  Sum_probs=123.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .+.+-+.+++.+.++.|++++|... .+....+..+. .+...|.++|.|....++++|+.. |...+-+|.+.+.....
T Consensus       311 ~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~r-n~~~~~~R~~q~~P~g~  388 (944)
T KOG4307|consen  311 KYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTR-NPSDDVNRPFQTGPPGN  388 (944)
T ss_pred             hheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhc-CchhhhhcceeecCCCc
Confidence            3456678999999999999998753 24555555554 233367899999999999999884 66666666666643321


Q ss_pred             chhh--------hH------h-------------hhcc----ccccceEEEcCCCCCCcHHHHHHhhccCCceeE-EEEe
Q psy12549        189 RKER--------EK------E-------------LGEK----AKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS-YRVM  236 (336)
Q Consensus       189 ~~~~--------~~------~-------------~~~~----~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~-~~i~  236 (336)
                      ..-.        ..      .             .+..    ......|||..||..+++.++.++|.....|++ |.+.
T Consensus       389 ~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt  468 (944)
T KOG4307|consen  389 LGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELT  468 (944)
T ss_pred             cccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEec
Confidence            1100        00      0             0000    111267999999999999999999998777877 5555


Q ss_pred             C-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchh
Q psy12549        237 N-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAE  283 (336)
Q Consensus       237 ~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~  283 (336)
                      + .++..++.|||.|.+++++..|...-+...++.+.|+|.-...+..
T Consensus       469 ~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~~m  516 (944)
T KOG4307|consen  469 RLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADYAM  516 (944)
T ss_pred             cCCcccccchhhheeccccccchhhhcccccccCceEEEeechhhHHH
Confidence            5 7888899999999999999999877666777789999977655543

>KOG0113|consensus

Probab=99.36  E-value=4.6e-12  Score=105.49  Aligned_cols=85  Identities=21%  Similarity=0.490  Sum_probs=77.8

Q ss_pred             CCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q psy12549        102 DPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKI  180 (336)
Q Consensus       102 ~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~  180 (336)
                      ++.......+||||.-|+.+++|+.|+..|+.||+|..+.|+.+. +|+++|||||+|.++.+...|.+..+|..|+|+.
T Consensus        93 dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrr  172 (335)
T KOG0113|consen   93 DPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRR  172 (335)
T ss_pred             CCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcE
Confidence            334444566899999999999999999999999999999999997 9999999999999999999999999999999999


Q ss_pred             EEEeec
Q psy12549        181 VFVGKF  186 (336)
Q Consensus       181 i~v~~~  186 (336)
                      |.|..-
T Consensus       173 i~VDvE  178 (335)
T KOG0113|consen  173 ILVDVE  178 (335)
T ss_pred             EEEEec
Confidence            998653

>KOG0149|consensus

Probab=99.36  E-value=1.2e-12  Score=105.72  Aligned_cols=77  Identities=29%  Similarity=0.568  Sum_probs=69.8

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+||++.++.++|++.|++||+|.+..++.  .+|+++||+||+|.+.++|.+|++. -+-.|+||+..|..|.-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhhh
Confidence            37899999999999999999999999999988876  8899999999999999999999986 56678999999887643

>KOG0126|consensus

Probab=99.36  E-value=1.1e-13  Score=106.82  Aligned_cols=80  Identities=20%  Similarity=0.468  Sum_probs=75.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      +++-|||+|||...||.||.-+|++||.+..+.+++|+ +|.|+||||+.|++..+...|+..|||..+.||.|+|....
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            34779999999999999999999999999999999998 99999999999999999999999999999999999996644


Q ss_pred             C
Q psy12549        188 P  188 (336)
Q Consensus       188 ~  188 (336)
                      .
T Consensus       114 ~  114 (219)
T KOG0126|consen  114 N  114 (219)
T ss_pred             c
Confidence            3

>KOG1365|consensus

Probab=99.36  E-value=6.6e-13  Score=113.90  Aligned_cols=162  Identities=17%  Similarity=0.134  Sum_probs=124.9

Q ss_pred             eeeeecCchhhhhhhHHhhhc-----ccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeee
Q psy12549         20 NVATRELSAKVVEGVSRSLSS-----LIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPI   94 (336)
Q Consensus        20 ~v~v~~lp~~~~e~~l~~~f~-----~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i   94 (336)
                      -|.+++||.++++.++..||.     .++.+.|.++...+    |+..|-|||.|..+  ++|+.|+. .+...++.|-|
T Consensus       163 ivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpd----grpTGdAFvlfa~e--e~aq~aL~-khrq~iGqRYI  235 (508)
T KOG1365|consen  163 IVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPD----GRPTGDAFVLFACE--EDAQFALR-KHRQNIGQRYI  235 (508)
T ss_pred             EEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCC----CCcccceEEEecCH--HHHHHHHH-HHHHHHhHHHH
Confidence            367799999999999999995     44666888887664    56678899999999  99999998 45444443333


Q ss_pred             EEEeccC-----------------------------CCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCC-eeE--EEE
Q psy12549         95 RIMWSQR-----------------------------DPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGS-ILS--CKV  142 (336)
Q Consensus        95 ~v~~~~~-----------------------------~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~-v~~--~~~  142 (336)
                      .+..+..                             ...........|.++|||+..+.++|..+|..|.. |..  |.+
T Consensus       236 ElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHm  315 (508)
T KOG1365|consen  236 ELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHM  315 (508)
T ss_pred             HHHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEE
Confidence            3321110                             00011122457999999999999999999999874 333  788


Q ss_pred             eeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        143 AQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       143 ~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      +.+..|+..|-|||+|.+.++|..|....+++..+.+.|.|-.+..
T Consensus       316 v~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~  361 (508)
T KOG1365|consen  316 VLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSV  361 (508)
T ss_pred             EEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccH
Confidence            8888999999999999999999999999999999999998865543

>KOG0126|consensus

Probab=99.35  E-value=2.8e-13  Score=104.68  Aligned_cols=78  Identities=26%  Similarity=0.510  Sum_probs=73.8

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      .-|||+|||++.|+.||.-+|++||+|.+|.+++  .+|+++||||+.|++..+...|+..|||..+.||.|+|......
T Consensus        36 A~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~Y  115 (219)
T KOG0126|consen   36 AYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSNY  115 (219)
T ss_pred             eEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecccc
Confidence            6799999999999999999999999999999998  89999999999999999999999999999999999999886543

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.35  E-value=5.6e-12  Score=103.59  Aligned_cols=76  Identities=14%  Similarity=0.276  Sum_probs=69.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      .+|+|+||++.+|+++|+++|+.||+|.+|++++. +...++|||+|.++++|+.|+. |+|..|.|++|.|..+...
T Consensus         6 ~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D-~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~~y   81 (243)
T PLN03121          6 YTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS-GEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWGQY   81 (243)
T ss_pred             eEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC-CCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCccc
Confidence            68999999999999999999999999999999875 4446899999999999999995 8999999999999887643

>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=99.34  E-value=1.5e-11  Score=84.44  Aligned_cols=74  Identities=34%  Similarity=0.608  Sum_probs=68.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      +|+|+|||..+++++|+++|+.+|.+..+.+..++.+..+++|||+|.+.++|..|+..+++..+.|+.+.+.+
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            48999999999999999999999999999999987667789999999999999999999999999999998753

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).

>KOG0113|consensus

Probab=99.34  E-value=4.7e-12  Score=105.43  Aligned_cols=81  Identities=26%  Similarity=0.555  Sum_probs=76.0

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      .+.+||||.-|+++++|.+|+..|+.||+|..+.++.  .+|+++|||||+|+++-+...|.+..+|..|+|+.|.|.+-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            4558999999999999999999999999999999998  79999999999999999999999999999999999999886


Q ss_pred             ccc
Q psy12549        279 QKK  281 (336)
Q Consensus       279 ~~~  281 (336)
                      ..+
T Consensus       179 RgR  181 (335)
T KOG0113|consen  179 RGR  181 (335)
T ss_pred             ccc
Confidence            544

>PF13893 RRM_5: RNA recognition motif

Probab=99.34  E-value=9.8e-12  Score=80.84  Aligned_cols=56  Identities=34%  Similarity=0.677  Sum_probs=51.0

Q ss_pred             HHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        220 LKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       220 l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      |+++|++||+|..+.+.+..   +++|||+|.+.++|..|++.|||..+.|++|+|.|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~---~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK---RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS---TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999998753   589999999999999999999999999999999986

(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 ....

>smart00360 RRM RNA recognition motif

Probab=99.33  E-value=1.1e-11  Score=84.42  Aligned_cols=69  Identities=38%  Similarity=0.674  Sum_probs=64.7

Q ss_pred             EcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        115 IKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       115 v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      |+|||..+++++|+++|+.||.+..+.+..++ ++.++|+|||+|.+.++|..|+..+++..+.|+.+.|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEe
Confidence            57999999999999999999999999999887 5788999999999999999999999999999999876

>KOG0111|consensus

Probab=99.33  E-value=1.2e-12  Score=104.26  Aligned_cols=81  Identities=27%  Similarity=0.504  Sum_probs=76.1

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ..++|||++|..++++.-|...|-+||.|..++++-  .+++.||||||+|.-.++|..|+..||+..+.||.|+|.+|.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            448999999999999999999999999999999887  788999999999999999999999999999999999999997


Q ss_pred             cch
Q psy12549        280 KKA  282 (336)
Q Consensus       280 ~~~  282 (336)
                      |..
T Consensus        89 P~k   91 (298)
T KOG0111|consen   89 PEK   91 (298)
T ss_pred             Ccc
Confidence            643

>KOG4207|consensus

Probab=99.32  E-value=3.5e-12  Score=100.68  Aligned_cols=80  Identities=19%  Similarity=0.420  Sum_probs=75.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      .+-..|.|-||..-++.++|+-+|++||.|-.|.|++|+ ++.++|||||.|....+|+.|+++|+|..++|+.|.|+.+
T Consensus        11 ~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~a   90 (256)
T KOG4207|consen   11 EGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMA   90 (256)
T ss_pred             ccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhh
Confidence            445689999999999999999999999999999999998 8889999999999999999999999999999999999776


Q ss_pred             c
Q psy12549        187 I  187 (336)
Q Consensus       187 ~  187 (336)
                      .
T Consensus        91 r   91 (256)
T KOG4207|consen   91 R   91 (256)
T ss_pred             h
Confidence            4

>KOG0120|consensus

Probab=99.31  E-value=1.8e-11  Score=111.41  Aligned_cols=165  Identities=15%  Similarity=0.206  Sum_probs=130.6

Q ss_pred             cCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeE
Q psy12549         17 PKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIR   95 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~   95 (336)
                      -...++|++||...++..++++. ++++.....++.+..   +|.++||||.+|.++  -.+..|+..+||..+.++.+.
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~---~g~skg~af~ey~dp--svtd~A~agLnGm~lgd~~lv  362 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSA---TGNSKGFAFCEYCDP--SVTDQAIAGLNGMQLGDKKLV  362 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeecccc---cccccceeeeeeeCC--cchhhhhcccchhhhcCceeE
Confidence            33459999999999999999988 777888999999884   589999999999999  999999999999999999999


Q ss_pred             EEeccCCCCcCC---C-------------------CCceEEEcCCCCCCCH-------------HHHHHHhhccCCeeEE
Q psy12549         96 IMWSQRDPSLRK---S-------------------GVGNVFIKNLDKSIDN-------------KAMYDTFSAFGSILSC  140 (336)
Q Consensus        96 v~~~~~~~~~~~---~-------------------~~~~l~v~nlp~~~t~-------------~~l~~~f~~~G~v~~~  140 (336)
                      +..+........   +                   ....|.+.|+   +|+             ++++.-+.+||.|..|
T Consensus       363 vq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~---Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v  439 (500)
T KOG0120|consen  363 VQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNV---VTPDELKDDEEYEEILEDVRTECAKFGAVRSV  439 (500)
T ss_pred             eehhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhc---CCHHHhcchHHHHHHHHHHHHHhcccCceeEE
Confidence            987544322111   0                   1112222222   222             3456667899999999


Q ss_pred             EEeeC-C---CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        141 KVAQD-E---QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       141 ~~~~~-~---~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      .++++ .   .....|..||+|.+.+++++|++.|+|..+.|+.+...+....
T Consensus       440 ~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  440 EIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDED  492 (500)
T ss_pred             ecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHH
Confidence            99998 3   2335678999999999999999999999999999999886543

>KOG0130|consensus

Probab=99.31  E-value=3.8e-12  Score=93.58  Aligned_cols=84  Identities=24%  Similarity=0.379  Sum_probs=77.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      .+..-|||.++...+++++|.+.|..||+|..+.+..|+ +|-.+|||+|+|++.++|++|+..+||..+.|..|.|.|+
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            345679999999999999999999999999999999997 8999999999999999999999999999999999999997


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      -.+.+
T Consensus       150 Fv~gp  154 (170)
T KOG0130|consen  150 FVKGP  154 (170)
T ss_pred             EecCC
Confidence            65443

>smart00360 RRM RNA recognition motif

Probab=99.31  E-value=1e-11  Score=84.52  Aligned_cols=69  Identities=48%  Similarity=0.800  Sum_probs=63.6

Q ss_pred             EcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEe
Q psy12549        208 IKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG  276 (336)
Q Consensus       208 V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~  276 (336)
                      |+|||..+++++|+++|+.||.|..+.+..  .++.++++|||+|.+.++|..|+..+++..+.|+.++|+
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            579999999999999999999999998887  357789999999999999999999999999999998873

>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=99.30  E-value=2.9e-11  Score=83.06  Aligned_cols=73  Identities=41%  Similarity=0.728  Sum_probs=67.0

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEee
Q psy12549        205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR  277 (336)
Q Consensus       205 ~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~  277 (336)
                      +|+|+|||..+++++|+++|+.+|.+..+.+.. ..+.++++|||+|.+.++|..|+..+++..+.|+.+.|.+
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            489999999999999999999999999999887 4446689999999999999999999999999999999864

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).

>KOG0111|consensus

Probab=99.26  E-value=3.9e-12  Score=101.30  Aligned_cols=84  Identities=25%  Similarity=0.449  Sum_probs=78.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||++|...+++.-|...|-+||.|..+.++.|. +++++|||||+|.-.+||..|+..||+.++.|+.|+|.++.
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            34789999999999999999999999999999999996 88999999999999999999999999999999999999998


Q ss_pred             Cchhh
Q psy12549        188 PRKER  192 (336)
Q Consensus       188 ~~~~~  192 (336)
                      |....
T Consensus        89 P~kik   93 (298)
T KOG0111|consen   89 PEKIK   93 (298)
T ss_pred             Ccccc
Confidence            86543

>KOG4660|consensus

Probab=99.22  E-value=7.4e-11  Score=106.48  Aligned_cols=143  Identities=16%  Similarity=0.091  Sum_probs=95.7

Q ss_pred             CCCccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCcccc
Q psy12549         11 EEGIIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDAL   89 (336)
Q Consensus        11 ~~~~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~   89 (336)
                      |.....+.++|+|-|||.++++++|+++| .+|++..|+..+        ..+|.+||+|.+.  .+|+.|++++++..+
T Consensus        68 p~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~--------~~~~~~~v~FyDv--R~A~~Alk~l~~~~~  137 (549)
T KOG4660|consen   68 PSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETP--------NKRGIVFVEFYDV--RDAERALKALNRREI  137 (549)
T ss_pred             CCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccc--------ccCceEEEEEeeh--HhHHHHHHHHHHHHh
Confidence            44456788999999999999999999999 677777755444        4569999999999  999999999999999


Q ss_pred             CCeeeEEEeccCCCC--------------------cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCC
Q psy12549         90 KGRPIRIMWSQRDPS--------------------LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN  149 (336)
Q Consensus        90 ~g~~i~v~~~~~~~~--------------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~  149 (336)
                      .|+.+.-........                    .......+++.- |++..+..-+...+.-+|.+.. .-    ++.
T Consensus       138 ~~~~~k~~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~P~~s~~~~~~~~~~~~~~~~-~~----~~~  211 (549)
T KOG4660|consen  138 AGKRIKRPGGARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFGM-LSPTRSSILLEHISSVDGSSPG-RE----TPL  211 (549)
T ss_pred             hhhhhcCCCcccccchhcccchhhhhccchhhcCCCCCCcCCcceee-eccchhhhhhhcchhccCcccc-cc----ccc
Confidence            998877211111000                    111111234433 8777777666666666776554 21    121


Q ss_pred             cccEEEEEeCCHHHHHHHHH
Q psy12549        150 SKGYGFVHFETEEAANKSIE  169 (336)
Q Consensus       150 ~~g~afV~F~~~~~a~~a~~  169 (336)
                      -...-|+.|.+..++..+..
T Consensus       212 ~~hq~~~~~~~~~s~a~~~~  231 (549)
T KOG4660|consen  212 LNHQRFVEFADNRSYAFSEP  231 (549)
T ss_pred             hhhhhhhhhccccchhhccc
Confidence            22245677777777655444

>PF13893 RRM_5: RNA recognition motif

Probab=99.22  E-value=9.5e-11  Score=76.16  Aligned_cols=56  Identities=34%  Similarity=0.624  Sum_probs=50.5

Q ss_pred             HHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        127 MYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       127 l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      |+++|++||+|..+.+..+.    +++|||+|.+.++|..|++.|||..+.|++|.|.++
T Consensus         1 L~~~f~~fG~V~~i~~~~~~----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999998753    479999999999999999999999999999999875

(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

Probab=99.21  E-value=2.1e-11  Score=89.65  Aligned_cols=78  Identities=26%  Similarity=0.446  Sum_probs=72.4

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      --|||.++.+.+++++|.+.|..||+|.++++.-  .+|..+|||+|+|.+..+|++|+..+||..+-|..+.|.|+-.+
T Consensus        73 wIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~  152 (170)
T KOG0130|consen   73 WIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVK  152 (170)
T ss_pred             EEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEec
Confidence            3589999999999999999999999999988765  88999999999999999999999999999999999999998544

>KOG0108|consensus

Probab=99.19  E-value=6.3e-11  Score=107.25  Aligned_cols=83  Identities=30%  Similarity=0.595  Sum_probs=77.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      +.+||+|+|+++++++|..+|+..|.|.++++..  .+|+.+||||++|.+.++|.+|++.|||..+.||+|+|.|+...
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            7899999999999999999999999999999887  89999999999999999999999999999999999999999876


Q ss_pred             hhhHH
Q psy12549        282 AERTQ  286 (336)
Q Consensus       282 ~~~~~  286 (336)
                      ..+..
T Consensus        99 ~~~~~  103 (435)
T KOG0108|consen   99 KNAER  103 (435)
T ss_pred             chhHH
Confidence            55443

>smart00361 RRM_1 RNA recognition motif

Probab=99.18  E-value=1.2e-10  Score=79.37  Aligned_cols=60  Identities=23%  Similarity=0.443  Sum_probs=52.1

Q ss_pred             HHHHHHhhc----cCCceeEEE-EeC--CC--CccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEe
Q psy12549        217 DEKLKEMFE----PYGTITSYR-VMN--ND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG  276 (336)
Q Consensus       217 ~~~l~~~f~----~~g~i~~~~-i~~--~~--~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~  276 (336)
                      +++|+++|+    .||.|.++. +..  .+  +.++|+|||+|.+.++|.+|+..|||..+.|+.|+++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            467888888    999999985 332  44  8889999999999999999999999999999999873

>KOG0108|consensus

Probab=99.18  E-value=8.7e-11  Score=106.35  Aligned_cols=82  Identities=30%  Similarity=0.547  Sum_probs=77.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      +.+||+|+|+++++++|..+|+..|.|..++++.|+ +|..+||||++|.+.++|..|++.|||..+.|++|+|.|+...
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            779999999999999999999999999999999998 8999999999999999999999999999999999999998766


Q ss_pred             hhh
Q psy12549        190 KER  192 (336)
Q Consensus       190 ~~~  192 (336)
                      ...
T Consensus        99 ~~~  101 (435)
T KOG0108|consen   99 KNA  101 (435)
T ss_pred             chh
Confidence            543

>smart00361 RRM_1 RNA recognition motif

Probab=99.18  E-value=1.8e-10  Score=78.47  Aligned_cols=60  Identities=23%  Similarity=0.437  Sum_probs=53.3

Q ss_pred             HHHHHHHhh----ccCCeeEEE-EeeCC-C--CCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        124 NKAMYDTFS----AFGSILSCK-VAQDE-Q--GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       124 ~~~l~~~f~----~~G~v~~~~-~~~~~-~--~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      +++|+++|+    .||.|..+. ++.++ +  +.++|+|||.|.+.++|.+|+..|||..+.|+.|.+
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            568888888    999999995 65554 4  889999999999999999999999999999999876

>KOG0128|consensus

Probab=99.17  E-value=2.8e-12  Score=120.63  Aligned_cols=233  Identities=15%  Similarity=0.124  Sum_probs=180.1

Q ss_pred             cCceeeeecCchhhhhhh-HHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeee
Q psy12549         17 PKHNVATRELSAKVVEGV-SRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPI   94 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~-l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i   94 (336)
                      ..+...+.++.+.....+ .+..| ..+.++.++....+..   -..-.++++.+...  ..|+.|.. ..+..+.++..
T Consensus       570 ~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k---~h~q~~~~~~~s~~--~~~esat~-pa~~~~a~~~~  643 (881)
T KOG0128|consen  570 ERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFK---AHEQPQQQKVQSKH--GSAESATV-PAGGALANRSA  643 (881)
T ss_pred             hhhhhcccCCCcchhhHHhhHHHhhcccccccccCcccccc---ccccchhhhhhccc--cchhhccc-ccccccCCccc
Confidence            344566777777776664 55566 6667777777663211   11222789999999  99988887 77778888887


Q ss_pred             EEEeccCCCCcCCC--------CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHH
Q psy12549         95 RIMWSQRDPSLRKS--------GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAAN  165 (336)
Q Consensus        95 ~v~~~~~~~~~~~~--------~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~  165 (336)
                      .+..+.........        ...++|++||+..+.+.+|...|..+|.+..+.+.... .+.-+|+||+.|..++++.
T Consensus       644 av~~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~  723 (881)
T KOG0128|consen  644 AVGLADAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAG  723 (881)
T ss_pred             cCCCCCchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchh
Confidence            77766554432211        23489999999999999999999999988877776333 5678899999999999999


Q ss_pred             HHHHHhCCceeCCeEEEEeeccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccce
Q psy12549        166 KSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRG  244 (336)
Q Consensus       166 ~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g  244 (336)
                      +|+...+++.++                         ...++|+|.|+..|.++++.+++.+|.+.+..++. ..|+++|
T Consensus       724 aaV~f~d~~~~g-------------------------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg  778 (881)
T KOG0128|consen  724 AAVAFRDSCFFG-------------------------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKG  778 (881)
T ss_pred             hhhhhhhhhhhh-------------------------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhcccccc
Confidence            999965544443                         14589999999999999999999999999998776 8899999


Q ss_pred             EEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       245 ~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      -|+|.|.++.++.++....++..+.-+.+.+..+.+
T Consensus       779 ~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  779 KARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             ceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            999999999999999988888887766666665433

>KOG0129|consensus

Probab=99.16  E-value=9.3e-10  Score=98.67  Aligned_cols=153  Identities=18%  Similarity=0.290  Sum_probs=113.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC--C--CCccc---EEEEEeCCHHHHHHHHHHhCC----c---
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE--Q--GNSKG---YGFVHFETEEAANKSIEKVNG----M---  174 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~--~--~~~~g---~afV~F~~~~~a~~a~~~l~~----~---  174 (336)
                      ..++|||++||.+++|+.|...|..||.+. +.++...  .  -..+|   |+|+.|+++...+.-+.++.-    .   
T Consensus       258 ~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~yf~  336 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYYFK  336 (520)
T ss_pred             cccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccceEEE
Confidence            457899999999999999999999999866 4555211  1  23456   999999999999887776532    1   


Q ss_pred             ----eeCCeEEEEeeccCchhh-hHhhhccccccceEEEcCCCCCCcHHHHHHhhc-cCCceeEEEEeC--CCCccceEE
Q psy12549        175 ----LLNSKIVFVGKFIPRKER-EKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFE-PYGTITSYRVMN--NDGKSRGFG  246 (336)
Q Consensus       175 ----~~~~~~i~v~~~~~~~~~-~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~-~~g~i~~~~i~~--~~~~~~g~a  246 (336)
                          .+..+.+.+..+...+.. -........+.+||||++||..++.++|..+|+ -||.|..+-|-.  .-+.++|-|
T Consensus       337 vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaG  416 (520)
T KOG0129|consen  337 VSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAG  416 (520)
T ss_pred             EecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcc
Confidence                112333443333322211 111333445668999999999999999999998 899999988866  445678999


Q ss_pred             EEEeCCHHHHHHHHHH
Q psy12549        247 FVAYESPEFAEKAVQA  262 (336)
Q Consensus       247 fV~F~~~~~a~~a~~~  262 (336)
                      -|+|.+..+-.+||..
T Consensus       417 RVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  417 RVTFSNQQAYIKAISA  432 (520)
T ss_pred             eeeecccHHHHHHHhh
Confidence            9999999999999975

>KOG0129|consensus

Probab=99.13  E-value=1.5e-09  Score=97.33  Aligned_cols=158  Identities=15%  Similarity=0.148  Sum_probs=112.4

Q ss_pred             CCCccccCceeeeecCchhhhhhhHHhhhcccCCceEEEeCCCCcccccCCc---eEEEEEeCCcchhhHHHHHhhcCc-
Q psy12549         11 EEGIIIPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGS---GAILVQLGQPYMLDTERALDTMNF-   86 (336)
Q Consensus        11 ~~~~~~p~~~v~v~~lp~~~~e~~l~~~f~~~~~~~v~~~~~~~~~~~g~~~---g~afV~f~~~~~~~A~~A~~~~~~-   86 (336)
                      ..+..+..+.|+||+||++++|+.|...|...+...|-.....+..-.-..+   ||+|+.|+.+  ...+.-+..+.. 
T Consensus       252 ~~~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP~k~~~~~~~ppkGs~~YvflvFe~E--~sV~~Ll~aC~~~  329 (520)
T KOG0129|consen  252 GYRSPRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWPGKANSRGRAPPKGSYGYVFLVFEDE--RSVQSLLSACSEG  329 (520)
T ss_pred             CCCccccccceeecCCCccccHHHHHhhcccccceEeecCCCccccccCCCCCcccEEEEEecch--HHHHHHHHHHhhc
Confidence            3446677889999999999999999999955544444333222111111234   5999999999  877775554432 


Q ss_pred             ---c-------ccCCeeeEEEe-ccCC------CCcCCCCCceEEEcCCCCCCCHHHHHHHhh-ccCCeeEEEEeeCC-C
Q psy12549         87 ---D-------ALKGRPIRIMW-SQRD------PSLRKSGVGNVFIKNLDKSIDNKAMYDTFS-AFGSILSCKVAQDE-Q  147 (336)
Q Consensus        87 ---~-------~~~g~~i~v~~-~~~~------~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~-~~G~v~~~~~~~~~-~  147 (336)
                         .       .++.+.+.|.+ -..+      ....-+..+||||++||.-++.++|-.+|+ .||.|..+-|-.|+ -
T Consensus       330 ~~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~  409 (520)
T KOG0129|consen  330 EGNYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKL  409 (520)
T ss_pred             ccceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCccc
Confidence               1       11223344432 1111      112233457999999999999999999999 79999999999994 6


Q ss_pred             CCcccEEEEEeCCHHHHHHHHHH
Q psy12549        148 GNSKGYGFVHFETEEAANKSIEK  170 (336)
Q Consensus       148 ~~~~g~afV~F~~~~~a~~a~~~  170 (336)
                      +-.+|-|-|.|.+..+-.+|+.+
T Consensus       410 KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  410 KYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CCCCCcceeeecccHHHHHHHhh
Confidence            77899999999999999999984

>KOG4454|consensus

Probab=99.12  E-value=3e-11  Score=96.30  Aligned_cols=143  Identities=21%  Similarity=0.344  Sum_probs=121.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||.|+...++++-|.++|-..|+|..+.|+.++++..+ ||||.|.++....-|++.+||..+.+..+.++.-.
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            34579999999999999999999999999999999999988778 99999999999999999999999999888775432


Q ss_pred             CchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCc
Q psy12549        188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGK  266 (336)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~  266 (336)
                      ....                 .-|...++++.+...|+.-|++..+++.. .+|.++.++|+.+....+...++...++.
T Consensus        86 G~sh-----------------apld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l  148 (267)
T KOG4454|consen   86 GNSH-----------------APLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGL  148 (267)
T ss_pred             CCCc-----------------chhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhccc
Confidence            2110                 01456678889999999999999999988 67889999999999888888888877765


Q ss_pred             ee
Q psy12549        267 EV  268 (336)
Q Consensus       267 ~~  268 (336)
                      ..
T Consensus       149 ~~  150 (267)
T KOG4454|consen  149 EL  150 (267)
T ss_pred             Cc
Confidence            53

>KOG0112|consensus

Probab=99.05  E-value=9.5e-11  Score=110.97  Aligned_cols=165  Identities=19%  Similarity=0.311  Sum_probs=139.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..+++||++||+..+++.+|+..|..+|.+.+|.+-....+.-..|+||.|.+...+-.|+..+.+..|..-.+.+.+..
T Consensus       370 ~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~  449 (975)
T KOG0112|consen  370 RATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQ  449 (975)
T ss_pred             hhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccccc
Confidence            34679999999999999999999999999999998887655556699999999999999999998888866555554433


Q ss_pred             CchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCce
Q psy12549        188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKE  267 (336)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~  267 (336)
                      +          .....+.+++++|+..+....|..+|..||+|..|.+-..    ..||+|.|.+...|+.|+..|.|..
T Consensus       450 ~----------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg----q~yayi~yes~~~aq~a~~~~rgap  515 (975)
T KOG0112|consen  450 P----------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG----QPYAYIQYESPPAAQAATHDMRGAP  515 (975)
T ss_pred             c----------ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC----CcceeeecccCccchhhHHHHhcCc
Confidence            2          2233477999999999999999999999999999888543    6799999999999999999999999


Q ss_pred             ecC--EEEEEeecccchhhHH
Q psy12549        268 VDG--KILYVGRAQKKAERTQ  286 (336)
Q Consensus       268 ~~g--~~l~v~~~~~~~~~~~  286 (336)
                      ++|  ++++|.|+..-....+
T Consensus       516 ~G~P~~r~rvdla~~~~~~Pq  536 (975)
T KOG0112|consen  516 LGGPPRRLRVDLASPPGATPQ  536 (975)
T ss_pred             CCCCCcccccccccCCCCChh
Confidence            987  7899999876644433

>KOG4454|consensus

Probab=99.01  E-value=1.1e-10  Score=93.21  Aligned_cols=149  Identities=19%  Similarity=0.196  Sum_probs=122.4

Q ss_pred             CccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCC
Q psy12549         13 GIIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKG   91 (336)
Q Consensus        13 ~~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g   91 (336)
                      .....+++|+|+|+-..++|+.|-++| ..|+|..|.+..+++    +..+ ||||.|.++  -....|+..+||..+.+
T Consensus         4 aaae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d----~~~k-Fa~v~f~~E--~sv~~a~~L~ng~~l~~   76 (267)
T KOG4454|consen    4 AAAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD----QEQK-FAYVFFPNE--NSVQLAGQLENGDDLEE   76 (267)
T ss_pred             CCcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc----CCCc-eeeeecccc--cchhhhhhhcccchhcc
Confidence            345668999999999999999999999 777888898888774    4455 999999999  99999999999999999


Q ss_pred             eeeEEEeccCCCCcCCCCCceEEEcC----CCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHH
Q psy12549         92 RPIRIMWSQRDPSLRKSGVGNVFIKN----LDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS  167 (336)
Q Consensus        92 ~~i~v~~~~~~~~~~~~~~~~l~v~n----lp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a  167 (336)
                      +++.+.+               +.++    |....+++.+...|+..|++..+++..+.+|+.+.++|+.+...-..-.+
T Consensus        77 ~e~q~~~---------------r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~  141 (267)
T KOG4454|consen   77 DEEQRTL---------------RCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFA  141 (267)
T ss_pred             chhhccc---------------ccCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHH
Confidence            9888664               3333    45668999999999999999999999998888888999988777777777


Q ss_pred             HHHhCCceeCCeEEEE
Q psy12549        168 IEKVNGMLLNSKIVFV  183 (336)
Q Consensus       168 ~~~l~~~~~~~~~i~v  183 (336)
                      +....+....-+++.+
T Consensus       142 ~~~y~~l~~~~~~~~~  157 (267)
T KOG4454|consen  142 LDLYQGLELFQKKVTI  157 (267)
T ss_pred             hhhhcccCcCCCCccc
Confidence            7766666554444433

>KOG0128|consensus

Probab=98.98  E-value=6.4e-11  Score=111.63  Aligned_cols=146  Identities=16%  Similarity=0.053  Sum_probs=122.2

Q ss_pred             ceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEE
Q psy12549         19 HNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIM   97 (336)
Q Consensus        19 ~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~   97 (336)
                      -++|+.||++.+.+.++...| ..+.+..+.+....   ..++-+|+||++|..+  ++|.+|+...++..++       
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~---n~~~~rG~~Y~~F~~~--~~~~aaV~f~d~~~~g-------  735 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHK---NEKRFRGKAYVEFLKP--EHAGAAVAFRDSCFFG-------  735 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHh---hccccccceeeEeecC--Cchhhhhhhhhhhhhh-------
Confidence            468999999999999999988 55555555555333   3678899999999999  9999999944444333       


Q ss_pred             eccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeC
Q psy12549         98 WSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLN  177 (336)
Q Consensus        98 ~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~  177 (336)
                                  ...++|+|.|...|.++++.+++.+|++....++..+.|+.+|.|+|.|.++.+|.+++...+...+.
T Consensus       736 ------------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~r  803 (881)
T KOG0128|consen  736 ------------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKR  803 (881)
T ss_pred             ------------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhh
Confidence                        13499999999999999999999999999999999999999999999999999999999988888777


Q ss_pred             CeEEEEeeccC
Q psy12549        178 SKIVFVGKFIP  188 (336)
Q Consensus       178 ~~~i~v~~~~~  188 (336)
                      .+.+.+..++|
T Consensus       804 E~~~~v~vsnp  814 (881)
T KOG0128|consen  804 ENNGEVQVSNP  814 (881)
T ss_pred             hcCccccccCC
Confidence            77777766555

>KOG4208|consensus

Probab=98.97  E-value=2.5e-09  Score=84.96  Aligned_cols=83  Identities=28%  Similarity=0.532  Sum_probs=75.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhcc-CCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAF-GSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~-G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      .....-+++..+|..+.+.++...|.+| |.+..+++-+++ +|+|+|||||+|++++.|.-|-+.||+-.+.++-|.|.
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            3445679999999999999999999999 788888887876 99999999999999999999999999999999999998


Q ss_pred             eccCc
Q psy12549        185 KFIPR  189 (336)
Q Consensus       185 ~~~~~  189 (336)
                      ...+.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            87666

>KOG0226|consensus

Probab=98.97  E-value=7.6e-10  Score=90.43  Aligned_cols=178  Identities=20%  Similarity=0.332  Sum_probs=133.0

Q ss_pred             EEEcCCCCCCCHHH---HHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        113 VFIKNLDKSIDNKA---MYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       113 l~v~nlp~~~t~~~---l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      .++.++-..+..+-   +...|+.+-.+...+++++..+.-.+++|+.|.....-.++-..-++..++-..++...... 
T Consensus        99 p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gts-  177 (290)
T KOG0226|consen   99 PFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTS-  177 (290)
T ss_pred             ccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeeccccc-
Confidence            44555544333332   36778888778888888888888889999999988777777766666677666655432221 


Q ss_pred             hhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCce
Q psy12549        190 KEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKE  267 (336)
Q Consensus       190 ~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~  267 (336)
                       -..............||.+.|..+++.+-|...|.+|-.-...++++  .+|+++||+||.|.++.++.+|+..|+|..
T Consensus       178 -wedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gky  256 (290)
T KOG0226|consen  178 -WEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKY  256 (290)
T ss_pred             -cCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccc
Confidence             12223333444447899999999999999999999998888788877  889999999999999999999999999999


Q ss_pred             ecCEEEEEeecccchhhHHHHHHHH
Q psy12549        268 VDGKILYVGRAQKKAERTQELKRRF  292 (336)
Q Consensus       268 ~~g~~l~v~~~~~~~~~~~~~~~~~  292 (336)
                      ++.+.|.++.+.-+........+.+
T Consensus       257 VgsrpiklRkS~wkeRn~dvv~kk~  281 (290)
T KOG0226|consen  257 VGSRPIKLRKSEWKERNLDVVKKKQ  281 (290)
T ss_pred             cccchhHhhhhhHHhhhhHHHhHHH
Confidence            9999999987766654444433333

>KOG0226|consensus

Probab=98.96  E-value=1e-09  Score=89.63  Aligned_cols=159  Identities=19%  Similarity=0.241  Sum_probs=120.5

Q ss_pred             eeecCchhhhhhh-H--Hhhhccc-CCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEE
Q psy12549         22 ATRELSAKVVEGV-S--RSLSSLI-DGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIM   97 (336)
Q Consensus        22 ~v~~lp~~~~e~~-l--~~~f~~~-~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~   97 (336)
                      +++++-+.+..+- +  -..|+.. .....++.+++    .+.-++++|+.|...  ..-.++-..-++..+...++++.
T Consensus       100 ~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~----p~~~~~~~~~~~k~s--~a~~k~~~~~~~Kki~~~~VR~a  173 (290)
T KOG0226|consen  100 FQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDR----PQPIRPEAFESFKAS--DALLKAETEKEKKKIGKPPVRLA  173 (290)
T ss_pred             cccccccccCCCCCCcchhhhccchhhhhhhhhhcC----CCccCcccccCcchh--hhhhhhccccccccccCcceeec
Confidence            3445444444433 2  2334333 23344455544    356788999999888  77777777677778887777774


Q ss_pred             ----eccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhC
Q psy12549         98 ----WSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVN  172 (336)
Q Consensus        98 ----~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~  172 (336)
                          |..+....+.....+||.+.|...++.+-|-..|.+|-.-...++++++ +|+++||+||.|.++.++..|+..++
T Consensus       174 ~gtswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~  253 (290)
T KOG0226|consen  174 AGTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMN  253 (290)
T ss_pred             cccccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhc
Confidence                4444444555667799999999999999999999999988888899986 99999999999999999999999999


Q ss_pred             CceeCCeEEEEeec
Q psy12549        173 GMLLNSKIVFVGKF  186 (336)
Q Consensus       173 ~~~~~~~~i~v~~~  186 (336)
                      |.+++.+.|.+..+
T Consensus       254 gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  254 GKYVGSRPIKLRKS  267 (290)
T ss_pred             ccccccchhHhhhh
Confidence            99999999988543

>KOG0132|consensus

Probab=98.91  E-value=2e-09  Score=100.58  Aligned_cols=87  Identities=14%  Similarity=0.195  Sum_probs=79.5

Q ss_pred             ceeccCCCCccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhh
Q psy12549          5 QTVQLSEEGIIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDT   83 (336)
Q Consensus         5 ~~~~~~~~~~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~   83 (336)
                      ..+.++++.+..-+||||||+||..++|.||.++| .++.+.+|.++..+         |+|||.+.+.  ++|.+|+.+
T Consensus       408 glP~I~pd~isV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R---------~cAfI~M~~R--qdA~kalqk  476 (894)
T KOG0132|consen  408 GLPTIPPDHISVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPR---------GCAFIKMVRR--QDAEKALQK  476 (894)
T ss_pred             cCCCCCCcceeEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccCC---------ceeEEEEeeh--hHHHHHHHH
Confidence            45667788888999999999999999999999999 89999999999755         7899999999  999999999


Q ss_pred             cCccccCCeeeEEEeccCC
Q psy12549         84 MNFDALKGRPIRIMWSQRD  102 (336)
Q Consensus        84 ~~~~~~~g~~i~v~~~~~~  102 (336)
                      |.+..+.++.|+|.|+-..
T Consensus       477 l~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  477 LSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             HhcccccceeeEEeeeccC
Confidence            9999999999999997554

>KOG0112|consensus

Probab=98.91  E-value=1.7e-09  Score=102.71  Aligned_cols=165  Identities=16%  Similarity=0.096  Sum_probs=134.5

Q ss_pred             CCCccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCcccc
Q psy12549         11 EEGIIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDAL   89 (336)
Q Consensus        11 ~~~~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~   89 (336)
                      +....+-+++|+++||+..+++.+++..| .++.+..|.+..-.    .++...||||.|.+.  ..+-.|...+.+..|
T Consensus       365 ~~DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~----~~~esa~~f~~~~n~--dmtp~ak~e~s~~~I  438 (975)
T KOG0112|consen  365 KLDDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH----IKTESAYAFVSLLNT--DMTPSAKFEESGPLI  438 (975)
T ss_pred             cccchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC----CCcccchhhhhhhcc--ccCcccchhhcCCcc
Confidence            34455778999999999999999999999 66677777776654    356778899999999  999999999999887


Q ss_pred             CCeeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHH
Q psy12549         90 KGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE  169 (336)
Q Consensus        90 ~g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~  169 (336)
                      ..-.+++.....    .....+.+++++|+.++....|...|..||.|..+.+-..     ..|||++|++...|+.|+.
T Consensus       439 ~~g~~r~glG~~----kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-----q~yayi~yes~~~aq~a~~  509 (975)
T KOG0112|consen  439 GNGTHRIGLGQP----KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-----QPYAYIQYESPPAAQAATH  509 (975)
T ss_pred             ccCccccccccc----ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-----CcceeeecccCccchhhHH
Confidence            655555555432    2233477999999999999999999999999998776543     5699999999999999999


Q ss_pred             HhCCceeCC--eEEEEeeccCch
Q psy12549        170 KVNGMLLNS--KIVFVGKFIPRK  190 (336)
Q Consensus       170 ~l~~~~~~~--~~i~v~~~~~~~  190 (336)
                      .+-|..+++  +.+.|.++.+..
T Consensus       510 ~~rgap~G~P~~r~rvdla~~~~  532 (975)
T KOG0112|consen  510 DMRGAPLGGPPRRLRVDLASPPG  532 (975)
T ss_pred             HHhcCcCCCCCcccccccccCCC
Confidence            999999865  677777766543

>KOG0415|consensus

Probab=98.90  E-value=2.5e-09  Score=91.31  Aligned_cols=83  Identities=22%  Similarity=0.355  Sum_probs=77.3

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ++.+.|||..|.+-++.++|.-+|+.||.|.+|.+++  .+|.+-.||||+|.+.++.++|.-.|++.-|++++|+|.|+
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFS  316 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFS  316 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehh
Confidence            4558899999999999999999999999999999998  78889999999999999999999999999999999999998


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .+-.+
T Consensus       317 QSVsk  321 (479)
T KOG0415|consen  317 QSVSK  321 (479)
T ss_pred             hhhhh
Confidence            76544

>KOG0415|consensus

Probab=98.89  E-value=3.3e-09  Score=90.62  Aligned_cols=83  Identities=25%  Similarity=0.482  Sum_probs=77.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ....|||-.|.+-++.++|.-+|+.||.|.+|.++++. +|.+..||||+|++.+++.+|.-.|++..|+++.|+|.++.
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQ  317 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQ  317 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhh
Confidence            34679999999999999999999999999999999997 89999999999999999999999999999999999998876


Q ss_pred             Cchh
Q psy12549        188 PRKE  191 (336)
Q Consensus       188 ~~~~  191 (336)
                      +-..
T Consensus       318 SVsk  321 (479)
T KOG0415|consen  318 SVSK  321 (479)
T ss_pred             hhhh
Confidence            5443

>KOG4210|consensus

Probab=98.88  E-value=1.5e-09  Score=93.96  Aligned_cols=173  Identities=20%  Similarity=0.260  Sum_probs=135.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...+.|++++...+.+.+...++..+|......+.... ...++|++++.|...+.+..|+.........++.+......
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            45789999999999999999999999977766665543 67789999999999999999999544345555555443333


Q ss_pred             Cchhhh--HhhhccccccceEE-EcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHH
Q psy12549        188 PRKERE--KELGEKAKLFTNVY-IKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQA  262 (336)
Q Consensus       188 ~~~~~~--~~~~~~~~~~~~l~-V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~  262 (336)
                      ......  ...........+++ |.|++..+++++|+..|..+|.|..+++..  .++...++|++.|.....+..++..
T Consensus       167 ~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~  246 (285)
T KOG4210|consen  167 RRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND  246 (285)
T ss_pred             cccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc
Confidence            332111  11111222224455 999999999999999999999999999987  7888999999999999999999987


Q ss_pred             hCCceecCEEEEEeecccch
Q psy12549        263 WNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       263 l~g~~~~g~~l~v~~~~~~~  282 (336)
                       +...+.++++.+.+..+..
T Consensus       247 -~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  247 -QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             -ccCcccCcccccccCCCCc
Confidence             8899999999999987764

>KOG0132|consensus

Probab=98.84  E-value=7.5e-09  Score=96.88  Aligned_cols=78  Identities=23%  Similarity=0.419  Sum_probs=72.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchh
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAE  283 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~  283 (336)
                      +||||++|+..+++.||.++|+.||+|.+|.++..    +++|||.+.+.++|.+|+.+|++..+.++.|++.|+..+.-
T Consensus       422 rTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~----R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~G~  497 (894)
T KOG0132|consen  422 RTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP----RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGKGP  497 (894)
T ss_pred             eeeeeccccchhhHHHHHHHHHhcccceeEeeccC----CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccCCc
Confidence            79999999999999999999999999999999864    99999999999999999999999999999999999987754


Q ss_pred             hH
Q psy12549        284 RT  285 (336)
Q Consensus       284 ~~  285 (336)
                      ..
T Consensus       498 ks  499 (894)
T KOG0132|consen  498 KS  499 (894)
T ss_pred             ch
Confidence            43

>KOG4208|consensus

Probab=98.83  E-value=1.1e-08  Score=81.32  Aligned_cols=78  Identities=26%  Similarity=0.479  Sum_probs=72.0

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccC-CceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPY-GTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~-g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .-+++..+|..+.+.++..+|.+| |.+.++++.+  .+|+++|||||+|++++.|.-|.+.||+.-+.|+.|.|.+-.+
T Consensus        50 g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmpp  129 (214)
T KOG4208|consen   50 GVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPP  129 (214)
T ss_pred             cceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCc
Confidence            568999999999999999999988 7788888855  8999999999999999999999999999999999999999877


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      .
T Consensus       130 e  130 (214)
T KOG4208|consen  130 E  130 (214)
T ss_pred             h
Confidence            6

>KOG4210|consensus

Probab=98.82  E-value=6.4e-09  Score=90.09  Aligned_cols=169  Identities=18%  Similarity=0.239  Sum_probs=130.3

Q ss_pred             cCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeE
Q psy12549         17 PKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIR   95 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~   95 (336)
                      -..+.+++++...+.+.+...++ ..+......+....+   ...++|++++.|...  +++..|+.........++.+.
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~---~~~sk~~~s~~f~~k--s~~~~~l~~s~~~~~~~~~~~  161 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLED---SLSSKGGLSVHFAGK--SQFFAALEESGSKVLDGNKGE  161 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhcc---ccccccceeeccccH--HHHHHHHHhhhcccccccccc
Confidence            46679999999999999888877 666566665555443   367999999999999  999999984333344333333


Q ss_pred             EEec--------cCCCCcCCCCCceEE-EcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHH
Q psy12549         96 IMWS--------QRDPSLRKSGVGNVF-IKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAAN  165 (336)
Q Consensus        96 v~~~--------~~~~~~~~~~~~~l~-v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~  165 (336)
                      ....        ............+++ +++++.+++.++|+.+|..+|.|..++++.++ ++.++|+||+.|.....+.
T Consensus       162 ~dl~~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~  241 (285)
T KOG4210|consen  162 KDLNTRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKK  241 (285)
T ss_pred             CcccccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHH
Confidence            2221        111122333445666 99999999999999999999999999999987 7899999999999999999


Q ss_pred             HHHHHhCCceeCCeEEEEeeccCchh
Q psy12549        166 KSIEKVNGMLLNSKIVFVGKFIPRKE  191 (336)
Q Consensus       166 ~a~~~l~~~~~~~~~i~v~~~~~~~~  191 (336)
                      .++.. ....+.++++.+....+...
T Consensus       242 ~~~~~-~~~~~~~~~~~~~~~~~~~~  266 (285)
T KOG4210|consen  242 LALND-QTRSIGGRPLRLEEDEPRPK  266 (285)
T ss_pred             HHhhc-ccCcccCcccccccCCCCcc
Confidence            99997 88889999999987766543

>KOG0153|consensus

Probab=98.75  E-value=2.7e-08  Score=85.03  Aligned_cols=74  Identities=26%  Similarity=0.497  Sum_probs=66.6

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHh-CCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW-NGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l-~g~~~~g~~l~v~~~~~  280 (336)
                      ..+|||++|...+++.+|++.|.+||+|+.+.+...    +++|||+|.+.++|+.|.+.. +...++|.+|.+.|+.+
T Consensus       228 I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~----~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  228 IKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR----KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             eeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc----cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            378999999999999999999999999999999875    668999999999999987664 55667999999999988

>KOG4661|consensus

Probab=98.74  E-value=2.9e-08  Score=89.95  Aligned_cols=80  Identities=24%  Similarity=0.438  Sum_probs=73.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|+|.+|...+...+|+++|++||.|...+++.+. +...++|+||++.+.++|-+|+..|+...+.|+-|.|..++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            4689999999999999999999999999999999985 445788999999999999999999999999999999988765


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      .
T Consensus       485 E  485 (940)
T KOG4661|consen  485 E  485 (940)
T ss_pred             C
Confidence            4

>KOG0153|consensus

Probab=98.72  E-value=5e-08  Score=83.45  Aligned_cols=75  Identities=29%  Similarity=0.463  Sum_probs=66.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV-NGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l-~~~~~~~~~i~v~~~~  187 (336)
                      ...+|||+||.+.+++.+|+++|.+||+|.++.+...     +++|||+|.+.+.|..|...+ +...+.|+.|.+.|..
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~  301 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            3468999999999999999999999999999998874     569999999999999988754 5566899999999988


Q ss_pred             C
Q psy12549        188 P  188 (336)
Q Consensus       188 ~  188 (336)
                      +
T Consensus       302 ~  302 (377)
T KOG0153|consen  302 P  302 (377)
T ss_pred             C
Confidence            7

>KOG0533|consensus

Probab=98.68  E-value=1.1e-07  Score=79.61  Aligned_cols=81  Identities=22%  Similarity=0.363  Sum_probs=75.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      ..+|+|.|||+.++.+||+++|..||.+..+.+..++.|.+.|.|-|.|...+||..|++.+++..++|+.+.+....+.
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            46799999999999999999999999999999999999999999999999999999999999999999999988776554


Q ss_pred             h
Q psy12549        190 K  190 (336)
Q Consensus       190 ~  190 (336)
                      .
T Consensus       163 ~  163 (243)
T KOG0533|consen  163 S  163 (243)
T ss_pred             c
Confidence            3

>KOG4660|consensus

Probab=98.56  E-value=6.9e-08  Score=87.64  Aligned_cols=167  Identities=16%  Similarity=0.153  Sum_probs=111.5

Q ss_pred             CCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q psy12549        101 RDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKI  180 (336)
Q Consensus       101 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~  180 (336)
                      .++.......++|+|-|||.++++++|..+|+.||+|.+++.-+.    ..|.+||+|-+..+|++|++.|++..+.|+.
T Consensus        66 ~np~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~  141 (549)
T KOG4660|consen   66 DNPSEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN----KRGIVFVEFYDVRDAERALKALNRREIAGKR  141 (549)
T ss_pred             CCCCcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc----cCceEEEEEeehHhHHHHHHHHHHHHhhhhh
Confidence            344444556789999999999999999999999999999766554    4679999999999999999999999999988


Q ss_pred             EEEeeccCchhhh----------------HhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccce
Q psy12549        181 VFVGKFIPRKERE----------------KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRG  244 (336)
Q Consensus       181 i~v~~~~~~~~~~----------------~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g  244 (336)
                      +............                ...+...  ..+++. .|++..+...+...++.+|.+.. +..   +.-..
T Consensus       142 ~k~~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~--~~~~~g-~l~P~~s~~~~~~~~~~~~~~~~-~~~---~~~~h  214 (549)
T KOG4660|consen  142 IKRPGGARRAMGLQSGTSFLNHFGSPLANSPPGGWP--RGQLFG-MLSPTRSSILLEHISSVDGSSPG-RET---PLLNH  214 (549)
T ss_pred             hcCCCcccccchhcccchhhhhccchhhcCCCCCCc--CCccee-eeccchhhhhhhcchhccCcccc-ccc---cchhh
Confidence            8832211111000                0000001  122332 27777777667777777777655 322   22222


Q ss_pred             EEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       245 ~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      .-++.|.+..++..+.... |..+.+.....+++.
T Consensus       215 q~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~  248 (549)
T KOG4660|consen  215 QRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSG  248 (549)
T ss_pred             hhhhhhccccchhhcccCC-ceecCCCCceEEecC
Confidence            4667888877775555533 555665555555543

>KOG4676|consensus

Probab=98.54  E-value=1.2e-07  Score=82.28  Aligned_cols=199  Identities=9%  Similarity=0.027  Sum_probs=129.3

Q ss_pred             eeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEEe
Q psy12549         20 NVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMW   98 (336)
Q Consensus        20 ~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~~   98 (336)
                      .|.|.||.+++|.++++.+| -.|.+.++++..+.+..........|||.|.+.  ..+..|-. |.++.|-++.+.|.+
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~--~sv~vaQh-Ltntvfvdraliv~p   85 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDS--QSVTVAQH-LTNTVFVDRALIVRP   85 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCC--cceeHHhh-hccceeeeeeEEEEe
Confidence            58899999999999999999 556888999988655555566778899999999  88877766 777877777766665


Q ss_pred             ccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCC
Q psy12549         99 SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNS  178 (336)
Q Consensus        99 ~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~  178 (336)
                      ....                   +-++..  +|..++.-..+-=...+                         +|..+..
T Consensus        86 ~~~~-------------------~~p~r~--af~~l~~~navprll~p-------------------------dg~Lp~~  119 (479)
T KOG4676|consen   86 YGDE-------------------VIPDRF--AFVELADQNAVPRLLPP-------------------------DGVLPGD  119 (479)
T ss_pred             cCCC-------------------CCccHH--HHHhcCcccccccccCC-------------------------CCccCCC
Confidence            4322                   111121  45555433322111111                         1111111


Q ss_pred             eEEEEe-------eccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeC
Q psy12549        179 KIVFVG-------KFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYE  251 (336)
Q Consensus       179 ~~i~v~-------~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~  251 (336)
                      .++...       ...|...............++++|.+|+..+...++.+.|..+|++.+.++-  .+....+|.+.|.
T Consensus       120 ~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~a--sk~~s~~c~~sf~  197 (479)
T KOG4676|consen  120 RPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILPESGESFERKGEVSYAHTA--SKSRSSSCSHSFR  197 (479)
T ss_pred             CccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcchhhhhhhhhcchhhhhhhh--ccCCCcchhhhHh
Confidence            111000       0001111111222222333789999999999999999999999998777664  3344567889999


Q ss_pred             CHHHHHHHHHHhCCceecC
Q psy12549        252 SPEFAEKAVQAWNGKEVDG  270 (336)
Q Consensus       252 ~~~~a~~a~~~l~g~~~~g  270 (336)
                      ...+...|+. ++|..+.-
T Consensus       198 ~qts~~halr-~~gre~k~  215 (479)
T KOG4676|consen  198 KQTSSKHALR-SHGRERKR  215 (479)
T ss_pred             hhhhHHHHHH-hcchhhhh
Confidence            9888888887 58888763

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

Probab=98.54  E-value=9.1e-07  Score=63.28  Aligned_cols=77  Identities=19%  Similarity=0.260  Sum_probs=63.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcc--CCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeC----CeEEEE
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAF--GSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLN----SKIVFV  183 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~--G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~----~~~i~v  183 (336)
                      +||+|+|||...|.++|.+++...  |...-+-++.|. ++.+.|||||.|.++++|.+..+.++|..+.    .+...+
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            689999999999999999988664  556667788875 6778999999999999999999999998874    344455


Q ss_pred             eecc
Q psy12549        184 GKFI  187 (336)
Q Consensus       184 ~~~~  187 (336)
                      .++.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            5543

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

>KOG0533|consensus

Probab=98.52  E-value=3.1e-07  Score=76.82  Aligned_cols=78  Identities=28%  Similarity=0.447  Sum_probs=71.4

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ..|+|.|||+.++++||+++|..||.+..+.+-. ..|.+.|.|-|.|...++|.+|++.++|..++|+.|.+....+.
T Consensus        84 ~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~  162 (243)
T KOG0533|consen   84 TKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSP  162 (243)
T ss_pred             ceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCc
Confidence            6799999999999999999999999888887766 88999999999999999999999999999999999888776544

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

Probab=98.52  E-value=1e-06  Score=62.99  Aligned_cols=79  Identities=24%  Similarity=0.407  Sum_probs=64.3

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccC--CceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceec----CEEEEE
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPY--GTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD----GKILYV  275 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~--g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~----g~~l~v  275 (336)
                      +||.|+|+|...+.++|.+++...  |...-+.++-  .++.+.|||||.|.+++.|.+-.+.++|..+.    .+...+
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            689999999999999999888643  3444444433  67788999999999999999999999999985    477888


Q ss_pred             eecccch
Q psy12549        276 GRAQKKA  282 (336)
Q Consensus       276 ~~~~~~~  282 (336)
                      .||.-+.
T Consensus        82 ~yAriQG   88 (97)
T PF04059_consen   82 SYARIQG   88 (97)
T ss_pred             ehhHhhC
Confidence            8887553

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

>KOG4661|consensus

Probab=98.46  E-value=3.7e-07  Score=82.96  Aligned_cols=78  Identities=22%  Similarity=0.502  Sum_probs=71.0

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      +.|+|.+|...+...+|+.+|++||.|.-.+++.  .+...+-|+||++.+.++|.++|..||-..+.|+.|.|..++..
T Consensus       406 RNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKNE  485 (940)
T KOG4661|consen  406 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKNE  485 (940)
T ss_pred             cceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecccC
Confidence            6799999999999999999999999999999887  33445889999999999999999999999999999999988654

>KOG0116|consensus

Probab=98.39  E-value=7.4e-07  Score=80.63  Aligned_cols=79  Identities=24%  Similarity=0.404  Sum_probs=68.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..+|||+|||.+++.++|+++|..||+|....|.... .+...+||||+|.+.++++.|+.+ +...++++++.|+--.+
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            3469999999999999999999999999998777654 444558999999999999999996 68889999999976554


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      .
T Consensus       367 ~  367 (419)
T KOG0116|consen  367 G  367 (419)
T ss_pred             c
Confidence            3

>KOG0151|consensus

Probab=98.38  E-value=8.9e-07  Score=82.54  Aligned_cols=80  Identities=23%  Similarity=0.432  Sum_probs=72.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCC----CCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ----GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~----~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      ..+++||+||++.++++.|...|..||++..++++..++    ...+.++||-|.+..||++|++.|+|..+.+..+++.
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~g  252 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLG  252 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeec
Confidence            357899999999999999999999999999999998763    3445689999999999999999999999999999998


Q ss_pred             eccC
Q psy12549        185 KFIP  188 (336)
Q Consensus       185 ~~~~  188 (336)
                      |...
T Consensus       253 Wgk~  256 (877)
T KOG0151|consen  253 WGKA  256 (877)
T ss_pred             cccc
Confidence            8743

>KOG0151|consensus

Probab=98.35  E-value=6e-07  Score=83.66  Aligned_cols=83  Identities=17%  Similarity=0.117  Sum_probs=71.9

Q ss_pred             cccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCee
Q psy12549         15 IIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRP   93 (336)
Q Consensus        15 ~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~   93 (336)
                      ...++||||+||+++++|..|..-| .+|++.++++.+.+----..+.+-++||-|-+.  .+|+.|++.|+|..+.+..
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR--~D~era~k~lqg~iv~~~e  248 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNR--ADAERALKELQGIIVMEYE  248 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhh--hhHHHHHHHhcceeeeeee
Confidence            4567889999999999999999988 888999999988753323345666789999999  9999999999999999999


Q ss_pred             eEEEec
Q psy12549         94 IRIMWS   99 (336)
Q Consensus        94 i~v~~~   99 (336)
                      +++-|.
T Consensus       249 ~K~gWg  254 (877)
T KOG0151|consen  249 MKLGWG  254 (877)
T ss_pred             eeeccc
Confidence            999997

>KOG2193|consensus

Probab=98.34  E-value=7.3e-08  Score=84.39  Aligned_cols=153  Identities=24%  Similarity=0.383  Sum_probs=123.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCC-eeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCc-eeCCeEEEEeeccCc
Q psy12549        112 NVFIKNLDKSIDNKAMYDTFSAFGS-ILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGM-LLNSKIVFVGKFIPR  189 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l~~~f~~~G~-v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~-~~~~~~i~v~~~~~~  189 (336)
                      .+|++||.+..+.++|..+|..... ...-.++      ..||+||...+...|.+|++.++|. .+.|+.+.+..+.+.
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~k   76 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPK   76 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhH
Confidence            4899999999999999999976421 1111222      2479999999999999999999986 589999999888777


Q ss_pred             hhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceec
Q psy12549        190 KEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD  269 (336)
Q Consensus       190 ~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~  269 (336)
                      ..+.          +.+-++|+|.....+-|-.+...||.+..|...... ..+-..-|+|.+.+.+..|+..++|..+.
T Consensus        77 kqrs----------rk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~-~etavvnvty~~~~~~~~ai~kl~g~Q~e  145 (584)
T KOG2193|consen   77 KQRS----------RKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTD-SETAVVNVTYSAQQQHRQAIHKLNGPQLE  145 (584)
T ss_pred             HHHh----------hhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccc-hHHHHHHHHHHHHHHHHHHHHhhcchHhh
Confidence            6544          458899999999999999999999999998775411 11222347899999999999999999999


Q ss_pred             CEEEEEeecccc
Q psy12549        270 GKILYVGRAQKK  281 (336)
Q Consensus       270 g~~l~v~~~~~~  281 (336)
                      ...+.+.|-...
T Consensus       146 n~~~k~~YiPde  157 (584)
T KOG2193|consen  146 NQHLKVGYIPDE  157 (584)
T ss_pred             hhhhhcccCchh
Confidence            999999886544

>KOG0116|consensus

Probab=98.32  E-value=1e-06  Score=79.79  Aligned_cols=77  Identities=27%  Similarity=0.508  Sum_probs=66.7

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      .+|||.|||.+++..+|.++|..||+|....|..  ..+++..||||+|.+.++++.|+.+ +-..++|++|.|+--.+.
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecccc
Confidence            5699999999999999999999999999877765  2355559999999999999999986 688899999999776543

>KOG4209|consensus

Probab=98.27  E-value=1.6e-06  Score=72.80  Aligned_cols=82  Identities=20%  Similarity=0.339  Sum_probs=74.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ......+||+|+...+|.+++...|+.+|.+..+.++.+. .|+++||+||+|.+.+.+..++. |++..+.|+.+.+.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            3455789999999999999999999999999999999998 67899999999999999999999 999999999999987


Q ss_pred             ccCc
Q psy12549        186 FIPR  189 (336)
Q Consensus       186 ~~~~  189 (336)
                      ....
T Consensus       177 ~r~~  180 (231)
T KOG4209|consen  177 KRTN  180 (231)
T ss_pred             eeee
Confidence            6544

>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=98.20  E-value=8.5e-06  Score=55.52  Aligned_cols=70  Identities=23%  Similarity=0.412  Sum_probs=47.8

Q ss_pred             ceEEEcCCCCCCcHHH----HHHhhccCCc-eeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        204 TNVYIKNFGEDFNDEK----LKEMFEPYGT-ITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~----l~~~f~~~g~-i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ..|+|.|||.+.+...    |++++..+|. |..+  .      .+.|+|.|.+.+.|.+|.+.|+|....|+.|.|+|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~   74 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFS   74 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE----------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEc
Confidence            4589999999887754    5677777874 4333  1      456999999999999999999999999999999998


Q ss_pred             ccc
Q psy12549        279 QKK  281 (336)
Q Consensus       279 ~~~  281 (336)
                      ...
T Consensus        75 ~~~   77 (90)
T PF11608_consen   75 PKN   77 (90)
T ss_dssp             --S
T ss_pred             CCc
Confidence            543

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

>KOG2193|consensus

Probab=98.19  E-value=1.2e-07  Score=83.13  Aligned_cols=152  Identities=16%  Similarity=0.227  Sum_probs=119.0

Q ss_pred             ceeeeecCchhhhhhhHHhhhcccCC-ceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCcc-ccCCeeeEE
Q psy12549         19 HNVATRELSAKVVEGVSRSLSSLIDG-NTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFD-ALKGRPIRI   96 (336)
Q Consensus        19 ~~v~v~~lp~~~~e~~l~~~f~~~~~-~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~-~~~g~~i~v   96 (336)
                      ..+|++||.+.++-++++++|....+ .+-.+..         ..|||||.+...  .-|.+|++.++|. .+.|+.+.+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~---------k~gyafvd~pdq--~wa~kaie~~sgk~elqGkr~e~   70 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV---------KSGYAFVDCPDQ--QWANKAIETLSGKVELQGKRQEV   70 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee---------ecceeeccCCch--hhhhhhHHhhchhhhhcCceeec
Confidence            35899999999999999999944422 1222222         238899999999  9999999999995 788999888


Q ss_pred             EeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcee
Q psy12549         97 MWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLL  176 (336)
Q Consensus        97 ~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~  176 (336)
                      ..+.++..    ..+.+-|+|+|+....+-|..+...||++..|......+.  ....=|+|.+.+.++.|+..|+|..+
T Consensus        71 ~~sv~kkq----rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e--tavvnvty~~~~~~~~ai~kl~g~Q~  144 (584)
T KOG2193|consen   71 EHSVPKKQ----RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE--TAVVNVTYSAQQQHRQAIHKLNGPQL  144 (584)
T ss_pred             cchhhHHH----HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH--HHHHHHHHHHHHHHHHHHHhhcchHh
Confidence            77554332    2366999999999999999999999999998876544321  11233788899999999999999999


Q ss_pred             CCeEEEEeecc
Q psy12549        177 NSKIVFVGKFI  187 (336)
Q Consensus       177 ~~~~i~v~~~~  187 (336)
                      .+..+.+.+..
T Consensus       145 en~~~k~~YiP  155 (584)
T KOG2193|consen  145 ENQHLKVGYIP  155 (584)
T ss_pred             hhhhhhcccCc
Confidence            88888886643

>KOG4209|consensus

Probab=98.11  E-value=6e-06  Score=69.37  Aligned_cols=79  Identities=25%  Similarity=0.379  Sum_probs=71.1

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ..+.++|+|+.+.++.+++...|+.||.+..+.+..  ..+.++|+|||+|.+.+.+..|+. |+|..+.|+.+.|.+..
T Consensus       100 d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  100 DAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             CCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeeee
Confidence            347899999999999999999999999999888776  566789999999999999999999 99999999999998865


Q ss_pred             cc
Q psy12549        280 KK  281 (336)
Q Consensus       280 ~~  281 (336)
                      -.
T Consensus       179 ~~  180 (231)
T KOG4209|consen  179 TN  180 (231)
T ss_pred             ee
Confidence            44

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

Probab=98.06  E-value=2.3e-05  Score=57.48  Aligned_cols=76  Identities=22%  Similarity=0.404  Sum_probs=46.4

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCc-----eecCEEEEEeec
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGK-----EVDGKILYVGRA  278 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~-----~~~g~~l~v~~~  278 (336)
                      +.|++.+++..++.++|++.|+.||+|.+|.+...    ...|+|.|.++++|++|+..+...     .+.+..+.++..
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G----~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vL   77 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG----DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVL   77 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-----SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE--
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC----CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEEC
Confidence            35889999999999999999999999999999763    345999999999999999877543     566666666665


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .....
T Consensus        78 eGeeE   82 (105)
T PF08777_consen   78 EGEEE   82 (105)
T ss_dssp             -HHHH
T ss_pred             CCHHH
Confidence            54433

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

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.92  E-value=3.9e-05  Score=52.31  Aligned_cols=71  Identities=17%  Similarity=0.216  Sum_probs=45.4

Q ss_pred             ceeeeecCchhhhhhhHHh----hhcccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeee
Q psy12549         19 HNVATRELSAKVVEGVSRS----LSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPI   94 (336)
Q Consensus        19 ~~v~v~~lp~~~~e~~l~~----~f~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i   94 (336)
                      +.|+|.|||.+.+-..|+.    ++...++.-+.+..           +.|.|.|.+.  +.|..|.+.++|..+.|..|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~~-----------~tAilrF~~~--~~A~RA~KRmegEdVfG~kI   69 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVSG-----------GTAILRFPNQ--EFAERAQKRMEGEDVFGNKI   69 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE--T-----------T-EEEEESSH--HHHHHHHHHHTT--SSSS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEeC-----------CEEEEEeCCH--HHHHHHHHhhcccccccceE
Confidence            4689999999887777655    55333333333332           4499999999  99999999999999999999


Q ss_pred             EEEeccCC
Q psy12549         95 RIMWSQRD  102 (336)
Q Consensus        95 ~v~~~~~~  102 (336)
                      .|++....
T Consensus        70 ~v~~~~~~   77 (90)
T PF11608_consen   70 SVSFSPKN   77 (90)
T ss_dssp             EEESS--S
T ss_pred             EEEEcCCc
Confidence            99987543

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

>KOG4676|consensus

Probab=97.91  E-value=1e-05  Score=70.52  Aligned_cols=131  Identities=13%  Similarity=0.104  Sum_probs=93.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCC-----ccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG-----KSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~-----~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ..|.|.||...++.++++.+|...|.|..+.+++.-+     .....|||.|.+...+..|.. |.+..|-|+.|.|...
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            3689999999999999999999999999999987211     235679999999999887775 7889998988888765


Q ss_pred             ccchhhHH-HHHHHHHHHHHHhhcC------------------------C-------------CCceEEEecCCCCCCHH
Q psy12549        279 QKKAERTQ-ELKRRFEMLKIERLNR------------------------Y-------------QGVNLYVKNLDDSIDDE  320 (336)
Q Consensus       279 ~~~~~~~~-~~~~~~~~~~~~~~~~------------------------~-------------~~~~l~v~nlp~~~t~~  320 (336)
                      ........ ++..-..+...+....                        |             -..+++|.+|+..+...
T Consensus        87 ~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~  166 (479)
T KOG4676|consen   87 GDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILP  166 (479)
T ss_pred             CCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcch
Confidence            44333222 1110000000000000                        0             01468999999999999


Q ss_pred             HHHHhcCCCCCeeec
Q psy12549        321 RLRKEFTPFGTITSA  335 (336)
Q Consensus       321 ~l~~~F~~~G~V~~v  335 (336)
                      ++-+.|..+|+|.+.
T Consensus       167 e~~e~f~r~Gev~ya  181 (479)
T KOG4676|consen  167 ESGESFERKGEVSYA  181 (479)
T ss_pred             hhhhhhhhcchhhhh
Confidence            999999999998753

>KOG0115|consensus

Probab=97.79  E-value=8.1e-05  Score=61.62  Aligned_cols=89  Identities=22%  Similarity=0.376  Sum_probs=81.1

Q ss_pred             hhHHHHHhhcCccccCCeeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEE
Q psy12549         75 LDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYG  154 (336)
Q Consensus        75 ~~A~~A~~~~~~~~~~g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~a  154 (336)
                      .-|+.|-.+|++....|+.++|.++..         +.|+|.||+..++-+.+.+.|+.||++....++.|..+...+-+
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~---------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg   75 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH---------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREG   75 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc---------ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccc
Confidence            568888889999999999999999866         34999999999999999999999999999888888888888899


Q ss_pred             EEEeCCHHHHHHHHHHhC
Q psy12549        155 FVHFETEEAANKSIEKVN  172 (336)
Q Consensus       155 fV~F~~~~~a~~a~~~l~  172 (336)
                      +|.|...-.|.+|...+.
T Consensus        76 ~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   76 IVEFAKKPNARKAARRCR   93 (275)
T ss_pred             hhhhhcchhHHHHHHHhc
Confidence            999999999999999774

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.77  E-value=0.00013  Score=62.61  Aligned_cols=112  Identities=14%  Similarity=0.252  Sum_probs=81.2

Q ss_pred             eEEEcCCCCCCCHHHH------HHHhhccCCeeEEEEeeCCC-C-Cccc--EEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q psy12549        112 NVFIKNLDKSIDNKAM------YDTFSAFGSILSCKVAQDEQ-G-NSKG--YGFVHFETEEAANKSIEKVNGMLLNSKIV  181 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l------~~~f~~~G~v~~~~~~~~~~-~-~~~g--~afV~F~~~~~a~~a~~~l~~~~~~~~~i  181 (336)
                      -+||-+||+.+..+++      .++|.+||.|..+.+.+..+ . ...+  -.||+|.+.+||.+|+...+|..++|+.|
T Consensus       116 LvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~l  195 (480)
T COG5175         116 LVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVL  195 (480)
T ss_pred             eeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCceE
Confidence            3889999988777663      47899999999887776541 1 1112  24999999999999999999999999999


Q ss_pred             EEeeccCchhhhHhhhccccccceEEEcCCC---CCCcHHHHHHh
Q psy12549        182 FVGKFIPRKEREKELGEKAKLFTNVYIKNFG---EDFNDEKLKEM  223 (336)
Q Consensus       182 ~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp---~~~t~~~l~~~  223 (336)
                      +..+...+.-...-.........++|+---.   ...+.++|...
T Consensus       196 katYGTTKYCtsYLRn~~CpNp~CMyLHEpg~e~Ds~tK~el~n~  240 (480)
T COG5175         196 KATYGTTKYCTSYLRNAVCPNPDCMYLHEPGPEKDSLTKDELCNS  240 (480)
T ss_pred             eeecCchHHHHHHHcCCCCCCCCeeeecCCCcccccccHHHHhhh
Confidence            9988877665555555555555667664332   23566666443

>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=97.67  E-value=9.5e-05  Score=54.22  Aligned_cols=68  Identities=25%  Similarity=0.423  Sum_probs=42.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCc-----eeCCeEEEE
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGM-----LLNSKIVFV  183 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~-----~~~~~~i~v  183 (336)
                      +-|.|.|++..++.++|++.|+.||.|..|.+....     .-|||.|.++++|+.|+..+...     .+.+..+.+
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~-----~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~   74 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD-----TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTL   74 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC-----CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEE
Confidence            458899999999999999999999999988887643     36999999999999999876433     445555444

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

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.65  E-value=0.00012  Score=62.73  Aligned_cols=78  Identities=24%  Similarity=0.387  Sum_probs=62.9

Q ss_pred             ceEEEcCCCCCCcHHHH------HHhhccCCceeEEEEeCCC--Cccc-e--EEEEEeCCHHHHHHHHHHhCCceecCEE
Q psy12549        204 TNVYIKNFGEDFNDEKL------KEMFEPYGTITSYRVMNND--GKSR-G--FGFVAYESPEFAEKAVQAWNGKEVDGKI  272 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l------~~~f~~~g~i~~~~i~~~~--~~~~-g--~afV~F~~~~~a~~a~~~l~g~~~~g~~  272 (336)
                      +-+||.+||..+..|++      .++|.+||.|..+.+-+.+  ..+. +  -.||+|.+.++|.++|...+|..++||.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            45899999988776663      4799999999998887622  1111 1  2499999999999999999999999999


Q ss_pred             EEEeecccc
Q psy12549        273 LYVGRAQKK  281 (336)
Q Consensus       273 l~v~~~~~~  281 (336)
                      |+..|..-+
T Consensus       195 lkatYGTTK  203 (480)
T COG5175         195 LKATYGTTK  203 (480)
T ss_pred             EeeecCchH
Confidence            999997654

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

Probab=97.63  E-value=0.00013  Score=46.14  Aligned_cols=52  Identities=29%  Similarity=0.470  Sum_probs=42.7

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHH
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAV  260 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~  260 (336)
                      +.|.|.|.+.+..+ ++...|..||+|..+.+..    ...+++|+|.++.+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~----~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPE----STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCC----CCcEEEEEECCHHHHHhhC
Confidence            56889999877764 5666888999999988852    3678999999999999985

>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=97.56  E-value=0.00043  Score=49.97  Aligned_cols=74  Identities=23%  Similarity=0.329  Sum_probs=51.3

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEE-EeC--------CCCccceEEEEEeCCHHHHHHHHHHhCCceecCE-EE
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYR-VMN--------NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK-IL  273 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~-i~~--------~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~-~l  273 (336)
                      +.|.|-++|...+ ..+.+.|++||.|.+.. +.+        +.....++..|+|+++.+|.+|+.. ||..+.|. .+
T Consensus         7 ~wVtVFGfp~~~~-~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~mv   84 (100)
T PF05172_consen    7 TWVTVFGFPPSAS-NQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSLMV   84 (100)
T ss_dssp             CEEEEE---GGGH-HHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCEEE
T ss_pred             eEEEEEccCHHHH-HHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcEEE
Confidence            5688999998844 57889999999987664 100        1112366899999999999999985 99999885 45


Q ss_pred             EEeecc
Q psy12549        274 YVGRAQ  279 (336)
Q Consensus       274 ~v~~~~  279 (336)
                      -|.+..
T Consensus        85 GV~~~~   90 (100)
T PF05172_consen   85 GVKPCD   90 (100)
T ss_dssp             EEEE-H
T ss_pred             EEEEcH
Confidence            566653

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.

>KOG0115|consensus

Probab=97.47  E-value=0.00026  Score=58.65  Aligned_cols=89  Identities=18%  Similarity=0.276  Sum_probs=76.8

Q ss_pred             HHHHHHHHHhCCceeCCeEEEEeeccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCC
Q psy12549        162 EAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDG  240 (336)
Q Consensus       162 ~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~  240 (336)
                      .-|..|-..|++....++.+.|.++..               ..|+|.||+..++.+.+.+.|+.||+|....++. ..+
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~---------------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~   69 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMH---------------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRG   69 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeecc---------------ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccc
Confidence            346778888999999999999988653               3499999999999999999999999998766655 778


Q ss_pred             ccceEEEEEeCCHHHHHHHHHHhCC
Q psy12549        241 KSRGFGFVAYESPEFAEKAVQAWNG  265 (336)
Q Consensus       241 ~~~g~afV~F~~~~~a~~a~~~l~g  265 (336)
                      +..+-++|.|.....|.+|+.....
T Consensus        70 k~t~eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   70 KPTREGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             cccccchhhhhcchhHHHHHHHhcc
Confidence            8889999999999999999988743

>KOG2314|consensus

Probab=97.47  E-value=0.0006  Score=62.64  Aligned_cols=79  Identities=28%  Similarity=0.400  Sum_probs=64.9

Q ss_pred             CCceEEEcCCCCCCC------HHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeC-CeEE
Q psy12549        109 GVGNVFIKNLDKSID------NKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLN-SKIV  181 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t------~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~-~~~i  181 (336)
                      ....|+|.|+|---.      ..-|..+|+++|++....++.++.|.++||.|++|.+..+|+.|++.|||..++ ++..
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            346799999986321      234567899999999999998887779999999999999999999999999874 7777


Q ss_pred             EEeecc
Q psy12549        182 FVGKFI  187 (336)
Q Consensus       182 ~v~~~~  187 (336)
                      .+....
T Consensus       137 ~v~~f~  142 (698)
T KOG2314|consen  137 FVRLFK  142 (698)
T ss_pred             Eeehhh
Confidence            775543

>KOG1995|consensus

Probab=97.38  E-value=0.00015  Score=63.10  Aligned_cols=82  Identities=20%  Similarity=0.389  Sum_probs=70.9

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeE--------EEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCE
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITS--------YRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK  271 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~--------~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~  271 (336)
                      ...++||.+||..+++.+|.++|.++|.|..        +.+.+  .++..++-|.|.|.+...|+.|+.-++++.|.|.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn  144 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGN  144 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCC
Confidence            3468999999999999999999999998752        23333  6788899999999999999999999999999999


Q ss_pred             EEEEeecccchh
Q psy12549        272 ILYVGRAQKKAE  283 (336)
Q Consensus       272 ~l~v~~~~~~~~  283 (336)
                      .|.|.++..+..
T Consensus       145 ~ikvs~a~~r~~  156 (351)
T KOG1995|consen  145 TIKVSLAERRTG  156 (351)
T ss_pred             CchhhhhhhccC
Confidence            999988876653

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

Probab=97.31  E-value=0.00069  Score=42.89  Aligned_cols=52  Identities=15%  Similarity=0.447  Sum_probs=41.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHH
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSI  168 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~  168 (336)
                      +.|-|.|.|++..+ .+...|..||+|..+.+..     .....||+|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~-----~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPE-----STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCC-----CCcEEEEEECCHHHHHhhC
Confidence            45888999886654 5566899999999987762     2448999999999999985

>KOG2202|consensus

Probab=97.20  E-value=0.00014  Score=60.44  Aligned_cols=64  Identities=25%  Similarity=0.324  Sum_probs=52.8

Q ss_pred             HHHHHhhc-cCCceeEEEEeCC-CCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        218 EKLKEMFE-PYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       218 ~~l~~~f~-~~g~i~~~~i~~~-~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      +++...++ +||+|+.+.+... ...-.|-+||.|...++|++|++.|||.++.|++|...+..-.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            45555665 8999999988762 2223677999999999999999999999999999999997654

>KOG2314|consensus

Probab=97.11  E-value=0.0013  Score=60.44  Aligned_cols=75  Identities=27%  Similarity=0.337  Sum_probs=61.0

Q ss_pred             ceEEEcCCCCCC--cH----HHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecC-EEEEE
Q psy12549        204 TNVYIKNFGEDF--ND----EKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG-KILYV  275 (336)
Q Consensus       204 ~~l~V~nlp~~~--t~----~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g-~~l~v  275 (336)
                      ..|+|.|.|.--  ..    .-|.++|+++|++..+.++. +.|...|+.|++|.+..+|+.|++.|||..++- ++..|
T Consensus        59 ~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v  138 (698)
T KOG2314|consen   59 SVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFFV  138 (698)
T ss_pred             eEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccceEEe
Confidence            568889988532  22    34578999999999998886 677789999999999999999999999999964 66666


Q ss_pred             eec
Q psy12549        276 GRA  278 (336)
Q Consensus       276 ~~~  278 (336)
                      ..-
T Consensus       139 ~~f  141 (698)
T KOG2314|consen  139 RLF  141 (698)
T ss_pred             ehh
Confidence            543

>KOG1995|consensus

Probab=97.05  E-value=0.00069  Score=59.05  Aligned_cols=82  Identities=26%  Similarity=0.269  Sum_probs=71.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCee--------EEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCC
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSIL--------SCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNS  178 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~--------~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~  178 (336)
                      ....+|||.+||.++++++|..+|.+.|.|.        .+++.+++ ++..|+-|.|.|.++..|+.|+.-+++..+.+
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            3456899999999999999999999998765        36677776 78899999999999999999999999999999


Q ss_pred             eEEEEeeccCc
Q psy12549        179 KIVFVGKFIPR  189 (336)
Q Consensus       179 ~~i~v~~~~~~  189 (336)
                      ..|.|..+...
T Consensus       144 n~ikvs~a~~r  154 (351)
T KOG1995|consen  144 NTIKVSLAERR  154 (351)
T ss_pred             CCchhhhhhhc
Confidence            88888665443

>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=96.96  E-value=0.005  Score=44.47  Aligned_cols=75  Identities=17%  Similarity=0.309  Sum_probs=51.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEE-EeeC-------CCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCK-VAQD-------EQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIV  181 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~-~~~~-------~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i  181 (336)
                      .+-|.|-|.|+. ....|.+.|++||+|.+.. +.++       +.........|+|+++.+|.+|+. -||..+.|..+
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            356899999997 6678889999999988764 1111       101124578899999999999999 59999988655


Q ss_pred             E-Eeec
Q psy12549        182 F-VGKF  186 (336)
Q Consensus       182 ~-v~~~  186 (336)
                      - |.++
T Consensus        84 vGV~~~   89 (100)
T PF05172_consen   84 VGVKPC   89 (100)
T ss_dssp             EEEEE-
T ss_pred             EEEEEc
Confidence            4 5554

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.

>KOG3152|consensus

Probab=96.94  E-value=0.00093  Score=55.47  Aligned_cols=72  Identities=19%  Similarity=0.374  Sum_probs=61.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-C--------CCccc----EEEEEeCCHHHHHHHHHHhCCce
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-Q--------GNSKG----YGFVHFETEEAANKSIEKVNGML  175 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~--------~~~~g----~afV~F~~~~~a~~a~~~l~~~~  175 (336)
                      ....||+++||+.++..-|+++|+.||.|-+|.+-+.. +        |.+.+    -|+|+|.+...|..+...||+..
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            34679999999999999999999999999999887764 2        22222    37899999999999999999999


Q ss_pred             eCCeE
Q psy12549        176 LNSKI  180 (336)
Q Consensus       176 ~~~~~  180 (336)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99876

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

Probab=96.94  E-value=0.0038  Score=47.89  Aligned_cols=57  Identities=21%  Similarity=0.380  Sum_probs=45.8

Q ss_pred             HHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        218 EKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       218 ~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      .+|.+.|..||++.-+++.      .+.-+|+|.+-++|.+|+. ++|..+.|+.|+|+...+.
T Consensus        51 ~~ll~~~~~~GevvLvRfv------~~~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFV------GDTMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEE------TTCEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE----
T ss_pred             HHHHHHHHhCCceEEEEEe------CCeEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCcc
Confidence            3678889999999888886      3458999999999999997 7999999999999886654

; PDB: 1UFW_A 2DNR_A.

>KOG1996|consensus

Probab=96.90  E-value=0.0027  Score=53.73  Aligned_cols=63  Identities=25%  Similarity=0.316  Sum_probs=51.5

Q ss_pred             HHHHHHhhccCCceeEEEEeCCCCcc---ceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        217 DEKLKEMFEPYGTITSYRVMNNDGKS---RGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       217 ~~~l~~~f~~~g~i~~~~i~~~~~~~---~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ++++++.+++||.|..|.|....+..   .--.||+|.+.++|.+|+-.|||+.|+||.++..|-.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            36788999999999998776522221   2347999999999999999999999999999887754

>KOG2202|consensus

Probab=96.89  E-value=0.00051  Score=57.13  Aligned_cols=66  Identities=18%  Similarity=0.312  Sum_probs=54.8

Q ss_pred             HHHHHHhh-ccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCch
Q psy12549        125 KAMYDTFS-AFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRK  190 (336)
Q Consensus       125 ~~l~~~f~-~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~  190 (336)
                      ++|...|+ +||+|+++.+..+-..+-.|-+||.|..+++|++|+..||+..+.|++|...+..-..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~  149 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTD  149 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCc
Confidence            34444455 8999999988777655678899999999999999999999999999999998765443

>KOG3152|consensus

Probab=96.85  E-value=0.00052  Score=56.93  Aligned_cols=69  Identities=22%  Similarity=0.403  Sum_probs=59.2

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCC--C--------Cccc----eEEEEEeCCHHHHHHHHHHhCCceec
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--D--------GKSR----GFGFVAYESPEFAEKAVQAWNGKEVD  269 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~--~--------~~~~----g~afV~F~~~~~a~~a~~~l~g~~~~  269 (336)
                      ..||++++|+.....-|+++|+.||.|-+|.+.+.  +        |.++    ..|+|+|.+-..|.+....|||..|+
T Consensus        75 GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~Ig  154 (278)
T KOG3152|consen   75 GVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPIG  154 (278)
T ss_pred             eEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCccC
Confidence            57999999999999999999999999999998772  2        2222    34789999999999999999999999


Q ss_pred             CEE
Q psy12549        270 GKI  272 (336)
Q Consensus       270 g~~  272 (336)
                      |+.
T Consensus       155 gkk  157 (278)
T KOG3152|consen  155 GKK  157 (278)
T ss_pred             CCC
Confidence            843

>KOG1855|consensus

Probab=96.82  E-value=0.0023  Score=57.05  Aligned_cols=69  Identities=25%  Similarity=0.288  Sum_probs=58.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeC---C-C--CC--------cccEEEEEeCCHHHHHHHHHHhCC
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD---E-Q--GN--------SKGYGFVHFETEEAANKSIEKVNG  173 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~---~-~--~~--------~~g~afV~F~~~~~a~~a~~~l~~  173 (336)
                      ...++|.+-|||.+-.-+-|.++|..+|.|..|+|+..   + +  +.        .+-+|+|+|...+.|.+|.+.++.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            46789999999999999999999999999999999887   3 1  11        245899999999999999997765


Q ss_pred             cee
Q psy12549        174 MLL  176 (336)
Q Consensus       174 ~~~  176 (336)
                      ..-
T Consensus       309 e~~  311 (484)
T KOG1855|consen  309 EQN  311 (484)
T ss_pred             hhh
Confidence            443

>KOG1996|consensus

Probab=96.62  E-value=0.008  Score=50.99  Aligned_cols=66  Identities=17%  Similarity=0.223  Sum_probs=54.4

Q ss_pred             HHHHHHHhhccCCeeEEEEeeCCCC--CcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        124 NKAMYDTFSAFGSILSCKVAQDEQG--NSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       124 ~~~l~~~f~~~G~v~~~~~~~~~~~--~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      ++++++.+++||.|..|.|.-.+..  ...---||+|...++|.+|+-.|||.+++|+.+...+.+..
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            3578899999999999988887632  22235899999999999999999999999999988775543

>KOG4849|consensus

Probab=96.58  E-value=0.0019  Score=55.93  Aligned_cols=77  Identities=10%  Similarity=0.039  Sum_probs=63.3

Q ss_pred             CceeeeecCchhhhhhhHHhhh-ccc--CCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeee
Q psy12549         18 KHNVATRELSAKVVEGVSRSLS-SLI--DGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPI   94 (336)
Q Consensus        18 ~~~v~v~~lp~~~~e~~l~~~f-~~~--~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i   94 (336)
                      +.++|||||-+.+|.+||.+.. +.+  ...++++..++   .-|+|+|||.|...+.  ....+.++.|....++|+.-
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR---~NGQSKG~AL~~~~Sd--Aa~Kq~MeiLP~k~iHGQ~P  154 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENR---TNGQSKGYALLVLNSD--AAVKQTMEILPTKTIHGQSP  154 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcc---cCCcccceEEEEecch--HHHHHHHHhcccceecCCCC
Confidence            3479999999999999998866 333  44577888777   4599999999999999  88899999999999999876


Q ss_pred             EEEec
Q psy12549         95 RIMWS   99 (336)
Q Consensus        95 ~v~~~   99 (336)
                      .|...
T Consensus       155 ~V~~~  159 (498)
T KOG4849|consen  155 TVLSY  159 (498)
T ss_pred             eeecc
Confidence            66543

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

Probab=96.55  E-value=0.012  Score=45.30  Aligned_cols=73  Identities=15%  Similarity=0.086  Sum_probs=50.5

Q ss_pred             cccCceeeeecCch-----hhhh----hhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhc
Q psy12549         15 IIPKHNVATRELSA-----KVVE----GVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTM   84 (336)
Q Consensus        15 ~~p~~~v~v~~lp~-----~~~e----~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~   84 (336)
                      ..|+.+|.|.-+.+     ..-.    .+|.+.| .+|.+.-+++..+.           -+|+|.+-  +.|.+|++ +
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~~-----------mwVTF~dg--~sALaals-~   89 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGDT-----------MWVTFRDG--QSALAALS-L   89 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETTC-----------EEEEESSC--HHHHHHHH-G
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCCe-----------EEEEECcc--HHHHHHHc-c
Confidence            45677777766651     1222    2444556 77788888888765           79999999  99999999 9


Q ss_pred             CccccCCeeeEEEeccC
Q psy12549         85 NFDALKGRPIRIMWSQR  101 (336)
Q Consensus        85 ~~~~~~g~~i~v~~~~~  101 (336)
                      +|..+.|+.++|+.-.+
T Consensus        90 dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   90 DGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             CCSEETTEEEEEEE---
T ss_pred             CCcEECCEEEEEEeCCc
Confidence            99999999999987544

; PDB: 1UFW_A 2DNR_A.

>KOG4849|consensus

Probab=96.54  E-value=0.0028  Score=54.95  Aligned_cols=77  Identities=16%  Similarity=0.265  Sum_probs=66.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCC--eeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGS--ILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~--v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..+||+||-..+|.+||.+.+.+.|.  +.++++.-++ .|.+||||+|...+.....+.++.|-...+.|+.-.|...+
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~N  160 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSYN  160 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeeccc
Confidence            36999999999999999999988873  5667777776 78999999999999999999999999999998777665444

>KOG1855|consensus

Probab=96.52  E-value=0.0039  Score=55.61  Aligned_cols=67  Identities=28%  Similarity=0.381  Sum_probs=55.7

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCC-----C--Cc--------cceEEEEEeCCHHHHHHHHHHhCCc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-----D--GK--------SRGFGFVAYESPEFAEKAVQAWNGK  266 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~-----~--~~--------~~g~afV~F~~~~~a~~a~~~l~g~  266 (336)
                      +.++|.+.|||.+-.-+.|.++|+.+|.|..|+|+.+     +  +.        .+-+|+|+|...+.|.+|.+.++..
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~e  309 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNPE  309 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhchh
Confidence            4588999999999888999999999999999999874     1  11        1457999999999999999987654


Q ss_pred             ee
Q psy12549        267 EV  268 (336)
Q Consensus       267 ~~  268 (336)
                      .-
T Consensus       310 ~~  311 (484)
T KOG1855|consen  310 QN  311 (484)
T ss_pred             hh
Confidence            43

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

Probab=95.96  E-value=0.053  Score=35.25  Aligned_cols=53  Identities=23%  Similarity=0.379  Sum_probs=43.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhcc----CCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHh
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAF----GSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV  171 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~----G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l  171 (336)
                      ..|+|+|+.. ++.++|+.+|..|    + ...+.++-|.      -|=|.|.+.+.|.+|+.+|
T Consensus         6 eavhirGvd~-lsT~dI~~y~~~y~~~~~-~~~IEWIdDt------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVDE-LSTDDIKAYFSEYFDEEG-PFRIEWIDDT------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCCC-CCHHHHHHHHHHhcccCC-CceEEEecCC------cEEEEECCHHHHHHHHHcC
Confidence            5699999955 8999999999999    4 4567777763      3779999999999999864

>KOG2591|consensus

Probab=95.95  E-value=0.014  Score=53.91  Aligned_cols=81  Identities=20%  Similarity=0.301  Sum_probs=62.3

Q ss_pred             eeccCCCC-ccccCc--e-eeeecCchhhhhhhHHhhhcc---cCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHH
Q psy12549          6 TVQLSEEG-IIIPKH--N-VATRELSAKVVEGVSRSLSSL---IDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTE   78 (336)
Q Consensus         6 ~~~~~~~~-~~~p~~--~-v~v~~lp~~~~e~~l~~~f~~---~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~   78 (336)
                      .|++++.| .++|.+  + |+++.||.+.-+++|+-+|+.   -.+.++.+-.+.+          .||+|++.  .||+
T Consensus       159 ~VqvDekgekVrp~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n----------WyITfesd--~DAQ  226 (684)
T KOG2591|consen  159 NVQVDEKGEKVRPNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN----------WYITFESD--TDAQ  226 (684)
T ss_pred             CceeccCccccccCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc----------eEEEeecc--hhHH
Confidence            45566555 455554  4 455999999999999999943   5667888777665          89999999  9999


Q ss_pred             HHHhhcCc--cccCCeeeEEEe
Q psy12549         79 RALDTMNF--DALKGRPIRIMW   98 (336)
Q Consensus        79 ~A~~~~~~--~~~~g~~i~v~~   98 (336)
                      .|.+.|..  ..|.|++|.-+.
T Consensus       227 qAykylreevk~fqgKpImARI  248 (684)
T KOG2591|consen  227 QAYKYLREEVKTFQGKPIMARI  248 (684)
T ss_pred             HHHHHHHHHHHhhcCcchhhhh
Confidence            99997766  478888876654

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

Probab=95.72  E-value=0.062  Score=36.94  Aligned_cols=55  Identities=24%  Similarity=0.420  Sum_probs=41.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCC
Q psy12549        112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG  173 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~  173 (336)
                      .||--..|..+...||.++|+.||.|. |..+.+      .-|||...+.+.|..++..++.
T Consensus        10 HVFhltFPkeWK~~DI~qlFspfG~I~-VsWi~d------TSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   10 HVFHLTFPKEWKTSDIYQLFSPFGQIY-VSWIND------TSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CEEEEE--TT--HHHHHHHCCCCCCEE-EEEECT------TEEEEEECCCHHHHHHHHHHTT
T ss_pred             eEEEEeCchHhhhhhHHHHhccCCcEE-EEEEcC------CcEEEEeecHHHHHHHHHHhcc
Confidence            455445999999999999999999876 555544      3699999999999999998753

; 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.

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=95.68  E-value=0.017  Score=46.66  Aligned_cols=68  Identities=10%  Similarity=0.209  Sum_probs=45.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhc-cCCe---eEEEEeeCC--C-CCcccEEEEEeCCHHHHHHHHHHhCCcee
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSA-FGSI---LSCKVAQDE--Q-GNSKGYGFVHFETEEAANKSIEKVNGMLL  176 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~-~G~v---~~~~~~~~~--~-~~~~g~afV~F~~~~~a~~a~~~l~~~~~  176 (336)
                      ...+|.|++||+++|++++.+.++. ++.-   ..+.-..+.  . ...-.-|||.|.+.+++......++|+.+
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F   80 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVF   80 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEE
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEE
Confidence            3468999999999999999997777 6654   233311221  1 12234699999999999999999999776

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.

>KOG2416|consensus

Probab=95.61  E-value=0.011  Score=54.97  Aligned_cols=77  Identities=8%  Similarity=-0.028  Sum_probs=60.1

Q ss_pred             ccccCceeeeecCchhhhhhhHHhhhc--ccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCcccc--
Q psy12549         14 IIIPKHNVATRELSAKVVEGVSRSLSS--LIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDAL--   89 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~~~e~~l~~~f~--~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~--   89 (336)
                      .-.++..|+|.||-...|..+|+.+..  .+.|++.+|.+-+         .+|||.|.+.  ++|.....+|+|..|  
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkIK---------ShCyV~yss~--eEA~atr~AlhnV~WP~  508 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKIK---------SHCYVSYSSV--EEAAATREALHNVQWPP  508 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHHhh---------cceeEecccH--HHHHHHHHHHhccccCC
Confidence            446778899999999999999999983  4456677555533         5599999999  999999999999877  


Q ss_pred             -CCeeeEEEeccC
Q psy12549         90 -KGRPIRIMWSQR  101 (336)
Q Consensus        90 -~g~~i~v~~~~~  101 (336)
                       +++.|.+.+...
T Consensus       509 sNPK~L~adf~~~  521 (718)
T KOG2416|consen  509 SNPKHLIADFVRA  521 (718)
T ss_pred             CCCceeEeeecch
Confidence             456666655433

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=95.50  E-value=0.058  Score=43.61  Aligned_cols=77  Identities=14%  Similarity=0.161  Sum_probs=52.4

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhcc-CCce---eEEE--EeC-CC-CccceEEEEEeCCHHHHHHHHHHhCCceecC-----
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEP-YGTI---TSYR--VMN-ND-GKSRGFGFVAYESPEFAEKAVQAWNGKEVDG-----  270 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~-~g~i---~~~~--i~~-~~-~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g-----  270 (336)
                      ..|.|++||+.+|++++.+.++. ++.-   ..+.  ... .. ......|||.|.+.+++..-...++|..|.+     
T Consensus         8 ~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~~   87 (176)
T PF03467_consen    8 TKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGNE   87 (176)
T ss_dssp             -EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-E
T ss_pred             ceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCCC
Confidence            57999999999999999998886 6665   2332  111 11 1124569999999999999999999998843     


Q ss_pred             EEEEEeeccc
Q psy12549        271 KILYVGRAQK  280 (336)
Q Consensus       271 ~~l~v~~~~~  280 (336)
                      .+..|++|.-
T Consensus        88 ~~~~VE~Apy   97 (176)
T PF03467_consen   88 YPAVVEFAPY   97 (176)
T ss_dssp             EEEEEEE-SS
T ss_pred             cceeEEEcch
Confidence            5677788765

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.

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

Probab=95.47  E-value=0.093  Score=36.08  Aligned_cols=56  Identities=20%  Similarity=0.418  Sum_probs=40.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCC
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG  265 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g  265 (336)
                      ..||--.+|..+...||.++|++||.|. |..+.     -..|||...+.+.|..|+..+.-
T Consensus         9 dHVFhltFPkeWK~~DI~qlFspfG~I~-VsWi~-----dTSAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    9 DHVFHLTFPKEWKTSDIYQLFSPFGQIY-VSWIN-----DTSAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             CCEEEEE--TT--HHHHHHHCCCCCCEE-EEEEC-----TTEEEEEECCCHHHHHHHHHHTT
T ss_pred             ceEEEEeCchHhhhhhHHHHhccCCcEE-EEEEc-----CCcEEEEeecHHHHHHHHHHhcc
Confidence            3466556999999999999999999873 33332     34599999999999999988753

; 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=95.41  E-value=0.049  Score=41.39  Aligned_cols=74  Identities=16%  Similarity=0.289  Sum_probs=56.0

Q ss_pred             cccceEEEcCCCCCC----cHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEe
Q psy12549        201 KLFTNVYIKNFGEDF----NDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG  276 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~----t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~  276 (336)
                      .+..+|.|+=|....    +...+...++.||+|.++-..-     +..|.|.|.+..+|-+|+.+++. ...|..+.+.
T Consensus        84 pPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-----rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCs  157 (166)
T PF15023_consen   84 PPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-----RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCS  157 (166)
T ss_pred             CCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-----CceEEEEehhhHHHHHHHHhhcC-CCCCceEEee
Confidence            344678886555543    3344566778999999998762     55699999999999999999876 6678888888


Q ss_pred             eccc
Q psy12549        277 RAQK  280 (336)
Q Consensus       277 ~~~~  280 (336)
                      |...
T Consensus       158 Wqqr  161 (166)
T PF15023_consen  158 WQQR  161 (166)
T ss_pred             cccc
Confidence            8653

>KOG2416|consensus

Probab=95.40  E-value=0.012  Score=54.76  Aligned_cols=77  Identities=22%  Similarity=0.264  Sum_probs=62.8

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhc-cCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCcee---cCEEEEEee
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFE-PYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEV---DGKILYVGR  277 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~-~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~---~g~~l~v~~  277 (336)
                      ..+.|+|.||-..+|.-+|+.++. ..|.|... ++.   +-+..|||.|.+.++|.....+|||..|   +++.|.+.|
T Consensus       443 ~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-WmD---kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf  518 (718)
T KOG2416|consen  443 PSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WMD---KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADF  518 (718)
T ss_pred             ccceEeeecccccchHHHHHHHHhhccCchHHH-HHH---HhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeee
Confidence            347899999999999999999998 66666655 222   1256699999999999999999999998   568999999


Q ss_pred             cccch
Q psy12549        278 AQKKA  282 (336)
Q Consensus       278 ~~~~~  282 (336)
                      .....
T Consensus       519 ~~~de  523 (718)
T KOG2416|consen  519 VRADE  523 (718)
T ss_pred             cchhH
Confidence            86543

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

Probab=95.38  E-value=0.052  Score=35.29  Aligned_cols=52  Identities=15%  Similarity=0.096  Sum_probs=42.6

Q ss_pred             eeeeecCchhhhhhhHHhhhccc----CCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhc
Q psy12549         20 NVATRELSAKVVEGVSRSLSSLI----DGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTM   84 (336)
Q Consensus        20 ~v~v~~lp~~~~e~~l~~~f~~~----~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~   84 (336)
                      .|.|+++. +++.+++..+|..+    .+..|..+.|..          |=|.|.+.  +.|.+|+..|
T Consensus         7 avhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDtS----------cNvvf~d~--~~A~~AL~~L   62 (62)
T PF10309_consen    7 AVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDTS----------CNVVFKDE--ETAARALVAL   62 (62)
T ss_pred             eEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCCc----------EEEEECCH--HHHHHHHHcC
Confidence            48999985 58889999999555    667888887764          89999999  9999999754

>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=95.23  E-value=0.19  Score=37.06  Aligned_cols=65  Identities=15%  Similarity=0.212  Sum_probs=49.8

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCC-ceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecC
Q psy12549        206 VYIKNFGEDFNDEKLKEMFEPYG-TITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG  270 (336)
Q Consensus       206 l~V~nlp~~~t~~~l~~~f~~~g-~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g  270 (336)
                      +.+...|..++.++|..+.+.+- .|..+++++....++-.+.+.|.+.++|+.-...+||+.|..
T Consensus        16 ~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   16 CCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             EEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            34444556666677776666654 466788887655678889999999999999999999999864

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2591|consensus

Probab=94.95  E-value=0.08  Score=49.12  Aligned_cols=95  Identities=11%  Similarity=0.197  Sum_probs=69.1

Q ss_pred             hhHHHHHhhcCccccCCeeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhc--cCCeeEEEEeeCCCCCccc
Q psy12549         75 LDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSA--FGSILSCKVAQDEQGNSKG  152 (336)
Q Consensus        75 ~~A~~A~~~~~~~~~~g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~--~G~v~~~~~~~~~~~~~~g  152 (336)
                      +--.++++...+..+..+-.+|++...        .|-|+++-||..+..++++.+|..  +-.+.+|.+-.+.      
T Consensus       148 dLI~Evlresp~VqvDekgekVrp~~k--------RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~------  213 (684)
T KOG2591|consen  148 DLIVEVLRESPNVQVDEKGEKVRPNHK--------RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND------  213 (684)
T ss_pred             HHHHHHHhcCCCceeccCccccccCcc--------eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC------
Confidence            445567777777777666666655422        256889999999999999999975  5567778776542      


Q ss_pred             EEEEEeCCHHHHHHHHHHhCC--ceeCCeEEEE
Q psy12549        153 YGFVHFETEEAANKSIEKVNG--MLLNSKIVFV  183 (336)
Q Consensus       153 ~afV~F~~~~~a~~a~~~l~~--~~~~~~~i~v  183 (336)
                      -.||+|++..||+.|.+.|.-  ..|.|++|..
T Consensus       214 nWyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  214 NWYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            489999999999999987643  3466665543

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.86  E-value=0.11  Score=39.51  Aligned_cols=71  Identities=18%  Similarity=0.268  Sum_probs=53.2

Q ss_pred             CceEEEcCCCCCC----CHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        110 VGNVFIKNLDKSI----DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       110 ~~~l~v~nlp~~~----t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      -.+|.|+=|..++    +...+...++.||+|.+|.+.-      +.-|.|.|.+..+|-+|+.++.. ...|..+.+.|
T Consensus        86 MsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qCsW  158 (166)
T PF15023_consen   86 MSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG------RQSAVVVFKDITSACKAVSAFQS-RAPGTMFQCSW  158 (166)
T ss_pred             ceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC------CceEEEEehhhHHHHHHHHhhcC-CCCCceEEeec
Confidence            3578887666555    3344556678899999998763      34699999999999999998766 55677777766


Q ss_pred             cc
Q psy12549        186 FI  187 (336)
Q Consensus       186 ~~  187 (336)
                      ..
T Consensus       159 qq  160 (166)
T PF15023_consen  159 QQ  160 (166)
T ss_pred             cc
Confidence            43

>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=94.74  E-value=0.049  Score=38.20  Aligned_cols=65  Identities=14%  Similarity=0.206  Sum_probs=45.9

Q ss_pred             EEEEeCCcchhhHHHHHhhcCc-cccCCeeeEEEeccCCCC-------cCCCCCceEEEcCCCCCCCHHHHHHHh
Q psy12549         65 ILVQLGQPYMLDTERALDTMNF-DALKGRPIRIMWSQRDPS-------LRKSGVGNVFIKNLDKSIDNKAMYDTF  131 (336)
Q Consensus        65 afV~f~~~~~~~A~~A~~~~~~-~~~~g~~i~v~~~~~~~~-------~~~~~~~~l~v~nlp~~~t~~~l~~~f  131 (336)
                      |.|+|..+  .-|+.-++.... ..+.+..+.|...+....       ......++|.|.|||...++++|++.+
T Consensus         1 AlITF~e~--~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~L   73 (88)
T PF07292_consen    1 ALITFEEE--GVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKL   73 (88)
T ss_pred             CEEEeCcH--HHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeE
Confidence            68999999  999998884443 355666666654322211       233456899999999999999998754

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>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=94.66  E-value=0.1  Score=42.34  Aligned_cols=63  Identities=30%  Similarity=0.361  Sum_probs=46.7

Q ss_pred             cHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhC--CceecCEEEEEeecccch
Q psy12549        216 NDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN--GKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       216 t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~--g~~~~g~~l~v~~~~~~~  282 (336)
                      ..+.|+++|..++.+..+..++.    =+-..|.|.+.++|.+|...|+  +..+.|..+++.|+....
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s----FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS----FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT----TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC----CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            34789999999999988888764    2338899999999999999999  999999999999985443

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.

>KOG0804|consensus

Probab=94.09  E-value=0.085  Score=47.75  Aligned_cols=68  Identities=15%  Similarity=0.237  Sum_probs=58.7

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCC-ceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecC
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYG-TITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG  270 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g-~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g  270 (336)
                      .+.|+|-.+|..++..||..+...+- .|.++++++..-.++-.+.|.|.+.++|..-...+||+.|..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            47799999999999999999997664 478999998544557779999999999999999999999864

>KOG2068|consensus

Probab=94.04  E-value=0.043  Score=47.82  Aligned_cols=80  Identities=16%  Similarity=0.313  Sum_probs=60.2

Q ss_pred             eEEEcCCCCCCCHHHH---HHHhhccCCeeEEEEeeCCC---C-CcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        112 NVFIKNLDKSIDNKAM---YDTFSAFGSILSCKVAQDEQ---G-NSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l---~~~f~~~G~v~~~~~~~~~~---~-~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      -+|+-+|+.....+++   .+.|.+||.+..+.+..+++   + ....-+||+|...++|..|+...+|...+|+.+...
T Consensus        79 lvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka~  158 (327)
T KOG2068|consen   79 LVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKAS  158 (327)
T ss_pred             hhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHHh
Confidence            4778888876655444   35688899999988888652   1 112249999999999999999999999999997776


Q ss_pred             eccCchh
Q psy12549        185 KFIPRKE  191 (336)
Q Consensus       185 ~~~~~~~  191 (336)
                      +..++..
T Consensus       159 ~gttkyc  165 (327)
T KOG2068|consen  159 LGTTKYC  165 (327)
T ss_pred             hCCCcch
Confidence            6555543

>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=93.95  E-value=0.32  Score=35.88  Aligned_cols=69  Identities=6%  Similarity=0.069  Sum_probs=47.7

Q ss_pred             ccCceeeeecCchhhhh-hhHHhhhccc--CCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCC
Q psy12549         16 IPKHNVATRELSAKVVE-GVSRSLSSLI--DGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKG   91 (336)
Q Consensus        16 ~p~~~v~v~~lp~~~~e-~~l~~~f~~~--~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g   91 (336)
                      ....++.+--.|+.++- ++|..+.+..  .+..++++++.     ..++.-+.+.|++.  ++|.......||..+..
T Consensus        10 ~~~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~-----~pnrymVLikF~~~--~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   10 ERRSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG-----TPNRYMVLIKFRDQ--ESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CCCceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC-----CCceEEEEEEECCH--HHHHHHHHHhCCCccCC
Confidence            33445555455555555 5555444333  55578888876     24777799999999  99999999999988864

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>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=93.51  E-value=0.64  Score=30.73  Aligned_cols=55  Identities=11%  Similarity=0.259  Sum_probs=44.8

Q ss_pred             CCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        121 SIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       121 ~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      .++-++++..+..|+..   ++..+++|     =||.|.+..+|++|....++..+.+..+.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~---~I~~d~tG-----fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWD---RIRDDRTG-----FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcc---eEEecCCE-----EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            57889999999999743   35566555     689999999999999999998887776654

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

>KOG4285|consensus

Probab=93.29  E-value=0.29  Score=42.08  Aligned_cols=73  Identities=22%  Similarity=0.299  Sum_probs=55.1

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCE-EEEEeecccch
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK-ILYVGRAQKKA  282 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~-~l~v~~~~~~~  282 (336)
                      .-|.|-++|..-. .-|...|++||.|......    .+..|-+|+|.+.-+|.+||.. +|..|+|. .|-|.....+.
T Consensus       198 ~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~----~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCtDks  271 (350)
T KOG4285|consen  198 TWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP----SNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCTDKS  271 (350)
T ss_pred             ceEEEeccCccch-hHHHHHHHhhCeeeeeecC----CCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecCCHH
Confidence            5678888887644 3677899999998655332    4466899999999999999986 99999874 45566655543

>KOG0804|consensus

Probab=93.07  E-value=0.85  Score=41.57  Aligned_cols=68  Identities=16%  Similarity=0.234  Sum_probs=58.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccC-CeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFG-SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNS  178 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G-~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~  178 (336)
                      .+.|+|-.+|..++..||-.+...+- .|..++++++..+ .+--+++.|.+.++|......+||..+..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p-nrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP-NRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC-ceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            57899999999999999999988765 5888999997543 45468999999999999999999987643

>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=92.76  E-value=0.16  Score=35.62  Aligned_cols=71  Identities=17%  Similarity=0.194  Sum_probs=44.7

Q ss_pred             EEEEeCCHHHHHHHHHHhCCc--eeCCeEEEEeeccCchhhhHhhh-ccccccceEEEcCCCCCCcHHHHHHhhc
Q psy12549        154 GFVHFETEEAANKSIEKVNGM--LLNSKIVFVGKFIPRKEREKELG-EKAKLFTNVYIKNFGEDFNDEKLKEMFE  225 (336)
Q Consensus       154 afV~F~~~~~a~~a~~~l~~~--~~~~~~i~v~~~~~~~~~~~~~~-~~~~~~~~l~V~nlp~~~t~~~l~~~f~  225 (336)
                      |+|+|.++.-|++.++. ..+  .+.+..+.|....-......... ......++|.|.|||....+++|++..+
T Consensus         1 AlITF~e~~VA~~i~~~-~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKK-KKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             CEEEeCcHHHHHHHHhC-CEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeEE
Confidence            68999999999999883 333  35666665533221111111111 1122337899999999999999987654

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2068|consensus

Probab=92.59  E-value=0.047  Score=47.61  Aligned_cols=79  Identities=24%  Similarity=0.349  Sum_probs=59.5

Q ss_pred             ceEEEcCCCCCCcHHHHH---HhhccCCceeEEEEeCCC-----CccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEE
Q psy12549        204 TNVYIKNFGEDFNDEKLK---EMFEPYGTITSYRVMNND-----GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV  275 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~---~~f~~~g~i~~~~i~~~~-----~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v  275 (336)
                      +-+||.+|+.....+.+.   +.|.+||.|..+.+....     ....--++|+|...++|..||...+|....|+.++.
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            457888888776555543   578889999888776622     111223899999999999999999999999999888


Q ss_pred             eecccch
Q psy12549        276 GRAQKKA  282 (336)
Q Consensus       276 ~~~~~~~  282 (336)
                      .+...+.
T Consensus       158 ~~gttky  164 (327)
T KOG2068|consen  158 SLGTTKY  164 (327)
T ss_pred             hhCCCcc
Confidence            7766553

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=91.30  E-value=0.24  Score=38.91  Aligned_cols=121  Identities=14%  Similarity=0.121  Sum_probs=78.6

Q ss_pred             CCCHHHHHHHhhc-cCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchhhhHhhhcc
Q psy12549        121 SIDNKAMYDTFSA-FGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEK  199 (336)
Q Consensus       121 ~~t~~~l~~~f~~-~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~  199 (336)
                      ..+-..|.+.+.. ++....+.+..-    ..++..++|.+.+++.+++. .....+.+..+.+....+.........  
T Consensus        28 ~~~~~~l~~~l~~~W~~~~~~~i~~l----~~~~fl~~F~~~~d~~~vl~-~~p~~~~~~~~~l~~W~~~~~~~~~~~--  100 (153)
T PF14111_consen   28 PISLSALEQELAKIWKLKGGVKIRDL----GDNLFLFQFESEEDRQRVLK-GGPWNFNGHFLILQRWSPDFNPSEVKF--  100 (153)
T ss_pred             CCCHHHHHHHHHHHhCCCCcEEEEEe----CCCeEEEEEEeccceeEEEe-cccccccccchhhhhhcccccccccce--
Confidence            3556666666544 333223333332    23589999999999999998 466778888888877765433221111  


Q ss_pred             ccccceEEEcCCCCC-CcHHHHHHhhccCCceeEEEEeCCCCccceEEEE
Q psy12549        200 AKLFTNVYIKNFGED-FNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFV  248 (336)
Q Consensus       200 ~~~~~~l~V~nlp~~-~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV  248 (336)
                      .....-|.|.|||.. .+++-++.+.+.+|.+..++..........||-|
T Consensus       101 ~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~t~~~~~~~~~Rv  150 (153)
T PF14111_consen  101 EHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDENTLKRTRLDFARV  150 (153)
T ss_pred             eccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcCCCCcccccEEEE
Confidence            111245788999976 7888899999999999888876543333445544

>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=91.04  E-value=0.85  Score=37.08  Aligned_cols=61  Identities=20%  Similarity=0.169  Sum_probs=45.7

Q ss_pred             CHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhC--CceeCCeEEEEeeccC
Q psy12549        123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN--GMLLNSKIVFVGKFIP  188 (336)
Q Consensus       123 t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~--~~~~~~~~i~v~~~~~  188 (336)
                      ..+.|+++|..++.+......+.     -+-..|.|.+.++|..|...|+  +..+.|..+.+-++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s-----FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS-----FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT-----TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC-----CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            45789999999999888877764     3468999999999999999999  8999999999977643

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.

>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=90.86  E-value=10  Score=32.91  Aligned_cols=158  Identities=13%  Similarity=0.226  Sum_probs=96.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC--------CCCcccEEEEEeCCHHHHHHHHHH----hCC--
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE--------QGNSKGYGFVHFETEEAANKSIEK----VNG--  173 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~--------~~~~~g~afV~F~~~~~a~~a~~~----l~~--  173 (336)
                      ...+.|.+.|+..+++-..+...|-+||+|+++.++.+.        .........+.|-+.+.+-.....    |.-  
T Consensus        13 YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK   92 (309)
T PF10567_consen   13 YRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFK   92 (309)
T ss_pred             ceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHH
Confidence            345789999999999999999999999999999999875        223345788999998887654432    221  


Q ss_pred             ceeCCeEEEEeeccC-----ch--h--hh------Hhhh---ccccccceEEEcCCCCCCcHHHH-HH---hhccCC---
Q psy12549        174 MLLNSKIVFVGKFIP-----RK--E--RE------KELG---EKAKLFTNVYIKNFGEDFNDEKL-KE---MFEPYG---  228 (336)
Q Consensus       174 ~~~~~~~i~v~~~~~-----~~--~--~~------~~~~---~~~~~~~~l~V~nlp~~~t~~~l-~~---~f~~~g---  228 (336)
                      ..+....+.+.+..-     ..  .  ..      +...   ......+.|.|. +...+..+++ .+   +...-+   
T Consensus        93 ~~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~Ie-F~~~~~~~dl~~~kL~fL~~~~n~R  171 (309)
T PF10567_consen   93 TKLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIE-FKDPVDKDDLIEKKLPFLKNSNNKR  171 (309)
T ss_pred             HhcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEE-ecCccchhHHHHHhhhhhccCCCce
Confidence            224444554443221     10  0  00      0000   011223556664 2334433332 22   222222   


Q ss_pred             -ceeEEEEeC----CCCccceEEEEEeCCHHHHHHHHHHhCCc
Q psy12549        229 -TITSYRVMN----NDGKSRGFGFVAYESPEFAEKAVQAWNGK  266 (336)
Q Consensus       229 -~i~~~~i~~----~~~~~~g~afV~F~~~~~a~~a~~~l~g~  266 (336)
                       -++++.++.    ...-+..||.++|-+...|...+..+...
T Consensus       172 YVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk~~  214 (309)
T PF10567_consen  172 YVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLKSN  214 (309)
T ss_pred             EEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHHhc
Confidence             366788887    23335789999999999999988877633

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.

>KOG2135|consensus

Probab=88.77  E-value=0.28  Score=44.77  Aligned_cols=72  Identities=18%  Similarity=0.253  Sum_probs=57.7

Q ss_pred             EEEcCCCCCC-CHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCch
Q psy12549        113 VFIKNLDKSI-DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRK  190 (336)
Q Consensus       113 l~v~nlp~~~-t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~  190 (336)
                      |-+.-.|... +..+|...|.+||.|..|.+-..     .-.|.|+|.+..+|-.|.. .++..+.++.|++.|.++..
T Consensus       375 l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~-----~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  375 LALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS-----SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             hhhhccCCCCchHhhhhhhhhhcCccccccccCc-----hhhheeeeeccccccchhc-cccceecCceeEEEEecCCc
Confidence            4444445543 66789999999999999887654     2369999999999977777 58999999999999988764

>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=88.27  E-value=1.9  Score=29.21  Aligned_cols=59  Identities=29%  Similarity=0.436  Sum_probs=35.2

Q ss_pred             CCCcHHHHHHhhccCC-----ceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        213 EDFNDEKLKEMFEPYG-----TITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       213 ~~~t~~~l~~~f~~~g-----~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ..++..+|..++..-+     .|-.+++.      ..|+||+-.. +.|..++..|++..+.|+.+.|+.|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~------~~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIF------DNFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-------SS-EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEe------eeEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            3466777777776554     35577775      5679998875 5789999999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>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=87.92  E-value=3.2  Score=28.11  Aligned_cols=60  Identities=20%  Similarity=0.314  Sum_probs=36.9

Q ss_pred             CCCCCHHHHHHHhhccCC-----eeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        119 DKSIDNKAMYDTFSAFGS-----ILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       119 p~~~t~~~l~~~f~~~G~-----v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      -..++..+|..++..-+.     |-.+.+..+       |+||+-+.. .|..+++.|++..+.|+++.++.+
T Consensus        10 ~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~-------~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   10 KDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN-------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS--------EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             ccCCCHHHHHHHHHhccCCCHHhEEEEEEeee-------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            356788899999887653     556777654       899988766 788899999999999999998753

; PDB: 2G0C_A 3MOJ_B.

>KOG2135|consensus

Probab=85.82  E-value=0.49  Score=43.26  Aligned_cols=70  Identities=13%  Similarity=0.166  Sum_probs=55.3

Q ss_pred             EEEcCCCCCC-cHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        206 VYIKNFGEDF-NDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       206 l~V~nlp~~~-t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      +-+.-.|... +-++|-..|.+||.|..|.+-..    .-.|.|+|.+..+|-+|.. .++..|+++.|+|.|-.+
T Consensus       375 l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~----~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  375 LALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS----SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             hhhhccCCCCchHhhhhhhhhhcCccccccccCc----hhhheeeeeccccccchhc-cccceecCceeEEEEecC
Confidence            4444444443 55789999999999999988643    3348999999999977876 589999999999998765

>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=85.27  E-value=7.9  Score=25.59  Aligned_cols=56  Identities=16%  Similarity=0.165  Sum_probs=43.8

Q ss_pred             CCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEE
Q psy12549        213 EDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV  275 (336)
Q Consensus       213 ~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v  275 (336)
                      ..++.++++..+..|+-. ++..-     .+| -||.|.+..+|+++....+|..+.+..|.+
T Consensus        10 ~~~~v~d~K~~Lr~y~~~-~I~~d-----~tG-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   10 HGVTVEDFKKRLRKYRWD-RIRDD-----RTG-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CCccHHHHHHHHhcCCcc-eEEec-----CCE-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            356778999999999743 33321     144 589999999999999999999999888765

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

>KOG4574|consensus

Probab=84.35  E-value=0.6  Score=45.83  Aligned_cols=74  Identities=24%  Similarity=0.327  Sum_probs=60.7

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCcee--cCEEEEEeecccch
Q psy12549        205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEV--DGKILYVGRAQKKA  282 (336)
Q Consensus       205 ~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~--~g~~l~v~~~~~~~  282 (336)
                      +..+.|.+-..+-..|..+|+.||.+.+....++    -..|.|.|.+.+.|..|+++++|+..  -|-+.+|.+++.-.
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 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD----LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTLP  375 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccc----ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccccc
Confidence            3455666667777889999999999998887764    44599999999999999999999986  57788998886544

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=82.81  E-value=1.5  Score=34.36  Aligned_cols=80  Identities=15%  Similarity=0.015  Sum_probs=57.6

Q ss_pred             eEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEEeccCCCCcCCCC----CceEEEcCCCCC-CCHHHHHHHhhccCCe
Q psy12549         63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSG----VGNVFIKNLDKS-IDNKAMYDTFSAFGSI  137 (336)
Q Consensus        63 g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~~~~~~~~~~~~~----~~~l~v~nlp~~-~t~~~l~~~f~~~G~v  137 (336)
                      ++..++|.++  +++.++++ ...-.+.|..+.+..-.+........    ..=|.|.|||.. .+++-+..+-+.+|.+
T Consensus        56 ~~fl~~F~~~--~d~~~vl~-~~p~~~~~~~~~l~~W~~~~~~~~~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~  132 (153)
T PF14111_consen   56 NLFLFQFESE--EDRQRVLK-GGPWNFNGHFLILQRWSPDFNPSEVKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEP  132 (153)
T ss_pred             CeEEEEEEec--cceeEEEe-cccccccccchhhhhhcccccccccceeccchhhhhccCCHHHhhhHHHHHHHHhcCCe
Confidence            5689999999  99998888 55566778777776544332222111    223778899987 6778899999999998


Q ss_pred             eEEEEeeC
Q psy12549        138 LSCKVAQD  145 (336)
Q Consensus       138 ~~~~~~~~  145 (336)
                      ..+.....
T Consensus       133 i~vD~~t~  140 (153)
T PF14111_consen  133 IEVDENTL  140 (153)
T ss_pred             EEEEcCCC
Confidence            88775543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	336
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		4e-56
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		5e-19
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		3e-09
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		5e-56
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		5e-19
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		4e-09
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		4e-41
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		2e-11
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		7e-38
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		2e-10
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		2e-18
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		5e-13
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		5e-17
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		1e-07
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		6e-17
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		4e-08
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		4e-16
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		5e-07
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		2e-15
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		9e-08
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		7e-15
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-06
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		1e-14
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		8e-06
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		1e-14
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		8e-06
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		1e-14
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		4e-07
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		6e-14
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		1e-06
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		9e-13
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-12
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		3e-06
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		3e-12
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		2e-06
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		9e-09
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-06
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		1e-08
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		2e-06
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		1e-08
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		2e-06
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-08
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-06
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-08
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		2e-06
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		1e-08
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		2e-06
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		9e-08
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-07
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		1e-07
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		2e-07
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		2e-07
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		2e-07
1x5o_A	114	Solution Structure Of Rrm Domain In Rna Binding Mot		2e-07
1fje_B	175	Solution Structure Of Nucleolin Rbd12 In Complex Wi		3e-07
2khc_A	118	Bruno Rrm3+ Length = 118		9e-07
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-06
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-06
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		2e-06
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		2e-06
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		2e-06
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-06
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		3e-06
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		4e-05
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		3e-06
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		5e-06
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		9e-06
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		1e-05
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		1e-05
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		1e-05
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		4e-04
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		1e-05
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		2e-05
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		2e-04
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		2e-05
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		9e-04
2krr_A	180	Solution Structure Of The Rbd1,2 Domains From Human		2e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		3e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		6e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		4e-05
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		4e-05
2jvo_A	108	Segmental Isotope Labeling Of Npl3 Length = 108		5e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		5e-05
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		7e-05
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-04
2dhg_A	104	Solution Structure Of The C-Terminal Rna Recognitio		8e-05
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		8e-05
1sxl_A	97	Resonance Assignments And Solution Structure Of The		9e-05
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		1e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		1e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		7e-04
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		1e-04
1fjc_A	96	Solution Structure Of Nucleolin Rbd2 Length = 96		2e-04
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		2e-04
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		2e-04
2ywk_A	95	Crystal Structure Of Rrm-Domain Derived From Human		2e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		2e-04
2osq_A	74	Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length		2e-04
2dno_A	102	Solution Structure Of Rna Binding Domain In Trinucl		2e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		3e-04
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		3e-04
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		3e-04
1x4g_A	109	Solution Structure Of Rrm Domain In Nucleolysin Tia		3e-04
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-04
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-04
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		5e-04
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		6e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		8e-04
1no8_A	106	Solution Structure Of The Nuclear Factor Aly Rbd Do		9e-04

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score =  214 bits (546), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 105/141 (74%), Positives = 118/141 (83%), Gaps = 3/141 (2%)
Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KG+P+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct: 53  GYAYVNFQQP--ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 110
Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+EAA ++IEK+NGMLLN + VF
Sbjct: 111 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169
Query: 183 VGKFIPRKEREKELGEKAKLF 203
           VG+F  RKERE ELG +AK F
Sbjct: 170 VGRFKSRKEREAELGARAKEF 190

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 91.7 bits (226), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 54/191 (28%), Positives = 105/191 (54%), Gaps = 7/191 (3%)
Query: 102 DPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFET 160
           +PS     + ++++ +L   +    +Y+ FS  G ILS +V +D     S GY +V+F+ 
Sbjct: 2   NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 61
Query: 161 EEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKL 220
              A ++++ +N  ++  K V     I   +R+  L +      N++IKN  +  +++ L
Sbjct: 62  PADAERALDTMNFDVIKGKPVR----IMWSQRDPSLRKSG--VGNIFIKNLDKSIDNKAL 115
Query: 221 KEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK 280
            + F  +G I S +V+ ++  S+G+GFV +E+ E AE+A++  NG  ++ + ++VGR + 
Sbjct: 116 YDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 175
Query: 281 KAERTQELKRR 291
           + ER  EL  R
Sbjct: 176 RKEREAELGAR 186

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 40/136 (29%), Positives = 64/136 (47%), Gaps = 20/136 (14%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
            ++Y+ +   D  +  L E F P G I S RV  +    +S G+ +V ++ P  AE+A+ 
Sbjct: 11  ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGV-NLYVKNLDDSIDDE 320
             N   + GK + +  +Q+                     R  GV N+++KNLD SID++
Sbjct: 71  TMNFDVIKGKPVRIMWSQRDPSL-----------------RKSGVGNIFIKNLDKSIDNK 113
Query: 321 RLRKEFTPFGTITSAK 336
            L   F+ FG I S K
Sbjct: 114 ALYDTFSAFGNILSCK 129

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score =  214 bits (545), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 105/141 (74%), Positives = 118/141 (83%), Gaps = 3/141 (2%)
Query: 63  GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSI 122
           G   V   QP   D ERALDTMNFD +KG+P+RIMWSQRDPSLRKSGVGN+FIKNLDKSI
Sbjct: 58  GYAYVNFQQP--ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 115
Query: 123 DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF 182
           DNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+EAA ++IEK+NGMLLN + VF
Sbjct: 116 DNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 174
Query: 183 VGKFIPRKEREKELGEKAKLF 203
           VG+F  RKERE ELG +AK F
Sbjct: 175 VGRFKSRKEREAELGARAKEF 195

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 91.7 bits (226), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 54/191 (28%), Positives = 105/191 (54%), Gaps = 7/191 (3%)
Query: 102 DPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFET 160
           +PS     + ++++ +L   +    +Y+ FS  G ILS +V +D     S GY +V+F+ 
Sbjct: 7   NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 161 EEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKL 220
              A ++++ +N  ++  K V     I   +R+  L +      N++IKN  +  +++ L
Sbjct: 67  PADAERALDTMNFDVIKGKPVR----IMWSQRDPSLRKSG--VGNIFIKNLDKSIDNKAL 120
Query: 221 KEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK 280
            + F  +G I S +V+ ++  S+G+GFV +E+ E AE+A++  NG  ++ + ++VGR + 
Sbjct: 121 YDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 180
Query: 281 KAERTQELKRR 291
           + ER  EL  R
Sbjct: 181 RKEREAELGAR 191

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 58.9 bits (141), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 40/137 (29%), Positives = 64/137 (46%), Gaps = 20/137 (14%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
             ++Y+ +   D  +  L E F P G I S RV  +    +S G+ +V ++ P  AE+A+
Sbjct: 15  MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 261 QAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGV-NLYVKNLDDSIDD 319
              N   + GK + +  +Q+                     R  GV N+++KNLD SID+
Sbjct: 75  DTMNFDVIKGKPVRIMWSQRDPSL-----------------RKSGVGNIFIKNLDKSIDN 117
Query: 320 ERLRKEFTPFGTITSAK 336
           + L   F+ FG I S K
Sbjct: 118 KALYDTFSAFGNILSCK 134

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score =  165 bits (417), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 81/104 (77%), Positives = 91/104 (87%), Gaps = 1/104 (0%)
Query: 109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSI 168
           G GN+FIKNLDKSIDNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+EAA ++I
Sbjct: 4   GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAI 62
Query: 169 EKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFG 212
           EK+NGMLLN + VFVG+F  RKERE ELG +AK FTNVYIKNFG
Sbjct: 63  EKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFG 106

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 66.6 bits (161), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 34/109 (31%), Positives = 63/109 (57%), Gaps = 10/109 (9%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           N++IKN  +  +++ L + F  +G I S +V+ ++  S+G+GFV +E+ E AE+A++  N
Sbjct: 7   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 66
Query: 265 GKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNL 313
           G  ++ + ++VGR + + ER  EL  R +             N+Y+KN 
Sbjct: 67  GMLLNDRKVFVGRFKSRKEREAELGARAKEF----------TNVYIKNF 105

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score =  154 bits (389), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 75/94 (79%), Positives = 84/94 (89%), Gaps = 1/94 (1%)
Query: 102 DPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETE 161
           DPSLRKSGVGN+FIKNLDKSIDNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+
Sbjct: 3   DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQ 61
Query: 162 EAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKE 195
           EAA ++IEK+NGMLLN + VFVG+F  RKERE E
Sbjct: 62  EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 95

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 54/83 (65%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           N++IKN  +  +++ L + F  +G I S +V+ ++  S+G+GFV +E+ E AE+A++  N
Sbjct: 13  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 72
Query: 265 GKEVDGKILYVGRAQKKAERTQE 287
           G  ++ + ++VGR + + ER  E
Sbjct: 73  GMLLNDRKVFVGRFKSRKEREAE 95

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 89.7 bits (221), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 42/80 (52%), Positives = 56/80 (70%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           N+Y+KN  +  +DE+L++ F P+GTITS +VM   G+S+GFGFV + SPE A KAV   N
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 265 GKEVDGKILYVGRAQKKAER 284
           G+ V  K LYV  AQ+K ER
Sbjct: 77  GRIVATKPLYVALAQRKEER 96

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 72.0 bits (175), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 32/39 (82%), Positives = 35/39 (89%)
Query: 298 ERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           +R+ RYQ VNLYVKNLDD IDDERLRK F+PFGTITSAK
Sbjct: 8   DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAK 46

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 85.1 bits (209), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 48/172 (27%), Positives = 95/172 (55%), Gaps = 6/172 (3%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV 171
           V++ ++   +    +   F+ FG I S  ++ D      KG+ FV +E  EAA  ++E++
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 172 NGMLLNSKIVFVGKFIPRKEREK---ELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYG 228
           N ++L  + + VG+     + +    +L E+A+ F  +Y+ +  +D +D+ +K +FE +G
Sbjct: 76  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 229 TITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA 278
            I S  +  +   GK +G+GF+ YE  + ++ AV + N  ++ G+ L VG+A
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 72/154 (46%), Gaps = 27/154 (17%)
Query: 191 EREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG---KSRGFGF 247
           +R++ L     +   VY+ +   +  ++ +++ F P+G I S   M+ D    K +GF F
Sbjct: 5   QRQRALA----IMCRVYVGSIYYELGEDTIRQAFAPFGPIKSID-MSWDSVTMKHKGFAF 59
Query: 248 VAYESPEFAEKAVQAWNGKEVDGKILYVGR------AQKKAERTQELKRRFEMLKIERLN 301
           V YE PE A+ A++  N   + G+ + VGR      AQ   ++  E  R F        N
Sbjct: 60  VEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF--------N 111
Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSA 335
           R     +YV ++   + D+ ++  F  FG I S 
Sbjct: 112 R-----IYVASVHQDLSDDDIKSVFEAFGKIKSC 140

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 84.7 bits (208), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 48/172 (27%), Positives = 95/172 (55%), Gaps = 6/172 (3%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV 171
           V++ ++   +    +   F+ FG I S  ++ D      KG+ FV +E  EAA  ++E++
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 172 NGMLLNSKIVFVGKFIPRKEREK---ELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYG 228
           N ++L  + + VG+     + +    +L E+A+ F  +Y+ +  +D +D+ +K +FE +G
Sbjct: 91  NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 229 TITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA 278
            I S  +  +   GK +G+GF+ YE  + ++ AV + N  ++ G+ L VG+A
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 55.5 bits (132), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 41/143 (28%), Positives = 69/143 (48%), Gaps = 23/143 (16%)
Query: 202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG---KSRGFGFVAYESPEFAEK 258
           + + VY+ +   +  ++ +++ F P+G I S   M+ D    K +GF FV YE PE A+ 
Sbjct: 27  IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSID-MSWDSVTMKHKGFAFVEYEVPEAAQL 85
Query: 259 AVQAWNGKEVDGKILYVGR------AQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKN 312
           A++  N   + G+ + VGR      AQ   ++  E  R F        NR     +YV +
Sbjct: 86  ALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF--------NR-----IYVAS 132
Query: 313 LDDSIDDERLRKEFTPFGTITSA 335
           +   + D+ ++  F  FG I SA
Sbjct: 133 VHQDLSDDDIKSVFEAFGKIKSA 155

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 82.0 bits (201), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 48/172 (27%), Positives = 92/172 (53%), Gaps = 6/172 (3%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV 171
           V++ ++   +    +   F+ FG I S   + D      KG+ FV +E  EAA  ++E+ 
Sbjct: 15  VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 172 NGMLLNSKIVFVGKFIPRKEREK---ELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYG 228
           N + L  + + VG+     + +    +L E+A+ F  +Y+ +  +D +D+ +K +FE +G
Sbjct: 75  NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 229 TITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA 278
            I S  +  +   GK +G+GF+ YE  + ++ AV + N  ++ G+ L VG+A
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 41/153 (26%), Positives = 68/153 (44%), Gaps = 25/153 (16%)
Query: 191 EREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFV 248
           +R++ L    +++        GED     +++ F P+G I S     +    K +GF FV
Sbjct: 4   QRQRALAIXCRVYVGSIYYELGED----TIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFV 59
Query: 249 AYESPEFAEKAVQAWNGKEVDGKILYVGR------AQKKAERTQELKRRFEMLKIERLNR 302
            YE PE A+ A++  N   + G+ + VGR      AQ   ++  E  R F        NR
Sbjct: 60  EYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF--------NR 111
Query: 303 YQGVNLYVKNLDDSIDDERLRKEFTPFGTITSA 335
                +YV ++   + D+ ++  F  FG I S 
Sbjct: 112 -----IYVASVHQDLSDDDIKSVFEAFGKIKSC 139

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 46/156 (29%), Positives = 82/156 (52%), Gaps = 11/156 (7%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L + + ++ +Y  F A G I +C++ +D + G S GY FV F +E  + ++I+ 
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTI 230
           +NG+ + +K + V    P  E  K+        TN+Y+ N      D++L  +F  YG+I
Sbjct: 65  LNGITVRNKRLKVSYARPGGESIKD--------TNLYVTNLPRTITDDQLDTIFGKYGSI 116
Query: 231 TSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWN 264
               ++ +   G+ RG  FV Y   E A++A+ A N
Sbjct: 117 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 37/131 (28%), Positives = 60/131 (45%), Gaps = 20/131 (15%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    +D  D +L  +F   G I + R+M +   G S G+ FV + S   +++A++
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
             NG  V  K L V  A+   E  ++                   NLYV NL  +I D++
Sbjct: 64  VLNGITVRNKRLKVSYARPGGESIKD------------------TNLYVTNLPRTITDDQ 105
Query: 322 LRKEFTPFGTI 332
           L   F  +G+I
Sbjct: 106 LDTIFGKYGSI 116

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 78.2 bits (191), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 46/156 (29%), Positives = 81/156 (51%), Gaps = 11/156 (7%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L +   ++ +Y  F A G I +C++ +D + G S GY FV F +E  + ++I+ 
Sbjct: 16  NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTI 230
           +NG+ + +K + V    P  E  K+        TN+Y+ N      D++L  +F  YG+I
Sbjct: 76  LNGITVRNKRLKVSYARPGGESIKD--------TNLYVTNLPRTITDDQLDTIFGKYGSI 127
Query: 231 TSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWN 264
               ++ +   G+ RG  FV Y   E A++A+ A N
Sbjct: 128 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 36/131 (27%), Positives = 59/131 (45%), Gaps = 20/131 (15%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    +D  D +L  +F   G I + R+  +   G S G+ FV + S   +++A++
Sbjct: 15  TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
             NG  V  K L V  A+   E  ++                   NLYV NL  +I D++
Sbjct: 75  VLNGITVRNKRLKVSYARPGGESIKD------------------TNLYVTNLPRTITDDQ 116
Query: 322 LRKEFTPFGTI 332
           L   F  +G+I
Sbjct: 117 LDTIFGKYGSI 127

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 77.0 bits (188), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 48/165 (29%), Positives = 85/165 (51%), Gaps = 11/165 (6%)
Query: 109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKS 167
           G  N+ +  L +++    +   FS+ G + S K+ +D+  G+S GYGFV++ T + A ++
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPY 227
           I  +NG+ L SK + V    P  E  K+         N+YI         + +++MF  +
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSSEVIKD--------ANLYISGLPRTMTQKDVEDMFSRF 112
Query: 228 GTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
           G I + RV+     G SRG  F+ ++    AE+A+ ++NG +  G
Sbjct: 113 GRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPG 157

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 47.8 bits (112), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 30/135 (22%), Positives = 63/135 (46%), Gaps = 20/135 (14%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    ++   ++L+ +F   G + S +++ +   G S G+GFV Y + + AE+A+ 
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
             NG  +  K + V  A+  +E  ++                   NLY+  L  ++  + 
Sbjct: 63  TLNGLRLQSKTIKVSYARPSSEVIKD------------------ANLYISGLPRTMTQKD 104
Query: 322 LRKEFTPFGTITSAK 336
           +   F+ FG I +++
Sbjct: 105 VEDMFSRFGRIINSR 119

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 77.0 bits (188), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 48/165 (29%), Positives = 85/165 (51%), Gaps = 11/165 (6%)
Query: 109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKS 167
           G  N+ +  L +++    +   FS+ G + S K+ +D+  G+S GYGFV++ T + A ++
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPY 227
           I  +NG+ L SK + V    P  E  K+         N+YI         + +++MF  +
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSSEVIKD--------ANLYISGLPRTMTQKDVEDMFSRF 112
Query: 228 GTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
           G I + RV+     G SRG  F+ ++    AE+A+ ++NG +  G
Sbjct: 113 GRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPG 157

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 48.1 bits (113), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 30/135 (22%), Positives = 63/135 (46%), Gaps = 20/135 (14%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    ++   ++L+ +F   G + S +++ +   G S G+GFV Y + + AE+A+ 
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
             NG  +  K + V  A+  +E  ++                   NLY+  L  ++  + 
Sbjct: 63  TLNGLRLQSKTIKVSYARPSSEVIKD------------------ANLYISGLPRTMTQKD 104
Query: 322 LRKEFTPFGTITSAK 336
           +   F+ FG I +++
Sbjct: 105 VEDMFSRFGRIINSR 119

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 77.0 bits (188), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 45/162 (27%), Positives = 85/162 (52%), Gaps = 11/162 (6%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L +++  +     F + G I SCK+ +D+  G S GYGFV++   + A K+I  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTI 230
           +NG+ L +K + V    P     ++         N+Y+    +    ++L+++F  YG I
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASIRD--------ANLYVSGLPKTMTQKELEQLFSQYGRI 115
Query: 231 TSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
            + R++ +   G SRG GF+ ++    AE+A++  NG++  G
Sbjct: 116 ITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 33/135 (24%), Positives = 63/135 (46%), Gaps = 20/135 (14%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    ++   E+ + +F   G I S +++ +   G+S G+GFV Y  P+ AEKA+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
             NG  +  K + V  A+  +   ++                   NLYV  L  ++  + 
Sbjct: 63  TLNGLRLQTKTIKVSYARPSSASIRD------------------ANLYVSGLPKTMTQKE 104
Query: 322 LRKEFTPFGTITSAK 336
           L + F+ +G I +++
Sbjct: 105 LEQLFSQYGRIITSR 119

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 75.1 bits (183), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 44/162 (27%), Positives = 84/162 (51%), Gaps = 11/162 (6%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L +++        F + G I SCK+ +D+  G S GYGFV++     A+K+I  
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTI 230
           +NG+ L +K + V    P     ++         N+Y+    +  + ++++++F  YG I
Sbjct: 66  LNGLKLQTKTIKVSYARPSSASIRD--------ANLYVSGLPKTMSQKEMEQLFSQYGRI 117
Query: 231 TSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
            + R++     G SRG GF+ ++    AE+A++  NG++  G
Sbjct: 118 ITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLG 159

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/135 (22%), Positives = 63/135 (46%), Gaps = 20/135 (14%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    ++   ++ K +F   G I S +++ +   G+S G+GFV Y  P  A+KA+ 
Sbjct: 5   TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
             NG ++  K + V  A+  +   ++                   NLYV  L  ++  + 
Sbjct: 65  TLNGLKLQTKTIKVSYARPSSASIRD------------------ANLYVSGLPKTMSQKE 106
Query: 322 LRKEFTPFGTITSAK 336
           + + F+ +G I +++
Sbjct: 107 MEQLFSQYGRIITSR 121

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 70.9 bits (172), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 37/78 (47%), Positives = 54/78 (69%), Gaps = 2/78 (2%)
Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSIL-SCKVAQD-EQGNSKGYGFVHFETEEAAN 165
           SG   +FI NLD  ID K +YDTFSAFG IL + K+ +D + GNSKGY F++F + +A++
Sbjct: 3   SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 166 KSIEKVNGMLLNSKIVFV 183
            +IE +NG  L ++ + V
Sbjct: 63  AAIEAMNGQYLCNRPITV 80

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 42/148 (28%), Positives = 79/148 (53%), Gaps = 15/148 (10%)
Query: 117 NLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGML 175
           N D + DN   Y  F  +G++   K+ +D   G S+G+GF+ FE   + ++ ++  +  +
Sbjct: 12  NWDTTEDNLREY--FGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH--I 67
Query: 176 LNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV 235
           L+ K++   + IPR E++K           +++   G D   ++ +E F  +GTI   ++
Sbjct: 68  LDGKVIDPKRAIPRDEQDKT--------GKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQL 119
Query: 236 M--NNDGKSRGFGFVAYESPEFAEKAVQ 261
           M   + G+SRGFGFV Y+S +  ++  Q
Sbjct: 120 MLDKDTGQSRGFGFVTYDSADAVDRVCQ 147

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 48/83 (57%), Gaps = 4/83 (4%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
             ++I     D  ++ L+E F  YGT+T  ++M +   G+SRGFGF+++E P   ++ V+
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
             +   +DGK++   RA  + E+
Sbjct: 64  TQH--ILDGKVIDPKRAIPRDEQ 84

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 69.3 bits (168), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 43/170 (25%), Positives = 87/170 (51%), Gaps = 8/170 (4%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +++ NLDK+I    +   F   G I + K+  D+   +  Y FV +     AN +++ +N
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 173 GMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS 232
           G  + + IV +      ++   +       F N+++ +   + +DE L+  F+ + +  S
Sbjct: 63  GKQIENNIVKINWAFQSQQSSSD-----DTF-NLFVGDLNVNVDDETLRNAFKDFPSYLS 116
Query: 233 YRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK 280
             VM +   G SRG+GFV++ S + A+ A+ +  G++++G+ L +  A K
Sbjct: 117 GHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/131 (24%), Positives = 62/131 (47%), Gaps = 17/131 (12%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           +Y+ N  +   ++ LK+ F+  G I + ++M + + K+  + FV Y     A  A+Q  N
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 265 GKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRK 324
           GK+++  I+ +  A +  + + +                   NL+V +L+ ++DDE LR 
Sbjct: 63  GKQIENNIVKINWAFQSQQSSSD----------------DTFNLFVGDLNVNVDDETLRN 106
Query: 325 EFTPFGTITSA 335
            F  F +  S 
Sbjct: 107 AFKDFPSYLSG 117

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 57.8 bits (138), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 52/194 (26%), Positives = 92/194 (47%), Gaps = 23/194 (11%)
Query: 99  SQRDP-SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFV 156
           S ++P  LRK  +G +  +  D+S+ +      F  +G++  C V +D     S+G+GFV
Sbjct: 6   SPKEPEQLRKLFIGGLSFETTDESLRSH-----FEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 157 HFETEE----AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFG 212
            + T E    A N    KV+G ++  K     + + R++ ++           +++    
Sbjct: 61  TYATVEEVDAAMNARPHKVDGRVVEPK-----RAVSREDSQRPGAHLT--VKKIFVGGIK 113
Query: 213 EDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV-QAWNGKEVD 269
           ED  +  L++ FE YG I    +M +   GK RGF FV ++  +  +K V Q ++   V+
Sbjct: 114 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVN 171
Query: 270 GKILYVGRAQKKAE 283
           G    V +A  K E
Sbjct: 172 GHNCEVRKALSKQE 185

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 43/148 (29%), Positives = 71/148 (47%), Gaps = 19/148 (12%)
Query: 187 IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRG 244
           + + E  KE  +  KLF    I     +  DE L+  FE +GT+T   VM   N  +SRG
Sbjct: 1   MSKSESPKEPEQLRKLF----IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 56
Query: 245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQ 304
           FGFV Y + E  + A+ A   K VDG+++   RA  +    ++ +R    L +++     
Sbjct: 57  FGFVTYATVEEVDAAMNARPHK-VDGRVVEPKRAVSR----EDSQRPGAHLTVKK----- 106
Query: 305 GVNLYVKNLDDSIDDERLRKEFTPFGTI 332
              ++V  + +  ++  LR  F  +G I
Sbjct: 107 ---IFVGGIKEDTEEHHLRDYFEQYGKI 131

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 45/170 (26%), Positives = 81/170 (47%), Gaps = 20/170 (11%)
Query: 99  SQRDP-SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFV 156
           S ++P  LRK  +G +  +  D+S+ +      F  +G++  C V +D     S+G+GFV
Sbjct: 6   SPKEPEQLRKLFIGGLSFETTDESLRSH-----FEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 157 HFETEE----AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFG 212
            + T E    A N    KV+G ++  K     + + R++ ++           +++    
Sbjct: 61  TYATVEEVDAAMNARPHKVDGRVVEPK-----RAVSREDSQRPGAHLT--VKKIFVGGIK 113
Query: 213 EDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
           ED  +  L++ FE YG I    +M +   GK RGF FV ++  +  +K V
Sbjct: 114 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/148 (29%), Positives = 71/148 (47%), Gaps = 19/148 (12%)
Query: 187 IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRG 244
           + + E  KE  +  KLF    I     +  DE L+  FE +GT+T   VM   N  +SRG
Sbjct: 1   MSKSESPKEPEQLRKLF----IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 56
Query: 245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQ 304
           FGFV Y + E  + A+ A   K VDG+++      K+A   ++ +R    L +++     
Sbjct: 57  FGFVTYATVEEVDAAMNARPHK-VDGRVV----EPKRAVSREDSQRPGAHLTVKK----- 106
Query: 305 GVNLYVKNLDDSIDDERLRKEFTPFGTI 332
              ++V  + +  ++  LR  F  +G I
Sbjct: 107 ---IFVGGIKEDTEEHHLRDYFEQYGKI 131

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/195 (28%), Positives = 89/195 (45%), Gaps = 25/195 (12%)
Query: 99  SQRDP-SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFV 156
           S ++P  LRK  +G +  +  D+S+ +      F  +G++  C V +D     S+G+GFV
Sbjct: 5   SPKEPEQLRKLFIGGLSFETTDESLRSH-----FEQWGTLTDCVVMRDPNTKRSRGFGFV 59
Query: 157 HFETEE----AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKL-FTNVYIKNF 211
            + T E    A N    KV+G ++  K            RE      A L    +++   
Sbjct: 60  TYATVEEVDAAMNARPHKVDGRVVEPKRAV--------SREDSQRPGAHLTVKKIFVGGI 111
Query: 212 GEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV-QAWNGKEV 268
            ED  +  L++ FE YG I    +M +   GK RGF FV ++  +  +K V Q ++   V
Sbjct: 112 KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TV 169
Query: 269 DGKILYVGRAQKKAE 283
           +G    V +A  K E
Sbjct: 170 NGHNCEVRKALSKQE 184

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/146 (29%), Positives = 70/146 (47%), Gaps = 19/146 (13%)
Query: 189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFG 246
           + E  KE  +  KLF    I     +  DE L+  FE +GT+T   VM   N  +SRGFG
Sbjct: 2   KSESPKEPEQLRKLF----IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 57
Query: 247 FVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGV 306
           FV Y + E  + A+ A   K VDG+++   RA  +    ++ +R    L +++       
Sbjct: 58  FVTYATVEEVDAAMNARPHK-VDGRVVEPKRAVSR----EDSQRPGAHLTVKK------- 105
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTI 332
            ++V  + +  ++  LR  F  +G I
Sbjct: 106 -IFVGGIKEDTEEHHLRDYFEQYGKI 130

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 45/170 (26%), Positives = 81/170 (47%), Gaps = 20/170 (11%)
Query: 99  SQRDP-SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFV 156
           S ++P  LRK  +G +  +  D+S+ +      F  +G++  C V +D     S+G+GFV
Sbjct: 4   SPKEPEQLRKLFIGGLSFETTDESLRSH-----FEQWGTLTDCVVMRDPNTKRSRGFGFV 58
Query: 157 HFETEE----AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFG 212
            + T E    A N    KV+G ++  K     + + R++ ++           +++    
Sbjct: 59  TYATVEEVDAAMNARPHKVDGRVVEPK-----RAVSREDSQRPGAHLT--VKKIFVGGIK 111
Query: 213 EDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
           ED  +  L++ FE YG I    +M +   GK RGF FV ++  +  +K V
Sbjct: 112 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/146 (29%), Positives = 70/146 (47%), Gaps = 19/146 (13%)
Query: 189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFG 246
           + E  KE  +  KLF    I     +  DE L+  FE +GT+T   VM   N  +SRGFG
Sbjct: 1   KSESPKEPEQLRKLF----IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 56
Query: 247 FVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGV 306
           FV Y + E  + A+ A   K VDG+++      K+A   ++ +R    L +++       
Sbjct: 57  FVTYATVEEVDAAMNARPHK-VDGRVV----EPKRAVSREDSQRPGAHLTVKK------- 104
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTI 332
            ++V  + +  ++  LR  F  +G I
Sbjct: 105 -IFVGGIKEDTEEHHLRDYFEQYGKI 129

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 47/179 (26%), Positives = 84/179 (46%), Gaps = 17/179 (9%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEE----AANKS 167
           +FI  L     ++++   F  +G++  C V +D     S+G+GFV + T E    A N  
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPY 227
             KV+G ++  K     + + R++ ++           +++    ED  +  L++ FE Y
Sbjct: 69  PHKVDGRVVEPK-----RAVSREDSQRPGAHLT--VKKIFVGGIKEDTEEHHLRDYFEQY 121
Query: 228 GTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV-QAWNGKEVDGKILYVGRAQKKAE 283
           G I    +M +   GK RGF FV ++  +  +K V Q ++   V+G    V +A  K E
Sbjct: 122 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQE 178

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 37/129 (28%), Positives = 64/129 (49%), Gaps = 15/129 (11%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW 263
           ++I     +  DE L+  FE +GT+T   VM   N  +SRGFGFV Y + E  + A+ A 
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68
Query: 264 NGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLR 323
             K VDG+++   RA  +    ++ +R    L +++        ++V  + +  ++  LR
Sbjct: 69  PHK-VDGRVVEPKRAVSR----EDSQRPGAHLTVKK--------IFVGGIKEDTEEHHLR 115
Query: 324 KEFTPFGTI 332
             F  +G I
Sbjct: 116 DYFEQYGKI 124

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 54/195 (27%), Positives = 94/195 (48%), Gaps = 25/195 (12%)
Query: 99  SQRDP-SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFV 156
           S ++P  LRK  +G +  +  D+S+ +      F  +G++  C V +D     S+G+GFV
Sbjct: 7   SPKEPEQLRKLFIGGLSFETTDESLRSH-----FEQWGTLTDCVVMRDPNTKRSRGFGFV 61
Query: 157 HFETEE----AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKL-FTNVYIKNF 211
            + T E    A N    KV+G ++  K     + + R++ ++     A L    +++   
Sbjct: 62  TYATVEEVDAAMNARPHKVDGRVVEPK-----RAVSREDSQRP---GAHLTVKKIFVGGI 113
Query: 212 GEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV-QAWNGKEV 268
            ED  +  L++ FE YG I    +M +   GK RGF FV ++  +  +K V Q ++   V
Sbjct: 114 KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TV 171
Query: 269 DGKILYVGRAQKKAE 283
           +G    V +A  K E
Sbjct: 172 NGHNCEVRKALSKQE 186

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/146 (29%), Positives = 70/146 (47%), Gaps = 19/146 (13%)
Query: 189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFG 246
           + E  KE  +  KLF    I     +  DE L+  FE +GT+T   VM   N  +SRGFG
Sbjct: 4   KSESPKEPEQLRKLF----IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG 59
Query: 247 FVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGV 306
           FV Y + E  + A+ A   K VDG+++   RA  +    ++ +R    L +++       
Sbjct: 60  FVTYATVEEVDAAMNARPHK-VDGRVVEPKRAVSR----EDSQRPGAHLTVKK------- 107
Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTI 332
            ++V  + +  ++  LR  F  +G I
Sbjct: 108 -IFVGGIKEDTEEHHLRDYFEQYGKI 132

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 50/80 (62%), Gaps = 2/80 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAW 263
           +Y+ +   +  ++ L+ +FEP+G I S ++M  +  G+S+G+GF+ +   E A+KA++  
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 264 NGKEVDGKILYVGRAQKKAE 283
           NG E+ G+ + VG   ++ +
Sbjct: 89  NGFELAGRPMKVGHVTERTD 108

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 50/80 (62%), Gaps = 2/80 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
           +++     D N++ L+++F  YG I+   V+ +    +SRGFGFV +E+ + A+ A+ A 
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 264 NGKEVDGKILYVGRAQKKAE 283
           NGK VDG+ + V +A K ++
Sbjct: 75  NGKSVDGRQIRVDQAGKSSD 94

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 53.9 bits (128), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 45/74 (60%), Gaps = 2/74 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
            N++I +  ++F D+ L +MF P+G + S +V        S+ FGFV+Y++P  A+ A+Q
Sbjct: 26  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 262 AWNGKEVDGKILYV 275
           + NG ++  K L V
Sbjct: 86  SMNGFQIGMKRLKV 99

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 42/171 (24%), Positives = 74/171 (43%), Gaps = 18/171 (10%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           + + NL  S+  +   +    FGS+  C +   E+ G SKGYGF  +  +++A ++   +
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 172 NGMLLNSKIVFV-----GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFND-EKLKEMFE 225
            G  L  + ++V     G+  P     + L           +      FND + L     
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSRCL----------CVDRLPPGFNDVDALCRALS 207
Query: 226 PYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV 275
              + T  ++    DG+ +GF  + YE+ E AE+A Q  +G  + G  L V
Sbjct: 208 AVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 42/171 (24%), Positives = 74/171 (43%), Gaps = 18/171 (10%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           + + NL  S+  +   +    FGS+  C +   E+ G SKGYGF  +  +++A ++   +
Sbjct: 96  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 172 NGMLLNSKIVFV-----GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFND-EKLKEMFE 225
            G  L  + ++V     G+  P     + L           +      FND + L     
Sbjct: 156 LGKPLGPRTLYVHWTDAGQLTPALLHSRCL----------CVDRLPPGFNDVDALCRALS 205
Query: 226 PYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV 275
              + T  ++    DG+ +GF  + YE+ E AE+A Q  +G  + G  L V
Sbjct: 206 AVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 256

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 42/171 (24%), Positives = 74/171 (43%), Gaps = 18/171 (10%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           + + NL  S+  +   +    FGS+  C +   E+ G SKGYGF  +  +++A ++   +
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 172 NGMLLNSKIVFV-----GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFND-EKLKEMFE 225
            G  L  + ++V     G+  P     + L           +      FND + L     
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSRCL----------CVDRLPPGFNDVDALCRALS 207
Query: 226 PYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV 275
              + T  ++    DG+ +GF  + YE+ E AE+A Q  +G  + G  L V
Sbjct: 208 AVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258

>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 1 Length = 114

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQA 262
           TN+YI N     ++++L+ M +P+G + S R++ ++ G SRG GF   ES E  E  +  
Sbjct: 26  TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 85
Query: 263 WNGK 266
           +NGK
Sbjct: 86  FNGK 89

>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre Rna Length = 175

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 46/171 (26%), Positives = 85/171 (49%), Gaps = 19/171 (11%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILS---CKVAQDEQGNSKGYGFVHFETEEAANKSI 168
           N+FI NL+    NK++ +   A   + +     V     G ++ +G+V FE+ E   K++
Sbjct: 15  NLFIGNLNP---NKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 71
Query: 169 EKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYG 228
           E     +  ++I    K    K R+    +K +    +  KN   +  +++LKE+FE   
Sbjct: 72  ELTGLKVFGNEI----KLEKPKGRD---SKKVRAARTLLAKNLSFNITEDELKEVFEDAL 124
Query: 229 TITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK---ILYVG 276
            I   R+++ DGKS+G  ++ ++S   AEK ++   G E+DG+   + Y G
Sbjct: 125 EI---RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 172

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 2/74 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
            N++I +  ++F D  L   F P+G + S +V        S+ FGFV++++P+ A+ A++
Sbjct: 41  CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100
Query: 262 AWNGKEVDGKILYV 275
           A NG +V  K L V
Sbjct: 101 AMNGFQVGTKRLKV 114

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 9/89 (10%)
Query: 89  LKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQG 148
           LK RP+RI ++    +L         +KNL   + N+ +   FS FG +    V  D++G
Sbjct: 83  LKSRPLRIRFATHGAALT--------VKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRG 134
Query: 149 NSKGYGFVHFETEEAANKSIEKV-NGMLL 176
            + G GFV F  +  A K++E+  +G  L
Sbjct: 135 RATGKGFVEFAAKPPARKALERCGDGAFL 163

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 44/143 (30%), Positives = 63/143 (44%), Gaps = 32/143 (22%)
Query: 193 EKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYES 252
           EK   ++ +LF    + N   D  +E  K +FE YG  +    +N D   RGFGF+  ES
Sbjct: 16  EKTYTQRCRLF----VGNLPTDITEEDFKRLFERYGEPSEV-FINRD---RGFGFIRLES 67
Query: 253 PEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKN 312
              AE A       E+DG IL          +++ L+ RF            G  L VKN
Sbjct: 68  RTLAEIA-----KAELDGTIL----------KSRPLRIRFAT---------HGAALTVKN 103
Query: 313 LDDSIDDERLRKEFTPFGTITSA 335
           L   + +E L + F+ FG +  A
Sbjct: 104 LSPVVSNELLEQAFSQFGPVEKA 126

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/87 (32%), Positives = 50/87 (57%), Gaps = 3/87 (3%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQA 262
           +V++ N   +  +E+LK++F   G + S+R++     GK +G+GF  Y+  E A  A++ 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 263 WNGKEVDGKILYVGRAQKKAERTQELK 289
            NG+E  G+ L V  A  +  + +ELK
Sbjct: 70  LNGREFSGRALRVDNAASEKNK-EELK 95

>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 41/72 (56%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             ++++N   DF  + LK+ F   G +    +   +GKS+G G V +ESPE AE+A +  
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMM 68
Query: 264 NGKEVDGKILYV 275
           NG ++ G+ + V
Sbjct: 69  NGMKLSGREIDV 80

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 42/72 (58%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           + ++++N   DF  + LK+ F   G +    +   +GKS+G G V +ESPE AE+A +  
Sbjct: 6   SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMM 65
Query: 264 NGKEVDGKILYV 275
           NG ++ G+ + V
Sbjct: 66  NGMKLSGREIDV 77

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 49/82 (59%), Gaps = 2/82 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
           + +Y+ +   +  ++ L+ +FEP+G I +  +M +   G+S+G+GF+ +   E A +A++
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 262 AWNGKEVDGKILYVGRAQKKAE 283
             NG E+ G+ + VG   ++ +
Sbjct: 66  QLNGFELAGRPMRVGHVTERLD 87

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 24/69 (34%), Positives = 44/69 (63%), Gaps = 1/69 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
           N+F+ +L+ ++D++ + + F  F S LS  V  D Q G+S+GYGFV F +++ A  +++ 
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 171 VNGMLLNSK 179
           + G  LN +
Sbjct: 63  MQGQDLNGR 71

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 23/78 (29%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQA 262
           N+++ +   + +DE L+  F+ + +  S  VM     G SRG+GFV++ S + A+ A+ +
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 263 WNGKEVDGKILYVGRAQK 280
             G++++G+ L +  A K
Sbjct: 63  MQGQDLNGRPLRINWAAK 80

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGK-----SRGFGFVAYESPEFAEK 258
           + ++IKN      +E LK +F   G I S  +     K     S GFGFV Y+ PE A+K
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 259 AVQAWNGKEVDGKILYV 275
           A++   G  VDG  L V
Sbjct: 66  ALKQLQGHTVDGHKLEV 82

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWN 264
           ++I     + N++ LK +F  +G I+   ++ +   KSRGF F+ +E+P  A+ A +  N
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 265 GKEVDGKILYVGRAQKKA 282
           GK + GK + V +A+K +
Sbjct: 70  GKSLHGKAIKVEQAKKPS 87

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 47.8 bits (112), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 43/181 (23%), Positives = 81/181 (44%), Gaps = 31/181 (17%)
Query: 113 VFIKNLDKSIDNKAMYDTFSA---FG--------SILSCKVAQDEQGNSKGYGFVHFETE 161
           +++ N+   I  +AM D F+A    G         +L+ ++ QD     K + F+ F   
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEF--- 58
Query: 162 EAANKSIEKVNGMLLNSKIVFVGKF--IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEK 219
               +S+++    +    I+F G+   I R    + L    KLF    I       ND++
Sbjct: 59  ----RSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLF----IGGLPNYLNDDQ 110
Query: 220 LKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR 277
           +KE+   +G + ++ ++ +   G S+G+ F  Y      ++A+   NG ++  K L V R
Sbjct: 111 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170
Query: 278 A 278
           A
Sbjct: 171 A 171

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 43/181 (23%), Positives = 81/181 (44%), Gaps = 31/181 (17%)
Query: 113 VFIKNLDKSIDNKAMYDTFSA---FG--------SILSCKVAQDEQGNSKGYGFVHFETE 161
           +++ N+   I  +AM D F+A    G         +L+ ++ QD     K + F+ F   
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEF--- 60
Query: 162 EAANKSIEKVNGMLLNSKIVFVGKF--IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEK 219
               +S+++    +    I+F G+   I R    + L    KLF    I       ND++
Sbjct: 61  ----RSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLF----IGGLPNYLNDDQ 112
Query: 220 LKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR 277
           +KE+   +G + ++ ++ +   G S+G+ F  Y      ++A+   NG ++  K L V R
Sbjct: 113 VKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 172
Query: 278 A 278
           A
Sbjct: 173 A 173

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 43/77 (55%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +++ N    F D  L++MF  +G I    ++ N+  S+GFGFV +E+   A++A +  +G
Sbjct: 32  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 91
Query: 266 KEVDGKILYVGRAQKKA 282
             V+G+ + V  A  + 
Sbjct: 92  TVVEGRKIEVNNATARV 108

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKS 167
           G  N+ +  L +++    +   FS+ G + S K+ +D+  G+S GYGFV++ T + A ++
Sbjct: 3   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 168 IEKVNGMLLNSKIVFVGKFIP 188
           I  +NG+ L SK + V    P
Sbjct: 63  INTLNGLRLQSKTIKVSYARP 83

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/78 (26%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    ++   ++L+ +F   G + S +++ +   G S G+GFV Y + + AE+A+ 
Sbjct: 5   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 262 AWNGKEVDGKILYVGRAQ 279
             NG  +  K + V  A+
Sbjct: 65  TLNGLRLQSKTIKVSYAR 82

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 43/76 (56%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +++ N    F D  L++MF  +G I    ++ N+  S+GFGFV +E+   A++A +  +G
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 77
Query: 266 KEVDGKILYVGRAQKK 281
             V+G+ + V  A  +
Sbjct: 78  TVVEGRKIEVNNATAR 93

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 42/69 (60%), Gaps = 1/69 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L + + ++ +Y  F A G I +C++ +D + G S GY FV F +E  + ++I+ 
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 171 VNGMLLNSK 179
           +NG+ + +K
Sbjct: 65  LNGITVRNK 73

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 2/82 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    +D  D +L  +F   G I + R+M +   G S G+ FV + S   +++A++
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 262 AWNGKEVDGKILYVGRAQKKAE 283
             NG  V  K L V  A+   E
Sbjct: 64  VLNGITVRNKRLKVSYARPGGE 85

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/98 (30%), Positives = 47/98 (47%), Gaps = 10/98 (10%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            VF+ NLD  +  K + + FS  G ++   + +D+ G S+G G V FE    A ++I   
Sbjct: 17  TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 172 NGMLLNSKIVFV---------GKFIPRKEREKELGEKA 200
           NG LL  + + V         G F P  ER ++ G  +
Sbjct: 77  NGQLLFDRPMHVKMDERALPKGDFFP-PERPQQSGPSS 113

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 41.2 bits (95), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFA 256
           +  +L + V++ N       +KLKE+F   G +    ++ + DGKSRG G V +E    A
Sbjct: 10  QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEA 69
Query: 257 EKAVQAWNGKEVDGKILYV 275
            +A+  +NG+ +  + ++V
Sbjct: 70  VQAISMFNGQLLFDRPMHV 88

>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human Nucleoli Length = 180

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 46/187 (24%), Positives = 83/187 (44%), Gaps = 35/187 (18%)
Query: 96  IMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGF 155
           + +++  P L K+G+ +VF KN                        V     G ++ +G+
Sbjct: 15  LNFNKSAPEL-KTGISDVFAKN---------------------DLAVVDVRIGMTRKFGY 52
Query: 156 VHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDF 215
           V FE+ E   K++E      L    VF  +    K + K+  +K +    +  KN     
Sbjct: 53  VDFESAEDLEKALE------LTGLKVFGNEIKLEKPKGKD-SKKERDARTLLAKNLPYKV 105
Query: 216 NDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK---I 272
             ++LKE+FE    I   R+++ DGKS+G  ++ +++   AEK  +   G E+DG+   +
Sbjct: 106 TQDELKEVFEDAAEI---RLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISL 162
Query: 273 LYVGRAQ 279
            Y G  +
Sbjct: 163 YYTGEPK 169

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L +++        F + G I SCK+ +D+  G S GYGFV++     A+K+I  
Sbjct: 6   NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 171 VNGMLLNSKIVFVGKFIP 188
           +NG+ L +K + V    P
Sbjct: 66  LNGLKLQTKTIKVSYARP 83

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 2/81 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    ++   ++ K +F   G I S +++ +   G+S G+GFV Y  P  A+KA+ 
Sbjct: 5   TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 262 AWNGKEVDGKILYVGRAQKKA 282
             NG ++  K + V  A+  +
Sbjct: 65  TLNGLKLQTKTIKVSYARPSS 85

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQA 262
           +V++ +   +   E +K  F P+G I+  RV+ +   GKS+G+GFV++ +   AE A+Q 
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 263 WNGKEVDGKILYVGRAQKK 281
             G+ + G+ +    A +K
Sbjct: 77  MGGQWLGGRQIRTNWATRK 95

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 46/83 (55%), Gaps = 2/83 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTIT--SYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           ++++N     ++E L+++F  YG ++   Y + +   K +GF FV +  PE A KA    
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 264 NGKEVDGKILYVGRAQKKAERTQ 286
           +G+   G++L+V  +  K E +Q
Sbjct: 71  DGQVFQGRMLHVLPSTIKKEASQ 93

>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3 Length = 108

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           T ++++ F  D  + +L E+F P+G +   +++N      GF FV +E  E A KA++  
Sbjct: 32  TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN------GFAFVEFEEAESAAKAIEEV 85
Query: 264 NGKEVDGKILYVGRAQKKAER 284
           +GK    + L V  ++  A+R
Sbjct: 86  HGKSFANQPLEVVYSKLPAKR 106

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L ++     +   FS+ G + S K+ +D+  G+S GYGFV++ T + A ++I  
Sbjct: 21  NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 171 VNGMLLNSKIVFVGKFIP 188
           +NG+ L SK + V    P
Sbjct: 81  LNGLRLQSKTIKVSYARP 98

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 45.1 bits (105), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 25/92 (27%), Positives = 47/92 (51%), Gaps = 11/92 (11%)
Query: 81  LDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC 140
           LD M    L+G+ +R+ ++    SL         ++NL + + N+ + + FS FG +   
Sbjct: 78  LDNM---PLRGKQLRVRFACHSASLT--------VRNLPQYVSNELLEEAFSVFGQVERA 126
Query: 141 KVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
            V  D++G   G G V F  + AA K++++ +
Sbjct: 127 VVIVDDRGRPSGKGIVEFSGKPAARKALDRCS 158

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 38/147 (25%), Positives = 62/147 (42%), Gaps = 32/147 (21%)
Query: 189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFV 248
           RK  EK   ++++LF    + N   D  +E+++++FE YG      +     K +GFGF+
Sbjct: 12  RKPGEKTFTQRSRLF----VGNLPPDITEEEMRKLFEKYGKAGEVFI----HKDKGFGFI 63
Query: 249 AYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNL 308
             E+   AE A    +   + GK L V  A   A                        +L
Sbjct: 64  RLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA------------------------SL 99
Query: 309 YVKNLDDSIDDERLRKEFTPFGTITSA 335
            V+NL   + +E L + F+ FG +  A
Sbjct: 100 TVRNLPQYVSNELLEEAFSVFGQVERA 126

>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif In Trna Selenocysteine Associated Protein Length = 104

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 28/85 (32%), Positives = 45/85 (52%), Gaps = 2/85 (2%)
Query: 112 NVFIKNLDKSIDNKAMYDTF-SAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
           ++F+ +L   +D+  +Y+ F   + S    KV  D+ G SKGYGFV F  E    +++ +
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 171 VNGML-LNSKIVFVGKFIPRKEREK 194
             G + L SK V +   IP+  R K
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASRVK 95

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/92 (26%), Positives = 49/92 (53%), Gaps = 2/92 (2%)
Query: 195 ELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYES 252
           ++  +  +  N+ +       ++ +L+++FE YG I S +++ +    +SRG+GFV ++S
Sbjct: 34  QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93
Query: 253 PEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
              A++A+   NG  +  K L V  A    +R
Sbjct: 94  GSSAQQAIAGLNGFNILNKRLKVALAASGHQR 125

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
           TN+Y+ N      D++L  +F  YG+I    ++ +   G+ RG  FV Y   E A++A+ 
Sbjct: 14  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 262 AWN 264
           A N
Sbjct: 74  ALN 76

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
           + +YI+       D+ L ++ +PYG I S + +      K +G+GFV ++SP  A+KAV 
Sbjct: 6   SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 262 AWNGKEVDGKI 272
           A     V  ++
Sbjct: 66  ALKASGVQAQM 76

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
           N+++  L K++  K M   FS +G I++ ++  D+  G S+G GF+ F+    A ++I+ 
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 171 VNG 173
           +NG
Sbjct: 63  LNG 65

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 41.6 bits (96), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/69 (27%), Positives = 40/69 (57%), Gaps = 2/69 (2%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
            N+Y+    +  + ++++++F  YG I + R++     G SRG GF+ ++    AE+A++
Sbjct: 2   ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 262 AWNGKEVDG 270
             NG++  G
Sbjct: 62  GLNGQKPLG 70

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 45/77 (58%), Gaps = 3/77 (3%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GKSRGFGFVAYESPEFAEKAVQAWN 264
           +++K   ED  +E LKE F+  G++ +  V + + G S+GFGFV + S E A+ A +A  
Sbjct: 18  LFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 265 GKEVDGKILYVGRAQKK 281
             E+DG  + +  A+ K
Sbjct: 76  DGEIDGNKVTLDWAKPK 92

>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2 Length = 96

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 199 KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEK 258
           K +    +  KN   +  +++LKE+FE    I   R+++ DGKS+G  ++ ++S   AEK
Sbjct: 12  KVRAARTLLAKNLSFNITEDELKEVFEDALEI---RLVSQDGKSKGIAYIEFKSEADAEK 68
Query: 259 AVQAWNGKEVDGK---ILYVG 276
            ++   G E+DG+   + Y G
Sbjct: 69  NLEEKQGAEIDGRSVSLYYTG 89

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIE-- 169
           +FI  L      K + D FS FG ++ C +  D   G S+G+GFV F+  E+ +K ++  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 170 --KVNGMLLNSK 179
             K+NG +++ K
Sbjct: 62  EHKLNGKVIDPK 73

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/100 (32%), Positives = 50/100 (50%), Gaps = 11/100 (11%)
Query: 187 IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG--KSRG 244
           + RK+REKE       F  ++I     +  +E L+  +E +G +T   VM +    +SRG
Sbjct: 17  LERKKREKEQ------FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRG 70
Query: 245 FGFVAYESPEFAE-KAVQAWNGKEVDGKILYVGRAQKKAE 283
           FGFV + S   AE  A  A     +DG+++   RA  + E
Sbjct: 71  FGFVTFSS--MAEVDAAMAARPHSIDGRVVEPKRAVAREE 108

>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human Putative Rna-Binding Protein 11 Length = 95

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/71 (28%), Positives = 39/71 (54%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           VF+ NL+  +  + +Y+ F   G +    + +D +G  K +GFV F+  E+ + +I  +N
Sbjct: 19  VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 173 GMLLNSKIVFV 183
           G+ L  + + V
Sbjct: 79  GIRLYGRPINV 89

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQA 262
           +V++ +   +   E +K  F P+G I+  RV+ +   GKS+G+GFV++ +   AE A+  
Sbjct: 17  HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 263 WNGKEVDGKILYVGRAQKK 281
             G+ + G+ +    A +K
Sbjct: 77  MGGQWLGGRQIRTNWATRK 95

>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein Length = 74

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           T ++++ F  D  + +L E+F P+G +   +++N      GF FV +E  E A KA++  
Sbjct: 5   TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN------GFAFVEFEEAESAAKAIEEV 58
Query: 264 NGKEVDGKILYV 275
           +GK    + L V
Sbjct: 59  HGKSFANQPLEV 70

>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide Repeat Containing 4 Variant Length = 102

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/65 (36%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEF 255
           GE  KLF  +     G+   DE +++MFEP+GTI    V+   DG S+G  FV +++   
Sbjct: 10  GEDRKLFVGM----LGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAE 65
Query: 256 AEKAV 260
           A+ A+
Sbjct: 66  AQAAI 70

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 44/84 (52%), Gaps = 4/84 (4%)
Query: 196 LGEKAKLFTNVYIKNFGEDF--NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYE 251
           LG +A    N  +  FG      +  L+E+F  YG I    ++      +SRGF FV +E
Sbjct: 3   LGSRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 62
Query: 252 SPEFAEKAVQAWNGKEVDGKILYV 275
           + + A++A +  NG E+DG+ + V
Sbjct: 63  NVDDAKEAKERANGMELDGRRIRV 86

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 4/86 (4%)
Query: 194 KELGEKAKLFTNVYIKNFGEDF--NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVA 249
           + +G +A    N  +  FG      +  L+E+F  YG I    ++      +SRGF FV 
Sbjct: 35  RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 94
Query: 250 YESPEFAEKAVQAWNGKEVDGKILYV 275
           +E+ + A++A +  NG E+DG+ + V
Sbjct: 95  FENVDDAKEAKERANGMELDGRRIRV 120

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAW 263
           + + N  ED  +  L+E+F P+G+I+   +  +   G+S+GF F+++   E A +A+   
Sbjct: 18  IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 264 NGKEVDGKILYVGRAQ 279
           +G   D  IL V  A+
Sbjct: 78  SGFGYDHLILNVEWAK 93

>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar Length = 109

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           V+   +   + ++ M  TFS FG I+  +V  +     KGY FV F T E+A  +I  VN
Sbjct: 28  VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVN 82
Query: 173 GMLLNSKIV 181
           G  +   +V
Sbjct: 83  GTTIEGHVV 91

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 30/58 (51%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
            VF+  +D  +D   +   F+ +GS+   K+  D  G SKGYGFV F  +    K +E
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 30/58 (51%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
            VF+  +D  +D   +   F+ +GS+   K+  D  G SKGYGFV F  +    K +E
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 30/58 (51%)
Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
            VF+  +D  +D   +   F+ +GS+   K+  D  G SKGYGFV F  +    K +E
Sbjct: 12  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 69

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
           +Y+    E+ +D+ L   F P+G IT  ++  +    K RGF FV +E  E A  A+   
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 264 NGKEVDGKILYVGRA 278
           N  E+ G+ + V  A
Sbjct: 126 NESELFGRTIRVNLA 140

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 2/75 (2%)
Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAV 260
           F  +++     D  + KL+  FE YG I    ++     GK RG+ F+ YE       A 
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 261 QAWNGKEVDGKILYV 275
           +  +GK++DG+ + V
Sbjct: 162 KHADGKKIDGRRVLV 176

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 2/76 (2%)
Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAW 263
           +Y+    E+ +D+ L   F P+G IT  ++  +    K RGF FV +E  E A  A+   
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 264 NGKEVDGKILYVGRAQ 279
           N  E+ G+ + V  A+
Sbjct: 75  NESELFGRTIRVNLAK 90

>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain Length = 106

Iteration: 1
 Score = 41.2 bits (95), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 20/67 (29%), Positives = 37/67 (55%)
Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           + + NLD  + +  + + F+ FG++    V  D  G S G   VHFE +  A K++++ N
Sbjct: 31  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 173 GMLLNSK 179
           G+ L+ +
Sbjct: 91  GVPLDGR 97

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	336
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-92
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-54
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-84
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-73
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-31
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-82
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-42
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-35
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-73
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-35
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	9e-28
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	9e-69
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-58
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-27
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-04
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-59
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-39
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-25
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-59
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-54
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	7e-42
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	8e-59
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-44
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-39
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	6e-54
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	8e-36
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-08
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-52
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-48
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-32
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-50
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-45
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-37
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-50
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-33
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-23
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-46
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-34
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-23
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	6e-39
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	7e-22
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-06
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	5e-38
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-22
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-14
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-37
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-24
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-35
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-26
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-35
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	4e-26
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-16
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-34
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-19
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-17
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-34
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-27
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-33
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-24
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-33
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-25
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-11
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-32
1x5o_A	114	RNA binding motif, single-stranded interacting pro	8e-28
1x5o_A	114	RNA binding motif, single-stranded interacting pro	3e-21
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-31
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-21
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-31
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-20
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	6e-31
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	6e-18
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-04
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	7e-31
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-18
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-09
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	9e-31
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-23
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	8e-30
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-19
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-29
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	8e-19
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-15
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	6e-29
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-21
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-12
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	5e-28
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	7e-24
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-17
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	8e-28
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-21
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	9e-10
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-27
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-26
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-06
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-26
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	7e-20
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	8e-14
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-26
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-19
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-06
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-26
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	9e-20
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	9e-26
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-19
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	6e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-25
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	5e-19
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-15
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-25
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-17
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-14
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-24
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-17
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-07
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-24
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	8e-23
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	3e-08
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-24
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-18
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-07
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	9e-24
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-15
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-07
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-23
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-18
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-05
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-23
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-14
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-05
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-23
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-14
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-22
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-15
1x5p_A	97	Negative elongation factor E; structure genomics,	9e-08
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	1e-22
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	9e-16
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	5e-04
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-22
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-17
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-22
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	5e-14
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-05
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-22
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-16
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-04
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-21
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-17
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-04
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-21
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-14
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-04
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	6e-21
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	9e-16
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	7e-21
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-14
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-04
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-20
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	9e-17
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	6e-04
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-20
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-16
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-06
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	9e-06
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-20
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-16
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-05
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-20
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-13
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	5e-20
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-11
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	7e-20
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-15
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	9e-08
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-05
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	8e-20
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	6e-15
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	6e-04
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-19
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-13
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-05
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-19
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-15
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-19
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-19
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-06
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	5e-05
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-19
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-13
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-04
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	5e-19
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-15
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	7e-19
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	9e-14
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-18
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-04
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-18
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-13
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-18
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-11
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-18
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-13
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-04
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-18
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-13
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-18
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-14
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-04
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-18
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-13
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	5e-18
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-14
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-04
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	6e-18
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-13
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	7e-18
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	3e-14
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-04
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	9e-18
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-10
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-17
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-17
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	7e-04
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-17
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-14
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-05
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-17
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-14
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-09
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-05
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-17
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-13
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	4e-17
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-17
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-17
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-12
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	6e-17
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-15
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-07
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-04
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	7e-17
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	5e-13
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	8e-17
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-11
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	8e-17
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	9e-13
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	8e-17
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	6e-13
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	9e-17
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	9e-09
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-16
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-13
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-16
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-12
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-16
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-12
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-05
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-16
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-11
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-16
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-11
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	5e-16
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-13
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-16
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-08
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	8e-16
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	9e-16
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-09
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-15
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-09
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-15
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-12
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-15
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-05
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-15
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	9e-09
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-15
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-10
2div_A	99	TRNA selenocysteine associated protein; structural	3e-15
2div_A	99	TRNA selenocysteine associated protein; structural	7e-12
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-15
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	6e-13
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-15
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-08
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	7e-15
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	3e-10
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-14
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-10
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-14
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-10
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-14
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	3e-08
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-14
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-11
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-14
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	6e-10
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-14
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	5e-09
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-14
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-06
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	4e-14
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-08
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	5e-14
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-06
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	7e-14
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	9e-10
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-13
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-11
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-13
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-10
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-13
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-08
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-13
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	7e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-13
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	9e-08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-13
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-05
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	4e-13
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	7e-04
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	5e-13
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	6e-13
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	5e-08
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-12
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-12
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-12
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-10
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	5e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-08
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	5e-12
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	5e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	7e-12
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	5e-11
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	9e-12
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-09
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	9e-12
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-08
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-06
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-11
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-07
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-11
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-09
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-11
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-08
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	3e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	4e-11
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-08
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-09
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-10
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	7e-08
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-10
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-09
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	5e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-09
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-09
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	8e-09
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	3e-09
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	5e-06
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-09
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	4e-07
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-09
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	8e-09
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	6e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-08
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-08
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	4e-06
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	4e-08
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-08
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	5e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-07
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-07
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	8e-07
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-07
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-06
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	6e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	1e-06
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	2e-06
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-04
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	2e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	1e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-05
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	5e-05
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	1e-04
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	2e-04
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	2e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	7e-04

>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 =  276 bits (709), Expect = 1e-92
 Identities = 50/267 (18%), Positives = 96/267 (35%), Gaps = 41/267 (15%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPS---LRKSGVGNVFIKNLDKSIDNKAMYDTFS 132
           D++R LD       +G P     + +  +    R   +  V +KNL KS +   +Y  F 
Sbjct: 11  DSKRPLD-------EGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFK 63

Query: 133 AFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
             G I+   VA      +  +  + F   + A  +I K + + +    + V         
Sbjct: 64  HCGPIIHVDVADSL-KKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIVSHLT----- 116

Query: 193 EKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAY 250
                        +++ NF   +    ++++ +    +     +       SR F ++  
Sbjct: 117 ----------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDV 166

Query: 251 ESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYV 310
            S E A   V+  NG +++G  L             ++    E  K       +G  + +
Sbjct: 167 TSKEDARYCVEKLNGLKIEGYTLVT-----------KVSNPLEKSKRTDSATLEGREIMI 215

Query: 311 KNLDDSIDDER-LRKEFTPFGTITSAK 336
           +NL   + DE  LR+ F  FG+I    
Sbjct: 216 RNLSTELLDENLLRESFEGFGSIEKIN 242

>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 =  179 bits (456), Expect = 1e-54
 Identities = 38/211 (18%), Positives = 79/211 (37%), Gaps = 17/211 (8%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
               A+   +   +    I +                +++ N   S   + + D      
Sbjct: 93  GALAAITKTHKV-VGQNEIIVSHLTEC---------TLWMTNFPPSYTQRNIRDLLQDIN 142

Query: 136 SI-LSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
            + LS ++       S+ + ++   ++E A   +EK+NG+ +    +   K     E+ K
Sbjct: 143 VVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVT-KVSNPLEKSK 201

Query: 195 ELGEKAKLFTNVYIKNFGEDFNDEK-LKEMFEPYGTITSYRVMNND---GKSRGFGFVAY 250
                      + I+N   +  DE  L+E FE +G+I    +         +    F+ +
Sbjct: 202 RTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVF 261

Query: 251 ESPEFAEKAVQAWNGKEVDGKILYVGRAQKK 281
           E+ + AE+A+Q  N   +  + + V  A KK
Sbjct: 262 ENKDSAERALQM-NRSLLGNREISVSLADKK 291

>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 =  254 bits (651), Expect = 6e-84
 Identities = 45/251 (17%), Positives = 83/251 (33%), Gaps = 40/251 (15%)

Query: 89  LKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQG 148
           L    IR      +   R      + I+ L   + N+ ++D  S +  +  C V      
Sbjct: 3   LDPEEIRKRLEHTERQFRNRR--KILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----D 54

Query: 149 NSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYI 208
             KG  FV     E A  +I   +   L  + + V              +       + +
Sbjct: 55  KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSV--------------QLQPTDALLCV 100

Query: 209 KNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGK 266
            N       ++ +E+  P+G++    ++     G+S+G+GF  Y   + A +A     GK
Sbjct: 101 ANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGK 160

Query: 267 EVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDD-ERLRKE 325
            +  + LYV            L  R                L V  L    +D + L + 
Sbjct: 161 PLGPRTLYVHWTDAGQLTPALLHSR---------------CLCVDRLPPGFNDVDALCRA 205

Query: 326 FTPFGTITSAK 336
            +   + T  +
Sbjct: 206 LSAVHSPTFCQ 216

>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 =  227 bits (580), Expect = 3e-73
 Identities = 48/228 (21%), Positives = 87/228 (38%), Gaps = 17/228 (7%)

Query: 78  ERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSI 137
           E A++  +   L+ R + +     D          + + NL  S+  +   +    FGS+
Sbjct: 71  EAAINAFHQSRLRERELSVQLQPTDA--------LLCVANLPPSLTQQQFEELVRPFGSL 122

Query: 138 LSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKEL 196
             C +   E+ G SKGYGF  +  +++A ++   + G  L  + ++V      +     L
Sbjct: 123 ERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALL 182

Query: 197 GEKAKLFTNVYIKNFGEDFND-EKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPE 254
             +      + +      FND + L        + T  ++    DG+ +GF  + YE+ E
Sbjct: 183 HSR-----CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAE 237

Query: 255 FAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNR 302
            AE+A Q  +G  + G  L V            L            NR
Sbjct: 238 MAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATAL-NR 284

>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 =  118 bits (299), Expect = 1e-31
 Identities = 25/123 (20%), Positives = 46/123 (37%), Gaps = 2/123 (1%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQR-DPSLRKSGVGNVFIKNLDKSI-DNKAMYDTFSA 133
              RA   +    L  R + + W+     +        + +  L     D  A+    SA
Sbjct: 149 SAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSA 208

Query: 134 FGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKERE 193
             S   C++A  + G  KG+  + +ET E A ++ ++ +G+ L    + V    P     
Sbjct: 209 VHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGR 268

Query: 194 KEL 196
             L
Sbjct: 269 SML 271

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  247 bits (633), Expect = 3e-82
 Identities = 50/192 (26%), Positives = 100/192 (52%), Gaps = 10/192 (5%)

Query: 100 QRDPSLRKSG----VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYG 154
            R  + ++ G    +  V++ ++   +    +   F+ FG I S  ++ D      KG+ 
Sbjct: 14  GRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFA 73

Query: 155 FVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKERE---KELGEKAKLFTNVYIKNF 211
           FV +E  EAA  ++E++N ++L  + + VG+     + +    +L E+A+ F  +Y+ + 
Sbjct: 74  FVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASV 133

Query: 212 GEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD 269
            +D +D+ +K +FE +G I S  +      GK +G+GF+ YE  + ++ AV + N  ++ 
Sbjct: 134 HQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLG 193

Query: 270 GKILYVGRAQKK 281
           G+ L VG+A   
Sbjct: 194 GQYLRVGKAVTP 205

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  144 bits (366), Expect = 4e-42
 Identities = 35/166 (21%), Positives = 69/166 (41%), Gaps = 16/166 (9%)

Query: 173 GMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS 232
             +   + +  G    R+     +         VY+ +   +  ++ +++ F P+G I S
Sbjct: 5   ASMTGGQQMGRGSAAQRQGALAIMS-------RVYVGSIYYELGEDTIRQAFAPFGPIKS 57

Query: 233 YRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKR 290
             +   +   K +GF FV YE PE A+ A++  N   + G+ + VGR     +    + +
Sbjct: 58  IDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQ 117

Query: 291 RFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             E  +           +YV ++   + D+ ++  F  FG I SA 
Sbjct: 118 LAEEAR-------AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSAT 156

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  127 bits (321), Expect = 1e-35
 Identities = 30/127 (23%), Positives = 58/127 (45%), Gaps = 10/127 (7%)

Query: 78  ERALDTMNFDALKGRPIRIMWS----QRDPSLRK-----SGVGNVFIKNLDKSIDNKAMY 128
           + AL+ MN   L GR I++       Q  P + +          +++ ++ + + +  + 
Sbjct: 84  QLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIK 143

Query: 129 DTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI 187
             F AFG I S  +A+D   G  KGYGF+ +E  +++  ++  +N   L  + + VGK +
Sbjct: 144 SVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203

Query: 188 PRKEREK 194
                  
Sbjct: 204 TPPMPLL 210

>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 =  224 bits (572), Expect = 1e-73
 Identities = 41/184 (22%), Positives = 82/184 (44%), Gaps = 10/184 (5%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHF 158
           S        +   N+FI NL+ +     +    S   +     V     G ++ +G+V F
Sbjct: 2   SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF 61

Query: 159 ETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDE 218
           E+ E   K++E + G+ +    + + K   R  ++            +  KN   +  ++
Sbjct: 62  ESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVR------AARTLLAKNLSFNITED 114

Query: 219 KLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA 278
           +LKE+FE    I    +++ DGKS+G  ++ ++S   AEK ++   G E+DG+ + +   
Sbjct: 115 ELKEVFEDALEIR---LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT 171

Query: 279 QKKA 282
            +K 
Sbjct: 172 GEKG 175

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =  126 bits (319), Expect = 1e-35
 Identities = 28/135 (20%), Positives = 52/135 (38%), Gaps = 18/135 (13%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQ 261
             N++I N   + +  +LK             V++   G +R FG+V +ES E  EKA++
Sbjct: 13  PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE 72

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
              G +V G  + + + + +  +                       L  KNL  +I ++ 
Sbjct: 73  L-TGLKVFGNEIKLEKPKGRDSKKVR----------------AARTLLAKNLSFNITEDE 115

Query: 322 LRKEFTPFGTITSAK 336
           L++ F     I    
Sbjct: 116 LKEVFEDALEIRLVS 130

>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 =  105 bits (265), Expect = 9e-28
 Identities = 24/114 (21%), Positives = 49/114 (42%), Gaps = 5/114 (4%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
           D E+AL+ +    + G  I++   +   S +      +  KNL  +I    + + F    
Sbjct: 66  DLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL 124

Query: 136 SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR 189
            I        + G SKG  ++ F++E  A K++E+  G  ++ + V +     +
Sbjct: 125 EIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174

>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 =  213 bits (544), Expect = 9e-69
 Identities = 102/157 (64%), Positives = 119/157 (75%), Gaps = 13/157 (8%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
           D ERALDTMNFD +KG+P+RIMWSQRDPSLRKSGVGN+FIKNLDKSIDNKA+YDTFSAFG
Sbjct: 69  DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG 128

Query: 136 SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKE 195
           +ILSCKV  DE   SKGYGFVHFET+EAA ++IEK+NGMLLN + VFVG+F  RKERE E
Sbjct: 129 NILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 187

Query: 196 LGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS 232
           LG +AK F    + ++                G I +
Sbjct: 188 LGARAKEFYPYDVPDY------------AGSSGRIVT 212

>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 =  186 bits (475), Expect = 2e-58
 Identities = 54/210 (25%), Positives = 106/210 (50%), Gaps = 7/210 (3%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVH 157
              +PS     + ++++ +L   +    +Y+ FS  G ILS +V +D     S GY +V+
Sbjct: 4   GSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN 63

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFND 217
           F+    A ++++ +N  ++  K V +          K          N++IKN  +  ++
Sbjct: 64  FQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGV------GNIFIKNLDKSIDN 117

Query: 218 EKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR 277
           + L + F  +G I S +V+ ++  S+G+GFV +E+ E AE+A++  NG  ++ + ++VGR
Sbjct: 118 KALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177

Query: 278 AQKKAERTQELKRRFEMLKIERLNRYQGVN 307
            + + ER  EL  R +      +  Y G +
Sbjct: 178 FKSRKEREAELGARAKEFYPYDVPDYAGSS 207

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score =  105 bits (264), Expect = 3e-27
 Identities = 38/135 (28%), Positives = 63/135 (46%), Gaps = 18/135 (13%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
            ++Y+ +   D  +  L E F P G I S RV  +    +S G+ +V ++ P  AE+A+ 
Sbjct: 16  ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
             N   + GK + +  +Q+                   L +    N+++KNLD SID++ 
Sbjct: 76  TMNFDVIKGKPVRIMWSQRDP----------------SLRKSGVGNIFIKNLDKSIDNKA 119

Query: 322 LRKEFTPFGTITSAK 336
           L   F+ FG I S K
Sbjct: 120 LYDTFSAFGNILSCK 134

>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 = 41.5 bits (98), Expect = 1e-04
 Identities = 11/35 (31%), Positives = 19/35 (54%)

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            Y   +LYV +L   + +  L ++F+P G I S +
Sbjct: 12  SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIR 46

>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 =  187 bits (477), Expect = 3e-59
 Identities = 41/178 (23%), Positives = 76/178 (42%), Gaps = 11/178 (6%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN---SKGYGFVHFETEEAA 164
           S    +F+  + ++   K + + F  +G++    V +D   N   SKG  FV F T +AA
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 165 NKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMF 224
            ++   ++ M +   +    +  P    +    E  KLF    I    +   +  ++ MF
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLF----IGMISKKCTENDIRVMF 116

Query: 225 EPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEV---DGKILYVGRA 278
             +G I   R++   DG SRG  FV + +   A+ A++A +  +        + V  A
Sbjct: 117 SSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score =  136 bits (346), Expect = 1e-39
 Identities = 24/137 (17%), Positives = 56/137 (40%), Gaps = 18/137 (13%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM----NNDGKSRGFGFVAYESPEFAEKA 259
             +++      ++++ L+E+FE YG +    V+     N  +S+G  FV + + + A +A
Sbjct: 4   IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63

Query: 260 VQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDD 319
             A +  +V   + +  + +                  E+ N  +   L++  +     +
Sbjct: 64  QNALHNMKVLPGMHHPIQMKPA--------------DSEKNNAVEDRKLFIGMISKKCTE 109

Query: 320 ERLRKEFTPFGTITSAK 336
             +R  F+ FG I   +
Sbjct: 110 NDIRVMFSSFGQIEECR 126

>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 = 98.5 bits (246), Expect = 4e-25
 Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 4/99 (4%)

Query: 78  ERALDTMN---FDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAF 134
             A + ++          PI++  +  + +        +FI  + K      +   FS+F
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDR-KLFIGMISKKCTENDIRVMFSSF 119

Query: 135 GSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG 173
           G I  C++ +   G S+G  FV F T   A  +I+ ++ 
Sbjct: 120 GQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQ 158

>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 =  190 bits (484), Expect = 3e-59
 Identities = 40/259 (15%), Positives = 93/259 (35%), Gaps = 43/259 (16%)

Query: 91  GRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS 150
           G  I I    +      +    +F+ NL   I  +     F  +G      + +D     
Sbjct: 3   GFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD----- 57

Query: 151 KGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKN 210
           +G+GF+  E+   A  +  +++G +L S+ + +                A     + +KN
Sbjct: 58  RGFGFIRLESRTLAEIAKAELDGTILKSRPLRI--------------RFATHGAALTVKN 103

Query: 211 FGEDFNDEKLKEMFEPYGTITSYRVMNND-GKSRGFGFVAYESPEFAEKAVQAWNGKEV- 268
                ++E L++ F  +G +    V+ +D G++ G GFV + +   A KA++        
Sbjct: 104 LSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFL 163

Query: 269 ---DGKILYVGRAQKKAERTQELKRRFE-------------------MLKIERLNRYQGV 306
                + + V   ++  +     ++  +                     + E  +R++ +
Sbjct: 164 LTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRWKAL 223

Query: 307 NLYVKNLDDSIDDERLRKE 325
           +   K   + +D      +
Sbjct: 224 DEMEKQQREQVDRNIREAK 242

>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 =  178 bits (453), Expect = 1e-54
 Identities = 46/225 (20%), Positives = 79/225 (35%), Gaps = 37/225 (16%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
             E A   ++   LK RP+RI ++             + +KNL   + N+ +   FS FG
Sbjct: 70  LAEIAKAELDGTILKSRPLRIRFATHGA--------ALTVKNLSPVVSNELLEQAFSQFG 121

Query: 136 SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG---MLLNSKIVFVGKFIPRKER 192
            +    V  D++G + G GFV F  +  A K++E+      +L  +    + + + + + 
Sbjct: 122 PVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDD 181

Query: 193 EKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYES 252
           E  L EK    T  Y K              F   GT                       
Sbjct: 182 EDGLPEKLMQKTQQYHKERE-------QPPRFAQPGTFEFEYAS---------------- 218

Query: 253 PEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKI 297
                KA+     ++ +     +  A++K E   E  R    L +
Sbjct: 219 ---RWKALDEMEKQQREQVDRNIREAKEKLEAEMEAARHEHQLML 260

>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 =  145 bits (368), Expect = 7e-42
 Identities = 37/154 (24%), Positives = 57/154 (37%), Gaps = 28/154 (18%)

Query: 183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKS 242
           +G  I  K   K   +       +++ N   D  +E  K +FE YG  +   +     + 
Sbjct: 2   MGFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN----RD 57

Query: 243 RGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNR 302
           RGFGF+  ES   AE A    +G  +  + L +  A                        
Sbjct: 58  RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT----------------------- 94

Query: 303 YQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             G  L VKNL   + +E L + F+ FG +  A 
Sbjct: 95  -HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAV 127

>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 =  186 bits (474), Expect = 8e-59
 Identities = 50/176 (28%), Positives = 88/176 (50%), Gaps = 13/176 (7%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANK 166
           +   N+ +  L + + ++ +Y  F A G I +C++ +D + G S GY FV F +E  + +
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60

Query: 167 SIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEP 226
           +I+ +NG+ + +K + V    P  E  K+        TN+Y+ N      D++L  +F  
Sbjct: 61  AIKVLNGITVRNKRLKVSYARPGGESIKD--------TNLYVTNLPRTITDDQLDTIFGK 112

Query: 227 YGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG--KILYVGRA 278
           YG+I    ++     G+ RG  FV Y   E A++A+ A N    +G  + L V  A
Sbjct: 113 YGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score =  147 bits (374), Expect = 6e-44
 Identities = 37/136 (27%), Positives = 60/136 (44%), Gaps = 20/136 (14%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
            TN+ +    +D  D +L  +F   G I + R+M +   G S G+ FV + S   +++A+
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62

Query: 261 QAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDE 320
           +  NG  V  K L V  A+   E  ++                   NLYV NL  +I D+
Sbjct: 63  KVLNGITVRNKRLKVSYARPGGESIKD------------------TNLYVTNLPRTITDD 104

Query: 321 RLRKEFTPFGTITSAK 336
           +L   F  +G+I    
Sbjct: 105 QLDTIFGKYGSIVQKN 120

>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 =  136 bits (346), Expect = 1e-39
 Identities = 22/103 (21%), Positives = 54/103 (52%), Gaps = 3/103 (2%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
           D++RA+  +N   ++ + +++ +++  P        N+++ NL ++I +  +   F  +G
Sbjct: 57  DSQRAIKVLNGITVRNKRLKVSYAR--PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYG 114

Query: 136 SILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLN 177
           SI+   + +D+  G  +G  FV +   E A ++I  +N ++  
Sbjct: 115 SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPE 157

>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 =  171 bits (436), Expect = 6e-54
 Identities = 80/111 (72%), Positives = 90/111 (81%), Gaps = 1/111 (0%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
            G GN+FIKNLDKSIDNKA+YDTFSAFG+ILSCKV  DE   SKGYGFVHFET+EAA ++
Sbjct: 3   LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERA 61

Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDE 218
           IEK+NGMLLN + VFVG+F  RKERE ELG +AK FTNVYIKNFG      
Sbjct: 62  IEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRA 112

>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 =  125 bits (315), Expect = 8e-36
 Identities = 34/117 (29%), Positives = 64/117 (54%), Gaps = 10/117 (8%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
            N++IKN  +  +++ L + F  +G I S +V+ ++  S+G+GFV +E+ E AE+A++  
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 65

Query: 264 NGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDE 320
           NG  ++ + ++VGR + + ER  EL  R +          +  N+Y+KN        
Sbjct: 66  NGMLLNDRKVFVGRFKSRKEREAELGARAK----------EFTNVYIKNFGPGSTRA 112

>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 = 51.9 bits (125), Expect = 1e-08
 Identities = 15/30 (50%), Positives = 21/30 (70%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           N+++KNLD SID++ L   F+ FG I S K
Sbjct: 7   NIFIKNLDKSIDNKALYDTFSAFGNILSCK 36

>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 =  170 bits (432), Expect = 1e-52
 Identities = 30/110 (27%), Positives = 60/110 (54%), Gaps = 1/110 (0%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
           D   AL T+N   ++   ++I W+ +          N+F+ +L+ ++D++ + + F  F 
Sbjct: 53  DANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFP 112

Query: 136 SILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG 184
           S LS  V  D + G+S+GYGFV F +++ A  +++ + G  LN + + + 
Sbjct: 113 SYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 162

>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 =  159 bits (404), Expect = 2e-48
 Identities = 42/170 (24%), Positives = 85/170 (50%), Gaps = 8/170 (4%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +++ NLDK+I    +   F   G I + K+  D+   +  Y FV +     AN +++ +N
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 173 GMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS 232
           G  + + IV +      ++   +         N+++ +   + +DE L+  F+ + +  S
Sbjct: 63  GKQIENNIVKINWAFQSQQSSSDDT------FNLFVGDLNVNVDDETLRNAFKDFPSYLS 116

Query: 233 YRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK 280
             VM     G SRG+GFV++ S + A+ A+ +  G++++G+ L +  A K
Sbjct: 117 GHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166

>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 =  118 bits (297), Expect = 1e-32
 Identities = 32/132 (24%), Positives = 62/132 (46%), Gaps = 17/132 (12%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAEKAVQAWN 264
           +Y+ N  +   ++ LK+ F+  G I + ++M + + K+  + FV Y     A  A+Q  N
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 265 GKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRK 324
           GK+++  I+ +  A +                 ++ +     NL+V +L+ ++DDE LR 
Sbjct: 63  GKQIENNIVKINWAFQS----------------QQSSSDDTFNLFVGDLNVNVDDETLRN 106

Query: 325 EFTPFGTITSAK 336
            F  F +  S  
Sbjct: 107 AFKDFPSYLSGH 118

>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 =  165 bits (420), Expect = 1e-50
 Identities = 47/172 (27%), Positives = 88/172 (51%), Gaps = 13/172 (7%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L +++  +     F + G I SCK+ +D+  G S GYGFV++   + A K+I  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTI 230
           +NG+ L +K + V    P     ++         N+Y+    +    ++L+++F  YG I
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASIRD--------ANLYVSGLPKTMTQKELEQLFSQYGRI 115

Query: 231 TSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG--KILYVGRA 278
            + R++     G SRG GF+ ++    AE+A++  NG++  G  + + V  A
Sbjct: 116 ITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score =  150 bits (381), Expect = 6e-45
 Identities = 28/103 (27%), Positives = 59/103 (57%), Gaps = 3/103 (2%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
           D E+A++T+N   L+ + I++ +++  PS       N+++  L K++  K +   FS +G
Sbjct: 56  DAEKAINTLNGLRLQTKTIKVSYAR--PSSASIRDANLYVSGLPKTMTQKELEQLFSQYG 113

Query: 136 SILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLN 177
            I++ ++  D+  G S+G GF+ F+    A ++I+ +NG   +
Sbjct: 114 RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPS 156

>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 =  131 bits (331), Expect = 2e-37
 Identities = 33/135 (24%), Positives = 61/135 (45%), Gaps = 20/135 (14%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    ++   E+ + +F   G I S +++     G+S G+GFV Y  P+ AEKA+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER 321
             NG  +  K + V  A+  +                     +  NLYV  L  ++  + 
Sbjct: 63  TLNGLRLQTKTIKVSYARPSSASI------------------RDANLYVSGLPKTMTQKE 104

Query: 322 LRKEFTPFGTITSAK 336
           L + F+ +G I +++
Sbjct: 105 LEQLFSQYGRIITSR 119

>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 =  164 bits (417), Expect = 7e-50
 Identities = 32/191 (16%), Positives = 76/191 (39%), Gaps = 21/191 (10%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ------GNSKGYGFVHFETEEAANK 166
           +++ N+   I  +AM D F+A   +     A             K + F+ F + +   +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 167 SIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKL------------FTNVYIKNFGED 214
           ++   +G++   + + + +    +         +                 ++I      
Sbjct: 67  AMAF-DGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125

Query: 215 FNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKI 272
            ND+++KE+   +G + ++ ++  +  G S+G+ F  Y      ++A+   NG ++  K 
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185

Query: 273 LYVGRAQKKAE 283
           L V RA   A+
Sbjct: 186 LLVQRASVGAK 196

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score =  121 bits (305), Expect = 2e-33
 Identities = 19/140 (13%), Positives = 51/140 (36%), Gaps = 10/140 (7%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-------GKSRGFGFVAYESPEFAEK 258
           +Y+ N      +E + + F     +        +        + + F F+ + S +   +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 259 AVQAWNGKEVDGKILYVGRAQKKAER--TQELKRRFEMLKIERLNRYQGVNLYVKNLDDS 316
           A+   +G    G+ L + R           E    +    +  +       L++  L + 
Sbjct: 67  AMAF-DGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125

Query: 317 IDDERLRKEFTPFGTITSAK 336
           ++D+++++  T FG + +  
Sbjct: 126 LNDDQVKELLTSFGPLKAFN 145

>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 = 93.9 bits (234), Expect = 5e-23
 Identities = 23/129 (17%), Positives = 52/129 (40%), Gaps = 20/129 (15%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQ------------------RDPSLRKSGVGNVFIKN 117
           +T +A+   +    +G+ ++I                         ++       +FI  
Sbjct: 63  ETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGG 121

Query: 118 LDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKVNGMLL 176
           L   +++  + +  ++FG + +  + +D   G SKGY F  +      +++I  +NGM L
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181

Query: 177 NSKIVFVGK 185
             K + V +
Sbjct: 182 GDKKLLVQR 190

>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 =  155 bits (393), Expect = 1e-46
 Identities = 31/174 (17%), Positives = 73/174 (41%), Gaps = 17/174 (9%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ------GNSKGYGFVHFETEEAANK 166
           +++ N+   I  +AM D F+A   +     A             K + F+ F + +   +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 167 SIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEP 226
           ++   +G++   + + + +    +               ++I       ND+++KE+   
Sbjct: 67  AM-AFDGIIFQGQSLKIRRPHDYQPLPG--------AHKLFIGGLPNYLNDDQVKELLTS 117

Query: 227 YGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA 278
           +G + ++ ++  +  G S+G+ F  Y      ++A+   NG ++  K L V RA
Sbjct: 118 FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score =  123 bits (310), Expect = 2e-34
 Identities = 24/111 (21%), Positives = 52/111 (46%), Gaps = 4/111 (3%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG 135
           +T +A+   +    +G+ ++I        L  +    +FI  L   +++  + +  ++FG
Sbjct: 63  ETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAH--KLFIGGLPNYLNDDQVKELLTSFG 119

Query: 136 SILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK 185
            + +  + +D   G SKGY F  +      +++I  +NGM L  K + V +
Sbjct: 120 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 93.8 bits (234), Expect = 2e-23
 Identities = 18/138 (13%), Positives = 47/138 (34%), Gaps = 26/138 (18%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-------GKSRGFGFVAYESPEFAEK 258
           +Y+ N      +E + + F     +        +        + + F F+ + S +   +
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 259 AVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSID 318
           A+   +G    G+ L + R                              L++  L + ++
Sbjct: 67  AMAF-DGIIFQGQSLKIRRPHDYQPLPG------------------AHKLFIGGLPNYLN 107

Query: 319 DERLRKEFTPFGTITSAK 336
           D+++++  T FG + +  
Sbjct: 108 DDQVKELLTSFGPLKAFN 125

>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 =  132 bits (334), Expect = 6e-39
 Identities = 37/92 (40%), Positives = 55/92 (59%), Gaps = 2/92 (2%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQD-EQGNSKGYGFVHFETEEAAN 165
           SG   +FI NLD  ID K +YDTFSAFG IL   K+ +D + GNSKGY F++F + +A++
Sbjct: 3   SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62

Query: 166 KSIEKVNGMLLNSKIVFVGKFIPRKEREKELG 197
            +IE +NG  L ++ + V     +  +     
Sbjct: 63  AAIEAMNGQYLCNRPITVSYAFKKDSKGSGPS 94

>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 = 87.6 bits (218), Expect = 7e-22
 Identities = 20/83 (24%), Positives = 45/83 (54%), Gaps = 3/83 (3%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITS-YRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
            ++I N   + +++ L + F  +G I    ++M +   G S+G+ F+ + S + ++ A++
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
           A NG+ +  + + V  A KK  +
Sbjct: 67  AMNGQYLCNRPITVSYAFKKDSK 89

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 10/30 (33%), Positives = 16/30 (53%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            +++ NLD  ID++ L   F+ FG I    
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTP 36

>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 =  132 bits (335), Expect = 5e-38
 Identities = 42/174 (24%), Positives = 88/174 (50%), Gaps = 14/174 (8%)

Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIE 169
             +FI  L+       + + F  +G++   K+ +D   G S+G+GF+ FE   + ++ ++
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63

Query: 170 KVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGT 229
             +  +L+ K++   + IPR E++K           +++   G D   ++ +E F  +GT
Sbjct: 64  TQH--ILDGKVIDPKRAIPRDEQDKT--------GKIFVGGIGPDVRPKEFEEFFSQWGT 113

Query: 230 ITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK 281
           I   ++M   + G+SRGFGFV Y+S +  ++  Q     +   + + + RA+ +
Sbjct: 114 IIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIKRAEPR 166

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 91.1 bits (227), Expect = 2e-22
 Identities = 36/141 (25%), Positives = 65/141 (46%), Gaps = 26/141 (18%)

Query: 198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEF 255
           E  K+F    I     D  ++ L+E F  YGT+T  ++M     G+SRGFGF+++E P  
Sbjct: 2   ESCKMF----IGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSS 57

Query: 256 AEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDD 315
            ++ V+      +DGK++   RA  + E+ +  K                  ++V  +  
Sbjct: 58  VDEVVKT--QHILDGKVIDPKRAIPRDEQDKTGK------------------IFVGGIGP 97

Query: 316 SIDDERLRKEFTPFGTITSAK 336
            +  +   + F+ +GTI  A+
Sbjct: 98  DVRPKEFEEFFSQWGTIIDAQ 118

>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 = 69.5 bits (171), Expect = 2e-14
 Identities = 23/116 (19%), Positives = 53/116 (45%), Gaps = 8/116 (6%)

Query: 76  DTERALDTMNFDALKGRPIRI-MWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAF 134
             +  + T +   L G+ I       RD   +    G +F+  +   +  K   + FS +
Sbjct: 57  SVDEVVKTQHI--LDGKVIDPKRAIPRDEQDK---TGKIFVGGIGPDVRPKEFEEFFSQW 111

Query: 135 GSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR 189
           G+I+  ++  D + G S+G+GFV +++ +A ++  +    +    + + + +  PR
Sbjct: 112 GTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRKIEIKRAEPR 166

>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 =  131 bits (331), Expect = 6e-37
 Identities = 32/211 (15%), Positives = 72/211 (34%), Gaps = 35/211 (16%)

Query: 100 QRDPSLRKSGVGNVFIKNLD-KSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHF 158
              P L  +G   + + NL+ + +  ++++  F  +G +   K+  +     K    V  
Sbjct: 24  IAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQM 79

Query: 159 ETEEAANKSIEKVNGMLLNSKIVFVG----KFIPRKEREKELGEKAKLFTN--------- 205
                A  ++  +NG  L+ K + +     + +      +E     K + N         
Sbjct: 80  ADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKP 139

Query: 206 --------------VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYE 251
                         +++ N     ++E LK +F   G +          K R    +   
Sbjct: 140 GSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ--KDRKMALIQMG 197

Query: 252 SPEFAEKAVQAWNGKEV-DGKILYVGRAQKK 281
           S E A +A+   +  ++ +   L V  ++  
Sbjct: 198 SVEEAVQALIDLHNHDLGENHHLRVSFSKST 228

>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 = 97.8 bits (243), Expect = 3e-24
 Identities = 24/151 (15%), Positives = 56/151 (37%), Gaps = 21/151 (13%)

Query: 204 TNVYIKNFG-EDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
           + + + N   E    + L  +F  YG +   +++      +    V       A+ A+  
Sbjct: 35  SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF---NKKENALVQMADGNQAQLAMSH 91

Query: 263 WNGKEVDGKILYVGRAQKKA-------ERTQELKRRFEMLKIERLNRYQGVN-------- 307
            NG ++ GK + +  ++ +        +  Q L + +    + R  +    N        
Sbjct: 92  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 151

Query: 308 --LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             L++ N+  S+ +E L+  F+  G +    
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF 182

>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 =  126 bits (317), Expect = 3e-35
 Identities = 30/202 (14%), Positives = 69/202 (34%), Gaps = 35/202 (17%)

Query: 109 GVGNVFIKNLD-KSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
           G   + + NL+ + +  ++++  F  +G +   K+  +     K    V       A  +
Sbjct: 2   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLA 57

Query: 168 IEKVNGMLLNSKIVFVG----KFIPRKEREKELGEKAKLFTN------------------ 205
           +  +NG  L+ K + +     + +      +E     K + N                  
Sbjct: 58  MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117

Query: 206 -----VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAV 260
                +++ N     ++E LK +F   G +          K R    +   S E A +A+
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ--KDRKMALIQMGSVEEAVQAL 175

Query: 261 QAWNGKEV-DGKILYVGRAQKK 281
              +  ++ +   L V  ++  
Sbjct: 176 IDLHNHDLGENHHLRVSFSKST 197

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score =  102 bits (255), Expect = 4e-26
 Identities = 24/151 (15%), Positives = 56/151 (37%), Gaps = 21/151 (13%)

Query: 204 TNVYIKNFG-EDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
           + + + N   E    + L  +F  YG +   +++      +    V       A+ A+  
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF---NKKENALVQMADGNQAQLAMSH 60

Query: 263 WNGKEVDGKILYVGRA-------QKKAERTQELKRRFEMLKIERLNRYQGVN-------- 307
            NG ++ GK + +  +        ++ +  Q L + +    + R  +    N        
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120

Query: 308 --LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             L++ N+  S+ +E L+  F+  G +    
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF 151

>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 =  122 bits (308), Expect = 5e-35
 Identities = 44/105 (41%), Positives = 59/105 (56%), Gaps = 5/105 (4%)

Query: 184 GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSR 243
           G      +R            N+Y+KN  +  +DE+L++ F P+GTITS +VM   G+S+
Sbjct: 1   GSSGSSGDRITRYQ-----VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSK 55

Query: 244 GFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQEL 288
           GFGFV + SPE A KAV   NG+ V  K LYV  AQ+K ER    
Sbjct: 56  GFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGP 100

>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 = 98.8 bits (247), Expect = 4e-26
 Identities = 33/89 (37%), Positives = 57/89 (64%), Gaps = 1/89 (1%)

Query: 105 LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAA 164
           + +  V N+++KNLD  ID++ +   FS FG+I S KV  +  G SKG+GFV F + E A
Sbjct: 10  ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEA 68

Query: 165 NKSIEKVNGMLLNSKIVFVGKFIPRKERE 193
            K++ ++NG ++ +K ++V     ++ER+
Sbjct: 69  TKAVTEMNGRIVATKPLYVALAQRKEERQ 97

>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 = 73.0 bits (180), Expect = 2e-16
 Identities = 32/39 (82%), Positives = 35/39 (89%)

Query: 298 ERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           +R+ RYQ VNLYVKNLDD IDDERLRK F+PFGTITSAK
Sbjct: 8   DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAK 46

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score =  120 bits (304), Expect = 2e-34
 Identities = 26/103 (25%), Positives = 48/103 (46%), Gaps = 6/103 (5%)

Query: 184 GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSR 243
              +PR        E     T ++++ F  D  + +L E+F P+G +   +++       
Sbjct: 12  SGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL------N 65

Query: 244 GFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQ 286
           GF FV +E  E A KA++  +GK    + L V  ++  A+R +
Sbjct: 66  GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRYR 108

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 81.6 bits (202), Expect = 1e-19
 Identities = 11/62 (17%), Positives = 22/62 (35%)

Query: 275 VGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITS 334
           +G +      +  L  R   +   +        L+V+     + +  L + F PFG +  
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKE 60

Query: 335 AK 336
            K
Sbjct: 61  VK 62

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 74.6 bits (184), Expect = 5e-17
 Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 7/96 (7%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHF 158
                   +     +F++     +    + + F  FG +   K+         G+ FV F
Sbjct: 20  HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEF 72

Query: 159 ETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
           E  E+A K+IE+V+G    ++ + V       +R +
Sbjct: 73  EEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRYR 108

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score =  119 bits (301), Expect = 4e-34
 Identities = 28/92 (30%), Positives = 44/92 (47%), Gaps = 6/92 (6%)

Query: 104 SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEA 163
           S   SG   +F++NL      K + D F+  G +L   +  +  G SKG G V FE+ E 
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEV 60

Query: 164 ANKSIEKVNGMLLNSKIVFVGKFIPRKEREKE 195
           A ++   +NGM L+ + + V     R +R   
Sbjct: 61  AERACRMMNGMKLSGREIDV-----RIDRNAS 87

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score =  101 bits (253), Expect = 5e-27
 Identities = 24/81 (29%), Positives = 43/81 (53%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             ++++N   DF  + LK+ F   G +    +   +GKS+G G V +ESPE AE+A +  
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMM 68

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           NG ++ G+ + V   +  +  
Sbjct: 69  NGMKLSGREIDVRIDRNASGP 89

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 46.4 bits (111), Expect = 5e-07
 Identities = 7/33 (21%), Positives = 14/33 (42%)

Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
               ++V+NL      + L+ +F   G +  A 
Sbjct: 7   GACQIFVRNLPFDFTWKMLKDKFNECGHVLYAD 39

>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 =  120 bits (304), Expect = 3e-33
 Identities = 44/198 (22%), Positives = 85/198 (42%), Gaps = 11/198 (5%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVH 157
           S+ +       +  +FI  L     ++++   F  +G++  C V +D     S+G+GFV 
Sbjct: 2   SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKA--KLFTNVYIKNFGEDF 215
           + T E  + ++       ++ ++V   + + R++ ++        K+F    +    ED 
Sbjct: 62  YATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIF----VGGIKEDT 116

Query: 216 NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
            +  L++ FE YG I    +M     GK RGF FV ++  +  +K V       V+G   
Sbjct: 117 EEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNC 175

Query: 274 YVGRAQKKAERTQELKRR 291
            V +A  K E       +
Sbjct: 176 EVRKALSKQEMASASSSQ 193

>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 = 97.0 bits (242), Expect = 3e-24
 Identities = 43/152 (28%), Positives = 68/152 (44%), Gaps = 19/152 (12%)

Query: 187 IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRG 244
           + + E  KE  +  KLF    I     +  DE L+  FE +GT+T   VM   N  +SRG
Sbjct: 1   MSKSESPKEPEQLRKLF----IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 56

Query: 245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQ 304
           FGFV Y + E  + A+ A    +VDG+++   RA  + +  Q       + KI       
Sbjct: 57  FGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDS-QRPGAHLTVKKI------- 107

Query: 305 GVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
               +V  + +  ++  LR  F  +G I   +
Sbjct: 108 ----FVGGIKEDTEEHHLRDYFEQYGKIEVIE 135

>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 =  117 bits (295), Expect = 6e-33
 Identities = 22/91 (24%), Positives = 43/91 (47%), Gaps = 1/91 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQA 262
           + V++ N       +KLKE+F   G +    ++ + DGKSRG G V +E    A +A+  
Sbjct: 16  STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75

Query: 263 WNGKEVDGKILYVGRAQKKAERTQELKRRFE 293
           +NG+ +  + ++V   ++   +         
Sbjct: 76  FNGQLLFDRPMHVKMDERALPKGDFFPPERP 106

>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 = 97.4 bits (243), Expect = 2e-25
 Identities = 27/99 (27%), Positives = 45/99 (45%), Gaps = 1/99 (1%)

Query: 99  SQRDPSLRKSGVG-NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVH 157
           S    +L+   +G  VF+ NLD  +  K + + FS  G ++   + +D+ G S+G G V 
Sbjct: 3   SGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVT 62

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKEL 196
           FE    A ++I   NG LL  + + V        +    
Sbjct: 63  FEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFF 101

>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 = 58.5 bits (142), Expect = 4e-11
 Identities = 9/33 (27%), Positives = 18/33 (54%)

Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            G  ++V NLD  +  ++L++ F+  G +  A 
Sbjct: 14  LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRAD 46

>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 =  115 bits (290), Expect = 3e-32
 Identities = 27/105 (25%), Positives = 48/105 (45%), Gaps = 11/105 (10%)

Query: 191 EREKEL---GEKAKL-------FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NND 239
                L   G +A++        TN+YI N     ++++L+ M +P+G + S R++ ++ 
Sbjct: 3   SGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS 62

Query: 240 GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
           G SRG GF   ES E  E  +  +NGK +          +    +
Sbjct: 63  GTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCK 107

>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 =  103 bits (260), Expect = 8e-28
 Identities = 21/92 (22%), Positives = 40/92 (43%)

Query: 101 RDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFET 160
           +    ++    N++I NL  S+D + + +    FG ++S ++ +D  G S+G GF   E+
Sbjct: 16  QMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMES 75

Query: 161 EEAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
            E     I   NG  + +         P   +
Sbjct: 76  TEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCK 107

>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 = 86.2 bits (214), Expect = 3e-21
 Identities = 14/55 (25%), Positives = 25/55 (45%)

Query: 282 AERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           +  +  LK      ++ +       NLY+ NL  S+D++ L     PFG + S +
Sbjct: 2   SSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTR 56

>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 =  113 bits (286), Expect = 1e-31
 Identities = 27/96 (28%), Positives = 52/96 (54%), Gaps = 1/96 (1%)

Query: 199 KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN-DGKSRGFGFVAYESPEFAE 257
           +A     ++I     + N++ LK +F  +G I+   ++ +   KSRGF F+ +E+P  A+
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAK 62

Query: 258 KAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFE 293
            A +  NGK + GK + V +A+K + ++   +R   
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPA 98

>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 = 86.2 bits (214), Expect = 3e-21
 Identities = 20/87 (22%), Positives = 37/87 (42%)

Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
           G +FI  L++  + K +   F   G I    + +D    S+G+ F+ FE    A  + + 
Sbjct: 8   GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67

Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELG 197
           +NG  L+ K + V +      +     
Sbjct: 68  MNGKSLHGKAIKVEQAKKPSFQSGGRR 94

>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 = 44.6 bits (106), Expect = 3e-06
 Identities = 6/30 (20%), Positives = 14/30 (46%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            L++  L+   +++ L+  F   G I+   
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVL 38

>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 =  118 bits (296), Expect = 3e-31
 Identities = 34/230 (14%), Positives = 67/230 (29%), Gaps = 7/230 (3%)

Query: 112 NVFIKNLDKSID----NKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
            ++I NL++ I      K++Y  FS FG IL   V++      +G  FV F+   +A  +
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRS--LKMRGQAFVIFKEVSSATNA 68

Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPY 227
           +  + G     K + +       +   ++            K   +       K+  +  
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGG 128

Query: 228 GTITSYRVMNND-GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQ 286
           G       +                      +         +    L  G+    A   Q
Sbjct: 129 GATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQ 188

Query: 287 ELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           +L                   L++ NL +  ++  L   F  F      +
Sbjct: 189 QLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVR 238

>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 = 86.9 bits (214), Expect = 7e-20
 Identities = 31/221 (14%), Positives = 69/221 (31%), Gaps = 22/221 (9%)

Query: 78  ERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSI 137
             AL +M       +P+RI +++ D S   + +   F++   K    K       A    
Sbjct: 66  TNALRSMQGFPFYDKPMRIQYAKTD-SDIIAKMKGTFVERDRKREKRKPKSQETPATKKA 124

Query: 138 LSCKVAQDEQGNSKGYGFVHFETEEAANKS-----------------IEKVNGMLLNSKI 180
           +    A    G  +G         +A                        +    +    
Sbjct: 125 VQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGA 184

Query: 181 VFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG 240
           +   + +P +    +   +      +++ N  E+ N+  L  +F  +      R++    
Sbjct: 185 MPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP--- 241

Query: 241 KSRGFGFVAYESPEFAEKAVQAWNGKEV-DGKILYVGRAQK 280
                 FV +++   A  A  A  G ++     + +  A+K
Sbjct: 242 GRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK 282

>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 =  112 bits (281), Expect = 6e-31
 Identities = 29/105 (27%), Positives = 50/105 (47%), Gaps = 4/105 (3%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             +YI+N       E++ ++F  YG I   RV N   ++RG  +V YE    A+ AV   
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN-TPETRGTAYVVYEDIFDAKNAVDHL 67

Query: 264 NGKEVDGKILYVG-RAQKKAERTQELKRRFEMLKIERLNRYQGVN 307
           +G  V  + L V      +A +  + K++ E  +++ L    G+N
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQKMDTKKKEE--QLKLLKEKYGIN 110

>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 = 77.4 bits (191), Expect = 6e-18
 Identities = 21/108 (19%), Positives = 51/108 (47%), Gaps = 2/108 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            ++I+NL   I  + MYD F  +G I   +V       ++G  +V +E    A  +++ +
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHL 67

Query: 172 NGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEK 219
           +G  ++++ + V  +   +  +K   +K +    +  + +G + +  K
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK 115

>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 = 39.3 bits (92), Expect = 2e-04
 Identities = 11/38 (28%), Positives = 16/38 (42%)

Query: 299 RLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           RL       LY++NL   I  E +   F  +G I   +
Sbjct: 2   RLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIR 39

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

 Score =  111 bits (280), Expect = 7e-31
 Identities = 16/91 (17%), Positives = 47/91 (51%), Gaps = 6/91 (6%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
              ++++N      +E L++ F  +G +   + +      + + F+ ++  + A KA++ 
Sbjct: 11  VKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL------KDYAFIHFDERDGAVKAMEE 64

Query: 263 WNGKEVDGKILYVGRAQKKAERTQELKRRFE 293
            NGK+++G+ + +  A+   ++ +E K + +
Sbjct: 65  MNGKDLEGENIEIVFAKPPDQKRKERKAQRQ 95

>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 = 78.5 bits (194), Expect = 2e-18
 Identities = 23/92 (25%), Positives = 45/92 (48%), Gaps = 7/92 (7%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
           + V  +F++NL  ++  + +   FS FG +   K         K Y F+HF+  + A K+
Sbjct: 9   AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK-------LKDYAFIHFDERDGAVKA 61

Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREKELGEK 199
           +E++NG  L  + + +    P  ++ KE   +
Sbjct: 62  MEEMNGKDLEGENIEIVFAKPPDQKRKERKAQ 93

>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 = 53.1 bits (128), Expect = 3e-09
 Identities = 11/30 (36%), Positives = 19/30 (63%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            L+V+NL +++ +E L K F+ FG +   K
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVK 42

>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 =  111 bits (280), Expect = 9e-31
 Identities = 27/87 (31%), Positives = 48/87 (55%), Gaps = 2/87 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQ 261
            N++I +  ++F D+ L +MF P+G + S +V        S+ FGFV+Y++P  A+ A+Q
Sbjct: 26  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQEL 288
           + NG ++  K L V   + K +     
Sbjct: 86  SMNGFQIGMKRLKVQLKRSKNDSKSGP 112

>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 = 92.0 bits (229), Expect = 3e-23
 Identities = 23/88 (26%), Positives = 45/88 (51%), Gaps = 1/88 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
           N+FI +L +   ++ +   F  FG+++S KV  D+Q   SK +GFV ++   +A  +I+ 
Sbjct: 27  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86

Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGE 198
           +NG  +  K + V     + + +     
Sbjct: 87  MNGFQIGMKRLKVQLKRSKNDSKSGPSS 114

>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 = 65.8 bits (161), Expect = 1e-13
 Identities = 14/49 (28%), Positives = 24/49 (48%)

Query: 288 LKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           L ++       +    +G NL++ +L     D+ L + F PFG + SAK
Sbjct: 8   LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAK 56

>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 =  112 bits (280), Expect = 8e-30
 Identities = 24/192 (12%), Positives = 61/192 (31%), Gaps = 36/192 (18%)

Query: 112 NVFIKNLDKS-IDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
            + +  LD+S ++   +++ F  +G++   K  +       G   V      A +++I  
Sbjct: 6   VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITH 61

Query: 171 VNGMLLNSKIVFVG-----KFIPRKEREKELGEKAKLFT--------------------- 204
           +N   +  + + V        +P +    E G  +                         
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQH 121

Query: 205 ---NVYIKNFGEDFNDEKLKEMFEPYGTITSYRV--MNNDGKSRGFGFVAYESPEFAEKA 259
               ++  N   +  +E   E+ +  G      V   +   +    G + ++S   A + 
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181

Query: 260 VQAWNGKEVDGK 271
           +   N  ++   
Sbjct: 182 LGFLNHYQMKNP 193

>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 = 84.4 bits (208), Expect = 2e-19
 Identities = 18/153 (11%), Positives = 47/153 (30%), Gaps = 23/153 (15%)

Query: 204 TNVYIKNFGED-FNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
             + +    +   N +++  +F  YG +   + M +     G   V        ++A+  
Sbjct: 5   PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS---KPGAAMVEMADGYAVDRAITH 61

Query: 263 WNGKEVDGKILYVGRAQ------KKAERTQELKRRFEMLKIERLNRYQ------------ 304
            N   + G+ + V  ++       ++   ++    ++     R NR+             
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQH 121

Query: 305 -GVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
               L+  N    + +E   +     G      
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTS 154

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score =  107 bits (270), Expect = 2e-29
 Identities = 26/98 (26%), Positives = 47/98 (47%), Gaps = 2/98 (2%)

Query: 184 GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSR 243
              +PR        E       +++ N    F D  L++MF  +G I    ++ N+  S+
Sbjct: 12  SGLVPRGSHMN--TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK 69

Query: 244 GFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK 281
           GFGFV +E+   A++A +  +G  V+G+ + V  A  +
Sbjct: 70  GFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 79.7 bits (197), Expect = 8e-19
 Identities = 24/91 (26%), Positives = 44/91 (48%), Gaps = 1/91 (1%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHF 158
                +  KS    + + N+     +  +   F  FG IL  ++  +E+G SKG+GFV F
Sbjct: 18  GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTF 76

Query: 159 ETEEAANKSIEKVNGMLLNSKIVFVGKFIPR 189
           E    A+++ EK++G ++  + + V     R
Sbjct: 77  ENSADADRAREKLHGTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 70.8 bits (174), Expect = 1e-15
 Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 2/62 (3%)

Query: 275 VGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITS 334
           +G +      +  L  R     +   N+ Q   L+V N+     D  LR+ F  FG I  
Sbjct: 1   MGSSHHHHHHSSGLVPRGS--HMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILD 58

Query: 335 AK 336
            +
Sbjct: 59  VE 60

>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 =  107 bits (268), Expect = 6e-29
 Identities = 20/103 (19%), Positives = 42/103 (40%), Gaps = 1/103 (0%)

Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFG 246
              +     GE  +    + + N     +D  ++E+F  +GT+    V  +  G+S G  
Sbjct: 20  DLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTA 79

Query: 247 FVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELK 289
            V +E    A KA++ + G  +DG+ + +     + +      
Sbjct: 80  DVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 122

>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 = 87.4 bits (217), Expect = 2e-21
 Identities = 20/87 (22%), Positives = 40/87 (45%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            + + NLD  + +  + + F+ FG++    V  D  G S G   VHFE    A K++++ 
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96

Query: 172 NGMLLNSKIVFVGKFIPRKEREKELGE 198
            G+ L+ + + +     + + E     
Sbjct: 97  KGVPLDGRPMDIQLVASQIDLEHHHHH 123

>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 = 62.8 bits (153), Expect = 2e-12
 Identities = 15/61 (24%), Positives = 23/61 (37%)

Query: 276 GRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSA 335
           G  Q   +  +     F+           G  L V NLD  + D  +++ F  FGT+  A
Sbjct: 6   GGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA 65

Query: 336 K 336
            
Sbjct: 66  A 66

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score =  104 bits (262), Expect = 5e-28
 Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 2/78 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
            N++I +  ++F D  L   F P+G + S +V        S+ FGFV++++P+ A+ A++
Sbjct: 41  CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100

Query: 262 AWNGKEVDGKILYVGRAQ 279
           A NG +V  K L V   +
Sbjct: 101 AMNGFQVGTKRLKVQLKK 118

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 93.6 bits (233), Expect = 7e-24
 Identities = 27/106 (25%), Positives = 52/106 (49%), Gaps = 2/106 (1%)

Query: 80  ALDTMNFDALKGRPIRIMWSQRDPSLRKSGVG-NVFIKNLDKSIDNKAMYDTFSAFGSIL 138
           +   ++   L    +    +       +   G N+FI +L +   +  +  TF  FG+++
Sbjct: 9   SASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVI 68

Query: 139 SCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
           S KV  D+Q   SK +GFV F+  ++A  +I+ +NG  + +K + V
Sbjct: 69  SAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV 114

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 76.6 bits (189), Expect = 1e-17
 Identities = 14/52 (26%), Positives = 23/52 (44%)

Query: 285 TQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           +  L         +++   +G NL++ +L     D  L   F PFG + SAK
Sbjct: 20  SVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAK 71

>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 =  103 bits (259), Expect = 8e-28
 Identities = 28/86 (32%), Positives = 42/86 (48%), Gaps = 5/86 (5%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-----NNDGKSRGFGFVAYESPEFAEK 258
           + ++IKN      +E LK +F   G I S  +           S GFGFV Y+ PE A+K
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 259 AVQAWNGKEVDGKILYVGRAQKKAER 284
           A++   G  VDG  L V  +++  + 
Sbjct: 66  ALKQLQGHTVDGHKLEVRISERATKP 91

>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 = 86.9 bits (216), Expect = 1e-21
 Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 4/90 (4%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN----SKGYGFVHFETEEA 163
           SG   +FIKNL+ S   + +   FS  G+I SC +++ +       S G+GFV ++  E 
Sbjct: 3   SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 164 ANKSIEKVNGMLLNSKIVFVGKFIPRKERE 193
           A K+++++ G  ++   + V       +  
Sbjct: 63  AQKALKQLQGHTVDGHKLEVRISERATKPA 92

>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 = 54.2 bits (131), Expect = 9e-10
 Identities = 11/32 (34%), Positives = 17/32 (53%)

Query: 305 GVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
              L++KNL+ S  +E L+  F+  G I S  
Sbjct: 5   SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCT 36

>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 =  102 bits (256), Expect = 3e-27
 Identities = 18/89 (20%), Positives = 42/89 (47%), Gaps = 3/89 (3%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQ 261
              V++       ++ +++  F  YG++   +++    G S+G+GFV++ +    +K V+
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKR 290
             +     GK L +G A +K   +    +
Sbjct: 69  --SQINFHGKKLKLGPAIRKQNLSTYHVQ 95

>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 = 99.6 bits (249), Expect = 2e-26
 Identities = 26/99 (26%), Positives = 44/99 (44%), Gaps = 2/99 (2%)

Query: 107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANK 166
           K     VF+  +D  +D   +   F+ +GS+   K+  D  G SKGYGFV F  +    K
Sbjct: 6   KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 65

Query: 167 SIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTN 205
            +E  + +  + K + +G  I ++       +   L  N
Sbjct: 66  IVE--SQINFHGKKLKLGPAIRKQNLSTYHVQPRPLIFN 102

>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 = 44.9 bits (107), Expect = 2e-06
 Identities = 7/30 (23%), Positives = 16/30 (53%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            ++V  +D  +D+  +R  F  +G++   K
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVK 40

>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 =  100 bits (250), Expect = 2e-26
 Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 1/92 (1%)

Query: 189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGF 247
             +     G   +    + + N     +D  ++E+F  +GT+    V  +  G+S G   
Sbjct: 15  LFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTAD 74

Query: 248 VAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ 279
           V +E    A KA++ +NG  +DG+ + +    
Sbjct: 75  VHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 82.3 bits (204), Expect = 7e-20
 Identities = 21/85 (24%), Positives = 43/85 (50%), Gaps = 1/85 (1%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHF 158
                +  ++G   + + NLD  + +  + + F+ FG++    V  D  G S G   VHF
Sbjct: 19  GFGGGAGVETGG-KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHF 77

Query: 159 ETEEAANKSIEKVNGMLLNSKIVFV 183
           E +  A K++++ NG+ L+ + + +
Sbjct: 78  ERKADALKAMKQYNGVPLDGRPMNI 102

>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 = 65.8 bits (161), Expect = 8e-14
 Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 5/59 (8%)

Query: 283 ERTQELKR-----RFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            R ++L        F+           G  L V NLD  + D  +++ F  FGT+  A 
Sbjct: 2   SRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAA 60

>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 = 98.9 bits (247), Expect = 5e-26
 Identities = 23/83 (27%), Positives = 43/83 (51%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
              +++ N    F D  L++MF  +G I    ++ N+  S+GFGFV +E+   A++A + 
Sbjct: 15  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREK 74

Query: 263 WNGKEVDGKILYVGRAQKKAERT 285
            +G  V+G+ + V  A  +    
Sbjct: 75  LHGTVVEGRKIEVNNATARVMTN 97

>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 = 81.6 bits (202), Expect = 1e-19
 Identities = 25/94 (26%), Positives = 44/94 (46%), Gaps = 1/94 (1%)

Query: 101 RDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFET 160
              S  KS    + + N+     +  +   F  FG IL  ++  +E+G SKG+GFV FE 
Sbjct: 6   SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFEN 64

Query: 161 EEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
              A+++ EK++G ++  + + V     R     
Sbjct: 65  SADADRAREKLHGTVVEGRKIEVNNATARVMTNS 98

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 10/39 (25%), Positives = 16/39 (41%)

Query: 298 ERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
              ++     L+V N+     D  LR+ F  FG I   +
Sbjct: 8   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE 46

>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 = 98.5 bits (246), Expect = 6e-26
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQ 261
              V++ N      +E L E+F   G +T   +    +GK + FGFV ++ PE    A+ 
Sbjct: 16  DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIA 75

Query: 262 AWNGKEVDGKILYVGRAQ 279
             NG  + G+ + V    
Sbjct: 76  LLNGIRLYGRPINVSGPS 93

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 81.9 bits (203), Expect = 9e-20
 Identities = 20/74 (27%), Positives = 39/74 (52%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            VF+ NL+  +  + +Y+ F   G +    + +D +G  K +GFV F+  E+ + +I  +
Sbjct: 18  TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALL 77

Query: 172 NGMLLNSKIVFVGK 185
           NG+ L  + + V  
Sbjct: 78  NGIRLYGRPINVSG 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 = 52.6 bits (127), Expect = 3e-09
 Identities = 8/36 (22%), Positives = 15/36 (41%)

Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
                  ++V NL+  + +E L + F   G +T   
Sbjct: 12  QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVT 47

>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 = 98.1 bits (245), Expect = 9e-26
 Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 4/88 (4%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQ 261
              +++    +  ++E +  +F+P+G I    V+   DG S+G  FV + S   A+ A+ 
Sbjct: 15  DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIH 74

Query: 262 AWNGKEV---DGKILYVGRAQKKAERTQ 286
           A +G +        L V  A    E   
Sbjct: 75  ALHGSQTMPGASSSLVVKFADTDKESGP 102

>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 = 81.2 bits (201), Expect = 2e-19
 Identities = 24/84 (28%), Positives = 36/84 (42%), Gaps = 3/84 (3%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            +F+  L+K    + +   F  FG I  C V +   G+SKG  FV F +   A  +I  +
Sbjct: 17  KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76

Query: 172 NG---MLLNSKIVFVGKFIPRKER 192
           +G   M   S  + V      KE 
Sbjct: 77  HGSQTMPGASSSLVVKFADTDKES 100

>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 = 51.9 bits (125), Expect = 6e-09
 Identities = 9/33 (27%), Positives = 15/33 (45%)

Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           +   L+V  L+    +E + + F PFG I    
Sbjct: 14  RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECT 46

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 99.5 bits (248), Expect = 2e-25
 Identities = 20/103 (19%), Positives = 42/103 (40%), Gaps = 1/103 (0%)

Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFG 246
              +     GE  +    + + N     +D  ++E+F  +GT+    V  +  G+S G  
Sbjct: 73  DLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTA 132

Query: 247 FVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELK 289
            V +E    A KA++ + G  +DG+ + +     + +      
Sbjct: 133 DVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHH 175

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 82.2 bits (203), Expect = 5e-19
 Identities = 23/113 (20%), Positives = 46/113 (40%), Gaps = 6/113 (5%)

Query: 90  KGRPIRIMWSQRDPSLRKSGVG------NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVA 143
           + +P+   W          G         + + NLD  + +  + + F+ FG++    V 
Sbjct: 62  RPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVD 121

Query: 144 QDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKEL 196
            D  G S G   VHFE    A K++++  G+ L+ + + +     + + E   
Sbjct: 122 YDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHH 174

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 71.4 bits (175), Expect = 4e-15
 Identities = 15/73 (20%), Positives = 25/73 (34%)

Query: 264 NGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLR 323
                 G+      ++ K    +     F+           G  L V NLD  + D  ++
Sbjct: 47  PAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQ 106

Query: 324 KEFTPFGTITSAK 336
           + F  FGT+  A 
Sbjct: 107 ELFAEFGTLKKAA 119

>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 = 98.0 bits (244), Expect = 4e-25
 Identities = 22/141 (15%), Positives = 56/141 (39%), Gaps = 10/141 (7%)

Query: 163 AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKEL---GEKAKLFTNVYIKNFGEDFNDEK 219
                 +++    ++ + +  G+    +     +    E  +    +Y+KN  +   ++ 
Sbjct: 2   PLGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKD 61

Query: 220 LKEMFEPYGTITSYR-------VMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKI 272
           LK +F  Y   +S          +  +G+ +G  F+   + + A KA++  NG  + GK 
Sbjct: 62  LKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP 121

Query: 273 LYVGRAQKKAERTQELKRRFE 293
           + V  A+    +    + + +
Sbjct: 122 MVVQFARSARPKQDPKEGKRK 142

>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 = 76.8 bits (189), Expect = 2e-17
 Identities = 14/82 (17%), Positives = 29/82 (35%), Gaps = 7/82 (8%)

Query: 255 FAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLD 314
                      + +  + L  GR  ++   T  + R +E  +           +YVKNL 
Sbjct: 2   PLGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGE-------PNCRIYVKNLA 54

Query: 315 DSIDDERLRKEFTPFGTITSAK 336
             + ++ L+  F  +   +S  
Sbjct: 55  KHVQEKDLKYIFGRYVDFSSET 76

>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 = 69.5 bits (170), Expect = 1e-14
 Identities = 22/96 (22%), Positives = 42/96 (43%), Gaps = 6/96 (6%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCK------VAQDEQGNSKGYGFVHFETEEAAN 165
            +++KNL K +  K +   F  +    S        +   ++G  KG  F+    E+AA 
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 166 KSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAK 201
           K++++ NG +L  K + V      + ++     K K
Sbjct: 107 KALKEANGYVLFGKPMVVQFARSARPKQDPKEGKRK 142

>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 = 94.5 bits (236), Expect = 1e-24
 Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQ 261
           + +YI+       D+ L ++ +PYG I S + +      K +G+GFV ++SP  A+KAV 
Sbjct: 6   SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65

Query: 262 AWNGKEVDGKILYVGRAQ 279
           A     V  ++       
Sbjct: 66  ALKASGVQAQMAKQSGPS 83

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 74.5 bits (184), Expect = 3e-17
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 3/83 (3%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANK 166
           SG   ++I+ L     ++ +      +G I+S K   D      KGYGFV F++  AA K
Sbjct: 3   SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62

Query: 167 SIEKVNGMLLNSKIVFVGKFIPR 189
           ++  +    + +++       P 
Sbjct: 63  AVTALKASGVQAQMAKQSG--PS 83

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 47.5 bits (114), Expect = 2e-07
 Identities = 11/30 (36%), Positives = 15/30 (50%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            LY++ L     D+ L K   P+G I S K
Sbjct: 7   GLYIRGLQPGTTDQDLVKLCQPYGKIVSTK 36

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 94.3 bits (235), Expect = 2e-24
 Identities = 20/88 (22%), Positives = 43/88 (48%), Gaps = 3/88 (3%)

Query: 205 NVYIKNFGEDFNDEKLKEMF-EPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQA 262
           ++++ +   D +D  L E F + Y +    +V+ +  G S+G+GFV +      ++A+  
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70

Query: 263 WNGK-EVDGKILYVGRAQKKAERTQELK 289
             G   +  K + +  A  KA R + ++
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASRVKPVE 98

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 90.4 bits (225), Expect = 8e-23
 Identities = 28/87 (32%), Positives = 46/87 (52%), Gaps = 2/87 (2%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSA-FGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
           ++F+ +L   +D+  +Y+ F   + S    KV  D+ G SKGYGFV F  E    +++ +
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70

Query: 171 VNG-MLLNSKIVFVGKFIPRKEREKEL 196
             G + L SK V +   IP+  R K +
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASRVKPV 97

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 50.4 bits (121), Expect = 3e-08
 Identities = 8/40 (20%), Positives = 16/40 (40%), Gaps = 1/40 (2%)

Query: 298 ERLNRYQGVNLYVKNLDDSIDDERLRKEFT-PFGTITSAK 336
              +     +L+V +L   +DD  L + F   + +    K
Sbjct: 2   SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGK 41

>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 = 92.6 bits (231), Expect = 7e-24
 Identities = 23/80 (28%), Positives = 46/80 (57%), Gaps = 2/80 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQ 261
            N+++ +   + +DE L+  F+ + +  S  VM     G SRG+GFV++ S + A+ A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 262 AWNGKEVDGKILYVGRAQKK 281
           +  G++++G+ L +  A K 
Sbjct: 62  SMQGQDLNGRPLRINWAAKL 81

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 77.5 bits (192), Expect = 2e-18
 Identities = 23/79 (29%), Positives = 46/79 (58%), Gaps = 1/79 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           N+F+ +L+ ++D++ + + F  F S LS  V  D + G+S+GYGFV F +++ A  +++ 
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 171 VNGMLLNSKIVFVGKFIPR 189
           + G  LN + + +      
Sbjct: 63  MQGQDLNGRPLRINWAAKL 81

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 46.3 bits (111), Expect = 4e-07
 Identities = 12/30 (40%), Positives = 18/30 (60%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           NL+V +L+ ++DDE LR  F  F +  S  
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGH 32

>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 = 92.7 bits (231), Expect = 9e-24
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 4/84 (4%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
              +Y++N     ++E +++ F         RV     K R + FV + + E A +A++A
Sbjct: 15  VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK----KIRDYAFVHFSNREDAVEAMKA 70

Query: 263 WNGKEVDGKILYVGRAQKKAERTQ 286
            NGK +DG  + V  A+   + + 
Sbjct: 71  LNGKVLDGSPIEVTLAKPVDKDSS 94

>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 = 70.4 bits (173), Expect = 2e-15
 Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 5/85 (5%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
           S V  ++++NL  S   + +   F+        +V +      + Y FVHF   E A ++
Sbjct: 13  SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEA 67

Query: 168 IEKVNGMLLNSKIVFVGKFIPRKER 192
           ++ +NG +L+   + V    P  + 
Sbjct: 68  MKALNGKVLDGSPIEVTLAKPVDKD 92

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

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 10/30 (33%), Positives = 14/30 (46%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            LYV+NL  S  +E + KEF         +
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVER 46

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 92.8 bits (231), Expect = 1e-23
 Identities = 18/94 (19%), Positives = 38/94 (40%), Gaps = 6/94 (6%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
             V      ++  +  LK+M   YG +    ++ +    K  G   V + S   A++ V+
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRRFEML 295
             +   V G I++     K  +R     + +E++
Sbjct: 67  NLHLTSVMGNIIHAQLDIKGQQR----MKYYELI 96

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 79.0 bits (195), Expect = 1e-18
 Identities = 12/86 (13%), Positives = 32/86 (37%), Gaps = 1/86 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
            V    L+ ++    + D    +G +   ++    +     G   V F +   A ++++ 
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 171 VNGMLLNSKIVFVGKFIPRKEREKEL 196
           ++   +   I+     I  ++R K  
Sbjct: 68  LHLTSVMGNIIHAQLDIKGQQRMKYY 93

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 4/30 (13%), Positives = 13/30 (43%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            +    L+D++ +  L+     +G +   +
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVE 37

>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 = 92.3 bits (230), Expect = 1e-23
 Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 4/84 (4%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
            + +++ N   D  +E+++++FE YG      +     K +GFGF+  E+   AE A   
Sbjct: 15  RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH----KDKGFGFIRLETRTLAEIAKVE 70

Query: 263 WNGKEVDGKILYVGRAQKKAERTQ 286
            +   + GK L V  A   A  T 
Sbjct: 71  LDNMPLRGKQLRVRFACHSASLTS 94

>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 = 66.1 bits (162), Expect = 5e-14
 Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 5/88 (5%)

Query: 106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAAN 165
             +    +F+ NL   I  + M   F  +G      + +D     KG+GF+  ET   A 
Sbjct: 11  TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAE 65

Query: 166 KSIEKVNGMLLNSKIVFVGKFIPRKERE 193
            +  +++ M L  K + V          
Sbjct: 66  IAKVELDNMPLRGKQLRVRFACHSASLT 93

>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 = 42.6 bits (101), Expect = 1e-05
 Identities = 11/33 (33%), Positives = 15/33 (45%)

Query: 304 QGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           Q   L+V NL   I +E +RK F  +G      
Sbjct: 14  QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF 46

>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 = 94.1 bits (234), Expect = 1e-23
 Identities = 29/140 (20%), Positives = 61/140 (43%), Gaps = 5/140 (3%)

Query: 157 HFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELG---EKAKLFTNVYIKNFGE 213
               +E A     +  G   N++         R E + EL    +++     +++ +  E
Sbjct: 23  IVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHE 82

Query: 214 DFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK 271
           +  +++++E F  YG I +  +  +   G S+G+  V YE+ + A  A +A NG E+ G+
Sbjct: 83  EAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ 142

Query: 272 ILYVGRAQKKAERTQELKRR 291
            + V     K  +  +   +
Sbjct: 143 TIQVDWCFVKGPKRVKKSEK 162

>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 = 68.7 bits (168), Expect = 3e-14
 Identities = 20/91 (21%), Positives = 41/91 (45%), Gaps = 1/91 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
            +F+ ++ +      + + F  +G I +  +  D   G SKGY  V +ET + A  + E 
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAK 201
           +NG  +  + + V     +  +  +  EK +
Sbjct: 134 LNGAEIMGQTIQVDWCFVKGPKRVKKSEKRR 164

>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 = 89.7 bits (223), Expect = 1e-22
 Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 6/83 (7%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             +Y+   GED     L+  F P+G I    +       R   FV YE  E A++AV   
Sbjct: 16  NTLYVY--GEDMTPTLLRGAFSPFGNIIDLSMD----PPRNCAFVTYEKMESADQAVAEL 69

Query: 264 NGKEVDGKILYVGRAQKKAERTQ 286
           NG +V+   L V  A+K+     
Sbjct: 70  NGTQVESVQLKVNIARKQPMLDS 92

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 68.9 bits (169), Expect = 6e-15
 Identities = 15/82 (18%), Positives = 36/82 (43%), Gaps = 7/82 (8%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            +++   D  +    +   FS FG+I+   +        +   FV +E  E+A++++ ++
Sbjct: 17  TLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAEL 69

Query: 172 NGMLLNSKIVFVGKFIPRKERE 193
           NG  + S  + V     +   +
Sbjct: 70  NGTQVESVQLKVNIARKQPMLD 91

>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 = 48.4 bits (116), Expect = 9e-08
 Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 2/39 (5%)

Query: 298 ERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           ER    +G  LYV   D  +    LR  F+PFG I    
Sbjct: 8   ERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLS 44

>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 = 89.1 bits (222), Expect = 1e-22
 Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 3/85 (3%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN---DGKSRGFGFVAYESPEFAEKA 259
            T V+I     +   + + E+F  YG I    +         S+G+ +V +E+P+ AEKA
Sbjct: 4   PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63

Query: 260 VQAWNGKEVDGKILYVGRAQKKAER 284
           ++  +G ++DG+ +          R
Sbjct: 64  LKHMDGGQIDGQEITATAVLAPWPR 88

>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 = 70.6 bits (174), Expect = 9e-16
 Identities = 18/83 (21%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD--EQGNSKGYGFVHFETEEAANKSIE 169
            V I  L +++    + + FS +G I    +  +      SKGY +V FE  + A K+++
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 170 KVNGMLLNSKIVFVGKFIPRKER 192
            ++G  ++ + +     +    R
Sbjct: 66  HMDGGQIDGQEITATAVLAPWPR 88

>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 = 37.5 bits (88), Expect = 5e-04
 Identities = 4/31 (12%), Positives = 14/31 (45%)

Query: 306 VNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             +++  L  ++  + + + F+ +G I    
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMID 35

>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 = 89.7 bits (223), Expect = 2e-22
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 2/85 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
             +Y+KN      +  L  +F  +       +      G+ RG  F+ + + E A +A+ 
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQ 286
             NG ++ GKIL +   + K +R+ 
Sbjct: 86  LVNGYKLYGKILVIEFGKNKKQRSS 110

>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 = 75.4 bits (186), Expect = 3e-17
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 1/83 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
            +++KNL   +  + +   F+ F       +      G  +G  F+ F  +E A +++  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 171 VNGMLLNSKIVFVGKFIPRKERE 193
           VNG  L  KI+ +     +K+R 
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQRS 109

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 12/48 (25%), Positives = 17/48 (35%), Gaps = 4/48 (8%)

Query: 293 EMLKIERLNRYQ----GVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           E+ KI   + Y        LY+KNL   + +  L   F  F       
Sbjct: 9   EIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPP 56

>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 = 88.1 bits (219), Expect = 4e-22
 Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 5/89 (5%)

Query: 205 NVYIKNFGEDFNDEKLKE----MFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAV 260
            +YI N  E    ++LK+    +F  +G I    V     K RG  FV ++    A  A+
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR-SLKMRGQAFVIFKEVSSATNAL 68

Query: 261 QAWNGKEVDGKILYVGRAQKKAERTQELK 289
           ++  G     K + +  A+  ++   ++K
Sbjct: 69  RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97

>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 = 66.1 bits (162), Expect = 5e-14
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 6/76 (7%)

Query: 112 NVFIKNLDKSIDN----KAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
            ++I NL++ I      K+++  FS FG IL   V++      +G  FV F+   +A  +
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS--LKMRGQAFVIFKEVSSATNA 67

Query: 168 IEKVNGMLLNSKIVFV 183
           +  + G     K + +
Sbjct: 68  LRSMQGFPFYDKPMRI 83

>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 = 42.6 bits (101), Expect = 1e-05
 Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 4/34 (11%)

Query: 307 NLYVKNLDDSIDDERLRKE----FTPFGTITSAK 336
            +Y+ NL++ I  + L+K     F+ FG I    
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDIL 43

>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 = 89.0 bits (221), Expect = 6e-22
 Identities = 27/110 (24%), Positives = 48/110 (43%), Gaps = 16/110 (14%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAV 260
            N+ +       ++ +L+++FE YG I S +++  D    +SRG+GFV ++S   A++A+
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVC-DRETRQSRGYGFVKFQSGSSAQQAI 101

Query: 261 QAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYV 310
              NG  +  K L V  A    +R                      N Y+
Sbjct: 102 AGLNGFNILNKRLKVALAASGHQRP------------GIAGAVGDGNGYL 139

>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 = 74.0 bits (182), Expect = 2e-16
 Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 3/98 (3%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  +  ++D   +   F  +G I S K+  D E   S+GYGFV F++  +A ++I  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYI 208
           +NG  + +K + V       +R    G       N Y+
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGIAGAVGD--GNGYL 139

>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 = 40.5 bits (95), Expect = 1e-04
 Identities = 11/30 (36%), Positives = 18/30 (60%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           NL V  +  ++D+ +LR+ F  +G I S K
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVK 73

>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 = 87.3 bits (217), Expect = 1e-21
 Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 2/93 (2%)

Query: 193 EKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYE 251
           +   G ++    N++I N   + +  +LK             V++   G +R FG+V +E
Sbjct: 7   DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFE 66

Query: 252 SPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
           S E  EKA++   G +V G  + + + + +   
Sbjct: 67  SAEDLEKALEL-TGLKVFGNEIKLEKPKGRDGT 98

>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 = 75.4 bits (186), Expect = 2e-17
 Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 1/97 (1%)

Query: 97  MWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFV 156
           M          +   N+FI NL+ +     +    S   +     V     G ++ +G+V
Sbjct: 4   MLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYV 63

Query: 157 HFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKERE 193
            FE+ E   K++E   G+ +    + + K   R    
Sbjct: 64  DFESAEDLEKALEL-TGLKVFGNEIKLEKPKGRDGTR 99

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 5/30 (16%), Positives = 11/30 (36%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           NL++ NL+ +     L+   +         
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLA 48

>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 = 85.4 bits (212), Expect = 6e-21
 Identities = 28/83 (33%), Positives = 49/83 (59%), Gaps = 2/83 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQA 262
            +++     D N++ L+++F  YG I+   V+      +SRGFGFV +E+ + A+ A+ A
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73

Query: 263 WNGKEVDGKILYVGRAQKKAERT 285
            NGK VDG+ + V +A K ++  
Sbjct: 74  MNGKSVDGRQIRVDQAGKSSDNR 96

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 71.1 bits (175), Expect = 9e-16
 Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 1/83 (1%)

Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIE 169
           G +F+  L    + +++   FS +G I    V +D E   S+G+GFV FE  + A  ++ 
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72

Query: 170 KVNGMLLNSKIVFVGKFIPRKER 192
            +NG  ++ + + V +     + 
Sbjct: 73  AMNGKSVDGRQIRVDQAGKSSDN 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 = 85.1 bits (211), Expect = 7e-21
 Identities = 25/94 (26%), Positives = 53/94 (56%), Gaps = 2/94 (2%)

Query: 192 REKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVA 249
               L + +     +Y+ +   +  ++ L+ +FEP+G I S ++M +   G+S+G+GF+ 
Sbjct: 15  MANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFIT 74

Query: 250 YESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAE 283
           +   E A+KA++  NG E+ G+ + VG   ++ +
Sbjct: 75  FSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>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 = 66.6 bits (163), Expect = 4e-14
 Identities = 27/81 (33%), Positives = 43/81 (53%), Gaps = 1/81 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
            +++ +L  +I    +   F  FG I S ++  D E G SKGYGF+ F   E A K++E+
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87

Query: 171 VNGMLLNSKIVFVGKFIPRKE 191
           +NG  L  + + VG    R +
Sbjct: 88  LNGFELAGRPMKVGHVTERTD 108

>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 = 39.6 bits (93), Expect = 2e-04
 Identities = 13/30 (43%), Positives = 18/30 (60%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            LYV +L  +I ++ LR  F PFG I S +
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQ 57

>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 = 84.2 bits (209), Expect = 1e-20
 Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
             + + N  ED  +  L+E+F P+G+I+   +  +   G+S+GF F+++   E A +A+ 
Sbjct: 16  ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75

Query: 262 AWNGKEVDGKILYVGRAQKKAERT 285
             +G   D  IL V  A+      
Sbjct: 76  GVSGFGYDHLILNVEWAKPSTNSG 99

>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 = 73.8 bits (182), Expect = 9e-17
 Identities = 25/91 (27%), Positives = 40/91 (43%), Gaps = 1/91 (1%)

Query: 103 PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETE 161
           P+ R      + + NL +      + + F  FGSI    +A+D   G SKG+ F+ F   
Sbjct: 8   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67

Query: 162 EAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
           E A ++I  V+G   +  I+ V    P    
Sbjct: 68  EDAARAIAGVSGFGYDHLILNVEWAKPSTNS 98

>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 = 38.0 bits (89), Expect = 6e-04
 Identities = 9/36 (25%), Positives = 16/36 (44%)

Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
                  + V NL +   +  L++ F PFG+I+   
Sbjct: 11  RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIY 46

>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 = 84.7 bits (210), Expect = 1e-20
 Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 2/85 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQ 261
            +V++ +   +   E +K  F P+G I+  RV+     GKS+G+GFV++ +   AE A+Q
Sbjct: 16  FHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQ 286
              G+ + G+ +    A +K    +
Sbjct: 76  QMGGQWLGGRQIRTNWATRKPPAPK 100

>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 = 74.3 bits (183), Expect = 1e-16
 Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 1/84 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           +VF+ +L   I  + +   F+ FG I   +V +D   G SKGYGFV F  +  A  +I++
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76

Query: 171 VNGMLLNSKIVFVGKFIPRKEREK 194
           + G  L  + +       +    K
Sbjct: 77  MGGQWLGGRQIRTNWATRKPPAPK 100

>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 = 44.3 bits (105), Expect = 4e-06
 Identities = 10/39 (25%), Positives = 21/39 (53%)

Query: 298 ERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           ++ +     +++V +L   I  E ++  F PFG I+ A+
Sbjct: 8   QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDAR 46

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 43.1 bits (102), Expect = 9e-06
 Identities = 14/37 (37%), Positives = 17/37 (45%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGN 112
           D E A+  M    L GR IR  W+ R P   KS   +
Sbjct: 69  DAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYES 105

>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 = 84.2 bits (209), Expect = 2e-20
 Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
             +Y+    E+ +D+ L   F P+G IT  ++  +    K RGF FV +E  E A  A+ 
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72

Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
             N  E+ G+ + V  A+    +
Sbjct: 73  NMNESELFGRTIRVNLAKPMRIK 95

>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 = 71.9 bits (177), Expect = 5e-16
 Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
            +++  L + +D+K ++  F  FG I   ++  D E    +G+ FV FE  E A  +I+ 
Sbjct: 14  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73

Query: 171 VNGMLLNSKIVFVGKFIPRKEREKELG 197
           +N   L  + + V    P + +E    
Sbjct: 74  MNESELFGRTIRVNLAKPMRIKESGPS 100

>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 = 41.8 bits (99), Expect = 2e-05
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            LYV  L + +DD+ L   F PFG IT  +
Sbjct: 14  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQ 43

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 82.9 bits (205), Expect = 4e-20
 Identities = 23/99 (23%), Positives = 46/99 (46%), Gaps = 1/99 (1%)

Query: 194 KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYES 252
           + + +      +VYIK F  D   + +KE  E  G + + ++        +G  FV ++S
Sbjct: 2   RWILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDS 61

Query: 253 PEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRR 291
            E A+K V+    K  +  +L + +    A++ +E K+ 
Sbjct: 62  IESAKKFVETPGQKYKETDLLILFKDDYFAKKNEERKQN 100

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 65.1 bits (159), Expect = 1e-13
 Identities = 16/88 (18%), Positives = 37/88 (42%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           +V+IK          + +     G +L+ ++ +      KG  FV F++ E+A K +E  
Sbjct: 13  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 72

Query: 172 NGMLLNSKIVFVGKFIPRKEREKELGEK 199
                 + ++ + K     ++ +E  + 
Sbjct: 73  GQKYKETDLLILFKDDYFAKKNEERKQN 100

>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 = 82.3 bits (204), Expect = 5e-20
 Identities = 24/92 (26%), Positives = 48/92 (52%), Gaps = 3/92 (3%)

Query: 193 EKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYES 252
           +    +K +    +  KN   +  +++LKE+FE    I   R+++ DGKS+G  ++ ++S
Sbjct: 6   DPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI---RLVSQDGKSKGIAYIEFKS 62

Query: 253 PEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
              AEK ++   G E+DG+ + +    +K   
Sbjct: 63  EADAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 94

>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 = 58.4 bits (142), Expect = 3e-11
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 4/81 (4%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            +  KNL  +I    + + F     I        + G SKG  ++ F++E  A K++E+ 
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEADAEKNLEEK 73

Query: 172 NGMLLNSKIVFVGKFIPRKER 192
            G  ++ + V +     +   
Sbjct: 74  QGAEIDGRSVSLYYTGEKGGT 94

>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 = 81.8 bits (203), Expect = 7e-20
 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQA 262
           +V++ +   +     +   F P+G I+  RV+     GKS+G+GFV++ +   AE A+Q 
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 263 WNGKEVDGKILYVGRAQKK 281
             G+ + G+ +    A +K
Sbjct: 68  MGGQWLGGRQIRTNWATRK 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 70.3 bits (173), Expect = 1e-15
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 1/79 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
           +VF+ +L   I   A+   F+ FG I   +V +D   G SKGYGFV F  +  A  +I++
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 171 VNGMLLNSKIVFVGKFIPR 189
           + G  L  + +       +
Sbjct: 68  MGGQWLGGRQIRTNWATRK 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 48.3 bits (116), Expect = 9e-08
 Identities = 12/28 (42%), Positives = 14/28 (50%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDP 103
           D E A+  M    L GR IR  W+ R P
Sbjct: 60  DAENAIQQMGGQWLGGRQIRTNWATRKP 87

>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 = 41.0 bits (97), Expect = 3e-05
 Identities = 9/30 (30%), Positives = 16/30 (53%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           +++V +L   I    +   F PFG I+ A+
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDAR 37

>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 = 81.8 bits (203), Expect = 8e-20
 Identities = 23/84 (27%), Positives = 49/84 (58%), Gaps = 4/84 (4%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAV 260
           + +Y+ +   +  ++ L+ +FEP+G I +  +M  D   G+S+G+GF+ +   E A +A+
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMK-DSDTGRSKGYGFITFSDSECARRAL 64

Query: 261 QAWNGKEVDGKILYVGRAQKKAER 284
           +  NG E+ G+ + VG   ++ + 
Sbjct: 65  EQLNGFELAGRPMRVGHVTERLDG 88

>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 = 68.7 bits (169), Expect = 6e-15
 Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
            +++ +L  +I    +   F  FG I +  + +D + G SKGYGF+ F   E A +++E+
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 171 VNGMLLNSKIVFVGKFIPRKER 192
           +NG  L  + + VG    R + 
Sbjct: 67  LNGFELAGRPMRVGHVTERLDG 88

>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 = 37.5 bits (88), Expect = 6e-04
 Identities = 12/30 (40%), Positives = 17/30 (56%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            LYV +L  +I ++ LR  F PFG I +  
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIV 36

>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 = 83.4 bits (206), Expect = 1e-19
 Identities = 31/137 (22%), Positives = 50/137 (36%), Gaps = 4/137 (2%)

Query: 155 FVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKL--FTNVYIKNFG 212
            V   T E   K     NG+          K     E          +   T++ + N  
Sbjct: 20  AVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT 79

Query: 213 EDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
              + + L+ +FE YG +    +  +    +SRGF FV +     AE A+ A +G  +DG
Sbjct: 80  YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG 139

Query: 271 KILYVGRAQKKAERTQE 287
           + L V  A+        
Sbjct: 140 RELRVQMARYGRPPDSH 156

>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 = 66.0 bits (161), Expect = 2e-13
 Identities = 15/98 (15%), Positives = 39/98 (39%), Gaps = 1/98 (1%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVH 157
                 +   G+ ++ + NL        +   F  +G +    + +D     S+G+ FV 
Sbjct: 59  HHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 118

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKE 195
           F  +  A  +++ ++G +L+ + + V      +  +  
Sbjct: 119 FHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 156

>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 = 43.7 bits (103), Expect = 2e-05
 Identities = 13/94 (13%), Positives = 23/94 (24%)

Query: 243 RGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNR 302
            G       + E  + A      K+        G                       ++ 
Sbjct: 8   NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67

Query: 303 YQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
               +L V NL      + LR+ F  +G +    
Sbjct: 68  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVY 101

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 81.6 bits (202), Expect = 1e-19
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYR-VMNNDGKSRGFGFVAYESPEFAEKAVQA 262
             ++I         E+L+E+ + +GT+   R V N  GK +G  +V YE+   A +AV  
Sbjct: 18  HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMK 77

Query: 263 WNGKEVDGKILYVGRAQKKAER 284
            +G  +   I+ V  +      
Sbjct: 78  MDGMTIKENIIKVAISNSGPSS 99

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 69.6 bits (171), Expect = 3e-15
 Identities = 18/81 (22%), Positives = 37/81 (45%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            +FI  L  S   + + +   A G++   ++  +  G  KG  +V +E E  A++++ K+
Sbjct: 19  KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKM 78

Query: 172 NGMLLNSKIVFVGKFIPRKER 192
           +GM +   I+ V         
Sbjct: 79  DGMTIKENIIKVAISNSGPSS 99

>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 = 81.1 bits (201), Expect = 2e-19
 Identities = 18/90 (20%), Positives = 42/90 (46%), Gaps = 2/90 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
             VY+ +   D  +E++ ++    G + + ++M +   G+S+G+ F+ +   E +  AV+
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRR 291
             NG ++  + L  G +         L+  
Sbjct: 63  NLNGYQLGSRFLKCGYSSNSDISGVSLEHH 92

>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 = 64.6 bits (158), Expect = 2e-13
 Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
            V++ ++      + + D  S  G +++ K+  D + G SKGY F+ F   E++  ++  
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 171 VNGMLLNSKIVFVGKFIPRKER 192
           +NG  L S+ +  G        
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDIS 85

>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 = 81.2 bits (201), Expect = 2e-19
 Identities = 20/94 (21%), Positives = 41/94 (43%), Gaps = 4/94 (4%)

Query: 193 EKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYES 252
           E  + + +     VY         D+ +++ F P+G I   RV       +G+ FV + +
Sbjct: 15  EDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF----PEKGYSFVRFST 70

Query: 253 PEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQ 286
            E A  A+ + NG  ++G ++     ++  + T 
Sbjct: 71  HESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTS 104

>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 = 65.0 bits (159), Expect = 2e-13
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            V+   +   + ++ M  TFS FG I+  +V  +     KGY FV F T E+A  +I  V
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSV 81

Query: 172 NGMLLNSKIVFVG 184
           NG  +   +V   
Sbjct: 82  NGTTIEGHVVKCY 94

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 5/34 (14%), Positives = 14/34 (41%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSG 109
               A+ ++N   ++G  ++  W +  P +    
Sbjct: 73  SAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGP 106

>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 = 40.8 bits (96), Expect = 5e-05
 Identities = 8/30 (26%), Positives = 16/30 (53%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            +Y   +   + D+ +R+ F+PFG I   +
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIR 56

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 80.2 bits (198), Expect = 4e-19
 Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 1/81 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             + I+N       E L  +   YG + S   +N D        V Y S + A +A+   
Sbjct: 16  RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS-ETAVVNVTYSSKDQARQALDKL 74

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           NG +++   L V     +   
Sbjct: 75  NGFQLENFTLKVAYIPDEMAA 95

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 63.2 bits (154), Expect = 6e-13
 Identities = 14/86 (16%), Positives = 41/86 (47%), Gaps = 3/86 (3%)

Query: 106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAAN 165
           ++  +  + I+N+   +  + +      +G + SC+    +  +      V + +++ A 
Sbjct: 11  KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTD--SETAVVNVTYSSKDQAR 68

Query: 166 KSIEKVNGMLLNSKIVFVGKFIPRKE 191
           ++++K+NG  L +  + V  +IP + 
Sbjct: 69  QALDKLNGFQLENFTLKV-AYIPDEM 93

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 7/35 (20%), Positives = 15/35 (42%)

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           R +   L ++N+   +  E L      +G + S +
Sbjct: 12  RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCE 46

>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 = 83.6 bits (206), Expect = 5e-19
 Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 4/92 (4%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGT--ITSYRVMNN--DGKSRGFGFVAYESPEFAEKA 259
             +YI N      DE L E     G   I   +   N  +G+S+GF  V   S   ++K 
Sbjct: 69  IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 128

Query: 260 VQAWNGKEVDGKILYVGRAQKKAERTQELKRR 291
           +     +E+ G+   V    K+     E++ R
Sbjct: 129 MDLLPKRELHGQNPVVTPVNKQFLSQFEMQSR 160

>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 = 73.6 bits (180), Expect = 2e-15
 Identities = 17/91 (18%), Positives = 39/91 (42%), Gaps = 3/91 (3%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFG--SILSCKVAQD-EQGNSKGYGFVHFETEEAANKSI 168
            ++I NL     ++ + +   + G   IL  K  ++   G SKG+  V   +E ++ K +
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 169 EKVNGMLLNSKIVFVGKFIPRKEREKELGEK 199
           + +    L+ +   V     +   + E+  +
Sbjct: 130 DLLPKRELHGQNPVVTPVNKQFLSQFEMQSR 160

>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 = 79.6 bits (197), Expect = 7e-19
 Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 2/84 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
             + + N     + + L+ +FE YG +    +         RGF FV +     A+ A  
Sbjct: 14  ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA 73

Query: 262 AWNGKEVDGKILYVGRAQKKAERT 285
           A +G E+DG+ L V  A+      
Sbjct: 74  AMDGAELDGRELRVQVARYGRRDL 97

>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 = 65.7 bits (161), Expect = 9e-14
 Identities = 14/95 (14%), Positives = 33/95 (34%), Gaps = 1/95 (1%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVH 157
           S         G+  + + NL       ++   F  +G +    + ++      +G+ FV 
Sbjct: 2   SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
           F     A  +   ++G  L+ + + V      +  
Sbjct: 62  FHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRD 96

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 80.2 bits (198), Expect = 1e-18
 Identities = 23/99 (23%), Positives = 41/99 (41%), Gaps = 2/99 (2%)

Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGF 245
                        +  T++ + N     + + L+ +FE YG +    +  +    +SRGF
Sbjct: 32  RGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGF 91

Query: 246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
            FV +     AE A+ A +G  +DG+ L V  A+     
Sbjct: 92  AFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP 130

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 64.8 bits (158), Expect = 4e-13
 Identities = 17/96 (17%), Positives = 40/96 (41%), Gaps = 1/96 (1%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVH 157
           S   P     G+ ++ + NL        +   F  +G +    + +D     S+G+ FV 
Sbjct: 36  SYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 95

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKERE 193
           F  +  A  +++ ++G +L+ + + V      +  +
Sbjct: 96  FHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD 131

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 39.3 bits (92), Expect = 3e-04
 Identities = 11/61 (18%), Positives = 19/61 (31%)

Query: 276 GRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSA 335
           G         Q++ R          +     +L V NL      + LR+ F  +G +   
Sbjct: 18  GSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDV 77

Query: 336 K 336
            
Sbjct: 78  Y 78

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 78.9 bits (195), Expect = 1e-18
 Identities = 21/83 (25%), Positives = 42/83 (50%), Gaps = 4/83 (4%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-GKSRGFGFVAYESPEFAEKAVQ 261
              + + N      +E L+E+FE    I   +V  N  GKS+G+ F+ + S E A++A+ 
Sbjct: 15  SKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALN 71

Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
           + N +E++G+ + +     +   
Sbjct: 72  SCNKREIEGRAIRLELQGPRGSP 94

>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 = 65.4 bits (160), Expect = 1e-13
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           + + NL  S   + + + F     I   KV Q++ G SKGY F+ F + E A +++   N
Sbjct: 18  LVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74

Query: 173 GMLLNSKIVFVGKFIPRKERE 193
              +  + + +    PR    
Sbjct: 75  KREIEGRAIRLELQGPRGSPN 95

>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 = 79.3 bits (196), Expect = 1e-18
 Identities = 21/91 (23%), Positives = 43/91 (47%), Gaps = 4/91 (4%)

Query: 198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM---NNDGKSRGFGFVAYESPE 254
            K +  + + ++N     N  +++E+F  +G + + R+       G  RGFGFV + + +
Sbjct: 10  PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 69

Query: 255 FAEKAVQA-WNGKEVDGKILYVGRAQKKAER 284
            A+KA  A  +   + G+ L +  A  +   
Sbjct: 70  DAKKAFNALCHSTHLYGRRLVLEWADSEVTV 100

>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 = 60.0 bits (146), Expect = 1e-11
 Identities = 15/86 (17%), Positives = 39/86 (45%), Gaps = 3/86 (3%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD--EQGNSKGYGFVHFETEEAANKSIE 169
            + ++N+    + + + + FS FG + + ++ +     G  +G+GFV F T++ A K+  
Sbjct: 17  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76

Query: 170 KV-NGMLLNSKIVFVGKFIPRKEREK 194
            + +   L  + + +         + 
Sbjct: 77  ALCHSTHLYGRRLVLEWADSEVTVQS 102

>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 = 78.3 bits (194), Expect = 1e-18
 Identities = 26/85 (30%), Positives = 41/85 (48%), Gaps = 2/85 (2%)

Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPE 254
           G  A     +Y+    E+ +D+ L   F P+G IT  ++  +    K RGF FV +E  E
Sbjct: 1   GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60

Query: 255 FAEKAVQAWNGKEVDGKILYVGRAQ 279
            A  A+   N  E+ G+ + V  A+
Sbjct: 61  DAAAAIDNMNESELFGRTIRVNLAK 85

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 62.9 bits (154), Expect = 4e-13
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
            +++  L + +D+K ++  F  FG I   ++  D E    +G+ FV FE  E A  +I+ 
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68

Query: 171 VNGMLLNSKIVFVGK 185
           +N   L  + + V  
Sbjct: 69  MNESELFGRTIRVNL 83

>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 = 38.7 bits (91), Expect = 2e-04
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            LYV  L + +DD+ L   F PFG IT  +
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQ 38

>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 = 78.4 bits (194), Expect = 2e-18
 Identities = 23/90 (25%), Positives = 44/90 (48%), Gaps = 2/90 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
             ++++N     ++E L+++F  YG ++      +    K +GF FV +  PE A KA  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRR 291
             +G+   G++L+V  +  K E +Q     
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 64.9 bits (159), Expect = 1e-13
 Identities = 24/90 (26%), Positives = 42/90 (46%), Gaps = 1/90 (1%)

Query: 106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAA 164
             SG G +F++NL  +   + +   FSA+G +       D      KG+ FV F   E A
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 165 NKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
            K+  +V+G +   +++ V     +KE  +
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTIKKEASQ 93

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 79.4 bits (196), Expect = 2e-18
 Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPE 254
           G  A     +Y+    E+ +D+ L   F P+G IT  ++  +    K RGF FV +E  E
Sbjct: 57  GGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 116

Query: 255 FAEKAVQAWNGKEVDGKILYVGRA 278
            A  A+   N  E+ G+ + V  A
Sbjct: 117 DAAAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 67.9 bits (166), Expect = 3e-14
 Identities = 25/121 (20%), Positives = 49/121 (40%), Gaps = 16/121 (13%)

Query: 81  LDTMNFDALKGRPIRIMWSQRDPSLRKSGVG---------------NVFIKNLDKSIDNK 125
           L    ++ L   P  + ++  + + R    G                +++  L + +D+K
Sbjct: 19  LSDEMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDK 78

Query: 126 AMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG 184
            ++  F  FG I   ++  D E    +G+ FV FE  E A  +I+ +N   L  + + V 
Sbjct: 79  VLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 138

Query: 185 K 185
            
Sbjct: 139 L 139

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 40.9 bits (96), Expect = 1e-04
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            LYV  L + +DD+ L   F PFG IT  +
Sbjct: 65  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQ 94

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 78.0 bits (193), Expect = 2e-18
 Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
           + VY+ N      +  L  +F  YG +    +M +    KS+G  F+ +   + A+   +
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76

Query: 262 AWNGKEVDGKILYVGRA 278
           A N K++ G+++    A
Sbjct: 77  AINNKQLFGRVIKASIA 93

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 64.2 bits (157), Expect = 2e-13
 Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 97  MWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGF 155
           M     PS        V++ NL  S+ N  +Y  FS +G ++   + +D +   SKG  F
Sbjct: 8   MSGGLAPSKST-----VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAF 62

Query: 156 VHFETEEAANKSIEKVNG 173
           + F  +++A      +N 
Sbjct: 63  ILFLDKDSAQNCTRAINN 80

>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 = 78.2 bits (193), Expect = 5e-18
 Identities = 24/96 (25%), Positives = 43/96 (44%), Gaps = 2/96 (2%)

Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGF 245
            R  R             + +        +  L+E+F  YG I    ++ +    +SRGF
Sbjct: 31  GRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 90

Query: 246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK 281
            FV +E+ + A++A +  NG E+DG+ + V  +  K
Sbjct: 91  AFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126

>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 = 68.2 bits (167), Expect = 2e-14
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
            + +  L      + + + FS +G I    +  D +   S+G+ FV+FE  + A ++ E+
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107

Query: 171 VNGMLLNSKIVFVGKFIPRK 190
            NGM L+ + + V   I ++
Sbjct: 108 ANGMELDGRRIRVDFSITKR 127

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 13/74 (17%), Positives = 19/74 (25%), Gaps = 4/74 (5%)

Query: 264 NGKEVDGK-ILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERL 322
           +     G        A     +      R       R N      L V  L     +  L
Sbjct: 7   HHHHSSGLVPRGSHMASMTGGQQMGRGSRHVG---NRANPDPNCCLGVFGLSLYTTERDL 63

Query: 323 RKEFTPFGTITSAK 336
           R+ F+ +G I    
Sbjct: 64  REVFSKYGPIADVS 77

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 76.9 bits (190), Expect = 6e-18
 Identities = 25/83 (30%), Positives = 47/83 (56%), Gaps = 2/83 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
            +V++ N   +  +E+LK++F   G + S+R++ +   GK +G+GF  Y+  E A  A++
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
             NG+E  G+ L V  A  +  +
Sbjct: 69  NLNGREFSGRALRVDNAASEKNK 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 = 64.6 bits (158), Expect = 2e-13
 Identities = 26/93 (27%), Positives = 48/93 (51%), Gaps = 2/93 (2%)

Query: 102 DPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFET 160
           DP++ +S   +VF+ N+      + + D FS  G ++S ++  D E G  KGYGF  ++ 
Sbjct: 1   DPAVDRSLR-SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59

Query: 161 EEAANKSIEKVNGMLLNSKIVFVGKFIPRKERE 193
           +E A  ++  +NG   + + + V      K +E
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKE 92

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 77.0 bits (190), Expect = 7e-18
 Identities = 24/91 (26%), Positives = 43/91 (47%), Gaps = 8/91 (8%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
             V+I+N   D  +E L E+ + +G +   RV+ +     S+G  F  + + E A+K + 
Sbjct: 16  KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75

Query: 262 AWN------GKEVDGKILYVGRAQKKAERTQ 286
           A +      G ++DG+ L V  A  + E   
Sbjct: 76  AASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106

>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 = 67.0 bits (164), Expect = 3e-14
 Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 7/90 (7%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
            VFI+NL    + +A+ +    FG +   +V    +  +SKG  F  F T+EAA K +  
Sbjct: 17  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76

Query: 171 VN------GMLLNSKIVFVGKFIPRKEREK 194
            +      G+ L+ + + V   + R E   
Sbjct: 77  ASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106

>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 = 38.1 bits (89), Expect = 5e-04
 Identities = 7/36 (19%), Positives = 18/36 (50%)

Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           +  +G  ++++NL    ++E L +    FG +   +
Sbjct: 11  DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVR 46

>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 = 76.7 bits (189), Expect = 9e-18
 Identities = 22/91 (24%), Positives = 40/91 (43%), Gaps = 10/91 (10%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN----------DGKSRGFGFVAYESP 253
           + +Y++   +    + L + F+  G +   +               GK +G   V+YE P
Sbjct: 16  SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75

Query: 254 EFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
             A+ AV+ ++GK+  G  L V  A+KK   
Sbjct: 76  PTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 106

>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 = 57.0 bits (138), Expect = 1e-10
 Identities = 16/92 (17%), Positives = 31/92 (33%), Gaps = 9/92 (9%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILS--------CKVAQD-EQGNSKGYGFVHFETEE 162
            ++++ L+ S+    + D F   G +            +  D E G  KG   V +E   
Sbjct: 17  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76

Query: 163 AANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
            A  ++E  +G       + V     +     
Sbjct: 77  TAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 108

>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 = 75.8 bits (187), Expect = 1e-17
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             +YI N       + L+++F       + +V        G+ FV Y    +A +A++  
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV----LLKSGYAFVDYPDQNWAIRAIETL 64

Query: 264 NGK-EVDGKILYVGRAQKKAERT 285
           +GK E+ GKI+ V  +  K  R+
Sbjct: 65  SGKVELHGKIMEVDYSVSKKLRS 87

>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 = 64.2 bits (157), Expect = 2e-13
 Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 6/87 (6%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
           SG+  ++I NL  ++    +   F      L+ +V         GY FV +  +  A ++
Sbjct: 6   SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRA 60

Query: 168 IEKVNGML-LNSKIVFVGKFIPRKERE 193
           IE ++G + L+ KI+ V   + +K R 
Sbjct: 61  IETLSGKVELHGKIMEVDYSVSKKLRS 87

>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 = 75.7 bits (187), Expect = 1e-17
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
              + +        +  L+E+F  YG I    ++ +    +SRGF FV +E+ + A++A 
Sbjct: 15  NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74

Query: 261 QAWNGKEVDGKILYVGRAQ 279
           +  NG E+DG+ + V    
Sbjct: 75  ERANGMELDGRRIRVSGPS 93

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 64.1 bits (157), Expect = 2e-13
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
            + +  L      + + + FS +G I    +  D +   S+G+ FV+FE  + A ++ E+
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76

Query: 171 VNGMLLNSKIVFV 183
            NGM L+ + + V
Sbjct: 77  ANGMELDGRRIRV 89

>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 = 37.6 bits (88), Expect = 7e-04
 Identities = 10/38 (26%), Positives = 14/38 (36%)

Query: 299 RLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           R N      L V  L     +  LR+ F+ +G I    
Sbjct: 9   RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVS 46

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 75.8 bits (187), Expect = 1e-17
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 4/78 (5%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           T  YI N      +  L  +F+ +G I  ++        +G  F+ Y++ E A   + A 
Sbjct: 28  TTAYIGNIPHFATEADLIPLFQNFGFILDFKHY----PEKGCCFIKYDTHEQAAVCIVAL 83

Query: 264 NGKEVDGKILYVGRAQKK 281
                 G+ L  G  +++
Sbjct: 84  ANFPFQGRNLRTGWGKER 101

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 66.9 bits (164), Expect = 2e-14
 Identities = 20/98 (20%), Positives = 34/98 (34%), Gaps = 7/98 (7%)

Query: 89  LKGRPIRIMWSQRDPSLRKSGVGN--VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE 146
             G P ++     D  +R +       +I N+        +   F  FG IL  K   + 
Sbjct: 4   TIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE- 62

Query: 147 QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG 184
               KG  F+ ++T E A   I  +       + +  G
Sbjct: 63  ----KGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG 96

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 40.4 bits (95), Expect = 7e-05
 Identities = 8/30 (26%), Positives = 11/30 (36%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             Y+ N+     +  L   F  FG I   K
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFK 58

>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 = 75.4 bits (186), Expect = 2e-17
 Identities = 17/81 (20%), Positives = 36/81 (44%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             +Y+ N   D  +  + ++F   G   S +++     +  + FV +     A  A+ A 
Sbjct: 16  RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 75

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           NG+++ GK + V  A   + +
Sbjct: 76  NGRKILGKEVKVNWATTPSSQ 96

>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 = 66.5 bits (163), Expect = 4e-14
 Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 1/83 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            +++ NL + +    +   FS  G   SCK+  +   N   Y FV F     A  ++  +
Sbjct: 17  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAAM 75

Query: 172 NGMLLNSKIVFVGKFIPRKEREK 194
           NG  +  K V V        ++ 
Sbjct: 76  NGRKILGKEVKVNWATTPSSQKS 98

>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 = 54.2 bits (131), Expect = 1e-09
 Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 1/37 (2%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGN 112
           D   AL  MN   + G+ +++ W+   PS +KSG  +
Sbjct: 67  DAAAALAAMNGRKILGKEVKVNWA-TTPSSQKSGPSS 102

>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 = 41.9 bits (99), Expect = 2e-05
 Identities = 10/36 (27%), Positives = 16/36 (44%)

Query: 301 NRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           +  Q   LYV NL   + +  + + F+  G   S K
Sbjct: 11  DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCK 46

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 75.4 bits (186), Expect = 2e-17
 Identities = 19/82 (23%), Positives = 41/82 (50%), Gaps = 4/82 (4%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAV 260
             +++    E+  +E + + F  YG I +  + N D   G  +G+  V YE+ + A+ A+
Sbjct: 24  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHL-NLDRRTGYLKGYTLVEYETYKEAQAAM 82

Query: 261 QAWNGKEVDGKILYVGRAQKKA 282
           +  NG+++ G+ + V     + 
Sbjct: 83  EGLNGQDLMGQPISVDWCFVRG 104

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 63.4 bits (155), Expect = 6e-13
 Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
            +F+  + +    + ++D F+ +G I +  +  D   G  KGY  V +ET + A  ++E 
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84

Query: 171 VNGMLLNSKIVFVGKFIPRK 190
           +NG  L  + + V     R 
Sbjct: 85  LNGQDLMGQPISVDWCFVRG 104

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 75.0 bits (185), Expect = 4e-17
 Identities = 23/82 (28%), Positives = 44/82 (53%), Gaps = 4/82 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQA 262
           +++ +  E+  +++++E F  YG I +  + N D   G S+G+  V YE+ + A  A +A
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHL-NLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 263 WNGKEVDGKILYVGRAQKKAER 284
            NG E+ G+ + V     K  +
Sbjct: 88  LNGAEIMGQTIQVDWCFVKGPK 109

>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 = 62.3 bits (152), Expect = 2e-12
 Identities = 18/81 (22%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           +F+ ++ +      + + F  +G I +  +  D   G SKGY  V +ET + A  + E +
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88

Query: 172 NGMLLNSKIVFVGKFIPRKER 192
           NG  +  + + V     +  +
Sbjct: 89  NGAEIMGQTIQVDWCFVKGPK 109

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 75.1 bits (185), Expect = 5e-17
 Identities = 20/93 (21%), Positives = 43/93 (46%), Gaps = 10/93 (10%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN----------DGKSRGFGFVAYESP 253
             ++++  GE+   E + + F+  G I + +               GK +G   V+++ P
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 254 EFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQ 286
             A+ A+  ++GKE  G  + V  A ++A+  +
Sbjct: 68  PSAKAAIDWFDGKEFSGNPIKVSFATRRADFNR 100

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 58.2 bits (141), Expect = 6e-11
 Identities = 19/98 (19%), Positives = 39/98 (39%), Gaps = 9/98 (9%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILS--------CKVAQD-EQGNSKGYGFVHFETEE 162
            +F++ L +++  +++ D F   G I +          +  D E G  KG   V F+   
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 163 AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKA 200
           +A  +I+  +G   +   + V     R +  +  G   
Sbjct: 69  SAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGR 106

>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 = 74.2 bits (183), Expect = 5e-17
 Identities = 16/81 (19%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             ++I N   +  +++++ +FE YG +    ++      + +GFV  E    AE A++  
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECDII------KNYGFVHIEDKTAAEDAIRNL 62

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           +  ++ G  + V  ++ K++ 
Sbjct: 63  HHYKLHGVNINVEASKNKSKA 83

>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 = 60.7 bits (148), Expect = 3e-12
 Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 7/91 (7%)

Query: 104 SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEA 163
           S   SG+  +FI NL +    + +   F  +G +L C +        K YGFVH E + A
Sbjct: 2   SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTA 54

Query: 164 ANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
           A  +I  ++   L+   + V     + +   
Sbjct: 55  AEDAIRNLHHYKLHGVNINVEASKNKSKASS 85

>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 = 74.2 bits (183), Expect = 6e-17
 Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 4/82 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAVQA 262
           VY+    E  ++  L E+F   G + +  +   D   G+ +G+GFV + S E A+ A++ 
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPK-DRVTGQHQGYGFVEFLSEEDADYAIKI 76

Query: 263 WNGKEVDGKILYVGRAQKKAER 284
            +  ++ GK + V +A    + 
Sbjct: 77  MDMIKLYGKPIRVNKASAHNKN 98

>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 = 70.4 bits (173), Expect = 2e-15
 Identities = 22/93 (23%), Positives = 46/93 (49%), Gaps = 1/93 (1%)

Query: 103 PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETE 161
           P   ++    V++  LD+ +    +++ F   G +++  + +D   G  +GYGFV F +E
Sbjct: 8   PISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 67

Query: 162 EAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
           E A+ +I+ ++ + L  K + V K     +   
Sbjct: 68  EDADYAIKIMDMIKLYGKPIRVNKASAHNKNLS 100

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 1/37 (2%)

Query: 76  DTERALDTMNFDALKGRPIRIMW-SQRDPSLRKSGVG 111
           D + A+  M+   L G+PIR+   S  + +L     G
Sbjct: 69  DADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSSG 105

>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 = 39.6 bits (93), Expect = 1e-04
 Identities = 9/35 (25%), Positives = 16/35 (45%)

Query: 302 RYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           R Q   +YV  LD+ + +  L + F   G + +  
Sbjct: 12  RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTH 46

>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 = 74.7 bits (184), Expect = 7e-17
 Identities = 19/84 (22%), Positives = 41/84 (48%), Gaps = 4/84 (4%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---GKSRGFGFVAYESPEFAEKAV 260
             +++    E+  +E + + F  YG I +  + N D   G  +G+  V YE+ + A+ A+
Sbjct: 23  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHL-NLDRRTGYLKGYTLVEYETYKEAQAAM 81

Query: 261 QAWNGKEVDGKILYVGRAQKKAER 284
           +  NG+++ G+ + V     +   
Sbjct: 82  EGLNGQDLMGQPISVDWCFVRGPP 105

>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 = 64.3 bits (157), Expect = 5e-13
 Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 1/85 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
            +F+  + +    + ++D F+ +G I +  +  D   G  KGY  V +ET + A  ++E 
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 171 VNGMLLNSKIVFVGKFIPRKEREKE 195
           +NG  L  + + V     R   + +
Sbjct: 84  LNGQDLMGQPISVDWCFVRGPPKGK 108

>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 = 73.8 bits (182), Expect = 8e-17
 Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 6/82 (7%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           T +++ N      +++L+  FE YG +    ++      + + FV  E  E A +A++  
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIECDIV------KDYAFVHMERAEDAVEAIRGL 64

Query: 264 NGKEVDGKILYVGRAQKKAERT 285
           +  E  GK ++V  +  +    
Sbjct: 65  DNTEFQGKRMHVQLSTSRLRTA 86

>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 = 58.0 bits (141), Expect = 4e-11
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 7/83 (8%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            + + N+  +  N+ +   F  +G ++ C +        K Y FVH E  E A ++I  +
Sbjct: 12  KLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRGL 64

Query: 172 NGMLLNSKIVFVGKFIPRKEREK 194
           +      K + V     R     
Sbjct: 65  DNTEFQGKRMHVQLSTSRLRTAS 87

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 73.4 bits (181), Expect = 8e-17
 Identities = 21/84 (25%), Positives = 33/84 (39%), Gaps = 4/84 (4%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGT--ITSYRVMNN--DGKSRGFGFVAYESPEFAEKAV 260
            +YI N      DE L E     G   I   +   N  +G+S+GF  V   S   ++K +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 261 QAWNGKEVDGKILYVGRAQKKAER 284
                +E+ G+   V  + K    
Sbjct: 63  DLLPKRELHGQNPVVTPSNKLEHH 86

>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 = 62.2 bits (152), Expect = 9e-13
 Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 3/84 (3%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFG--SILSCKVAQD-EQGNSKGYGFVHFETEEAANKSI 168
            ++I NL     ++ + +   + G   IL  K  ++   G SKG+  V   +E ++ K +
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 169 EKVNGMLLNSKIVFVGKFIPRKER 192
           + +    L+ +   V      +  
Sbjct: 63  DLLPKRELHGQNPVVTPSNKLEHH 86

>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 = 73.8 bits (182), Expect = 8e-17
 Identities = 27/85 (31%), Positives = 43/85 (50%), Gaps = 5/85 (5%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAV 260
              +++K   ED  +E LKE F+        R++ +   G S+GFGFV + S E A+ A 
Sbjct: 15  SKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71

Query: 261 QAWNGKEVDGKILYVGRAQKKAERT 285
           +A    E+DG  + +  A+ K E  
Sbjct: 72  EAMEDGEIDGNKVTLDWAKPKGEGG 96

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 63.0 bits (154), Expect = 6e-13
 Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 4/95 (4%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVH 157
               P+ R      +F+K L +    + + +   +F   +  ++  D E G+SKG+GFV 
Sbjct: 4   GSSGPNARSQPSKTLFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGFGFVD 60

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
           F +EE A  + E +    ++   V +    P+ E 
Sbjct: 61  FNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG 95

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 74.2 bits (183), Expect = 9e-17
 Identities = 28/100 (28%), Positives = 49/100 (49%), Gaps = 7/100 (7%)

Query: 187 IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRG 244
           +P + +++E  +  KLF    I     +  +E L+  +E +G +T   VM      +SRG
Sbjct: 15  VPLERKKREKEQFRKLF----IGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRG 70

Query: 245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
           FGFV + S    + A+ A     +DG+++   RA  + E 
Sbjct: 71  FGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREES 109

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 51.9 bits (125), Expect = 9e-09
 Identities = 18/95 (18%), Positives = 41/95 (43%), Gaps = 7/95 (7%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVH 157
            +     RK     +FI  L      +++ + +  +G +  C V +D     S+G+GFV 
Sbjct: 21  KREKEQFRK-----LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVT 75

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
           F +    + ++       ++ ++V   + + R+E 
Sbjct: 76  FSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAREES 109

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 75.0 bits (184), Expect = 1e-16
 Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 4/92 (4%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGT--ITSYRVMNND--GKSRGFGFVAYESPEFAEKA 259
             VY+ +F     D++L ++    G   +   +   N   G+S+G+  V   S     K 
Sbjct: 56  AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKL 115

Query: 260 VQAWNGKEVDGKILYVGRAQKKAERTQELKRR 291
           ++   GK ++G+ + V  A ++     E + R
Sbjct: 116 LELLPGKVLNGEKVDVRPATRQNLSQFEAQAR 147

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 64.9 bits (158), Expect = 5e-13
 Identities = 19/93 (20%), Positives = 41/93 (44%), Gaps = 3/93 (3%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGS--ILSCKVAQD-EQGNSKGYGFVHFETEEAANKSI 168
            V++ +      ++ +     + G   ++  K A++   G SKGY  V   +E + +K +
Sbjct: 57  AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116

Query: 169 EKVNGMLLNSKIVFVGKFIPRKEREKELGEKAK 201
           E + G +LN + V V     +   + E   + +
Sbjct: 117 ELLPGKVLNGEKVDVRPATRQNLSQFEAQARKR 149

>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 = 73.0 bits (180), Expect = 1e-16
 Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 3/82 (3%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQA 262
           N+Y+ N       E++KE+F  +G + + +++      K +GFGFV  +      +A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK 61

Query: 263 WNGKEVDGKILYVGRAQKKAER 284
            +  +  G+ + V  A  K   
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSL 83

>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 = 60.6 bits (148), Expect = 3e-12
 Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 2/85 (2%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           N+++ NL  S  ++ + + FS FG + + K+  D E    KG+GFV  + E   +++I K
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK 61

Query: 171 VNGMLLNSKIVFVGKFIPRKEREKE 195
           ++      + + V +  P+K  E  
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEHH 86

>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 = 74.8 bits (184), Expect = 2e-16
 Identities = 27/100 (27%), Positives = 43/100 (43%), Gaps = 6/100 (6%)

Query: 189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFG 246
            +E+EK L +   L    Y+ N      +E++ E+F   G I    +  +     + GF 
Sbjct: 29  NEEQEKLLKKSCTL----YVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFC 84

Query: 247 FVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQ 286
           FV Y S   AE A++  NG  +D +I+         E  Q
Sbjct: 85  FVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQ 124

>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 = 64.1 bits (156), Expect = 1e-12
 Identities = 18/97 (18%), Positives = 38/97 (39%), Gaps = 1/97 (1%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVH 157
              +          +++ NL      + +Y+ FS  G I    +  D  +  + G+ FV 
Sbjct: 28  DNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVE 87

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
           + +   A  ++  +NG  L+ +I+        KE  +
Sbjct: 88  YYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQ 124

>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 = 42.9 bits (101), Expect = 3e-05
 Identities = 12/37 (32%), Positives = 15/37 (40%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGN 112
           D E A+  +N   L  R IR  W       R+ G G 
Sbjct: 93  DAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGR 129

>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 = 72.6 bits (179), Expect = 2e-16
 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 6/82 (7%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             +++ N       ++L+ +FE  G +    V+      + + FV  E    A+ A+   
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDVV------KDYAFVHMEKEADAKAAIAQL 63

Query: 264 NGKEVDGKILYVGRAQKKAERT 285
           NGKEV GK + V  + K  +++
Sbjct: 64  NGKEVKGKRINVELSTKGQKKS 85

>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 = 58.0 bits (141), Expect = 3e-11
 Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 7/80 (8%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ N+  +  ++ +   F   G ++ C V        K Y FVH E E  A  +I ++N
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQLN 64

Query: 173 GMLLNSKIVFVGKFIPRKER 192
           G  +  K + V      +++
Sbjct: 65  GKEVKGKRINVELSTKGQKK 84

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 71.8 bits (177), Expect = 4e-16
 Identities = 18/81 (22%), Positives = 43/81 (53%), Gaps = 3/81 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW 263
           +++     +  + +L+E F+ +G +T   ++      + RGFGF+ +E  +  ++AV   
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM- 71

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           +  ++ GK + V RA+ +  +
Sbjct: 72  HFHDIMGKKVEVKRAEPRDSK 92

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 58.0 bits (141), Expect = 4e-11
 Identities = 17/86 (19%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSI 168
              +F+  +  +     + + F  FG +    +  D E+   +G+GF+ FE E++ ++++
Sbjct: 10  SNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69

Query: 169 EKVNGMLLNSKIVFVGKFIPRKEREK 194
              +   +  K V V +  PR  +  
Sbjct: 70  NM-HFHDIMGKKVEVKRAEPRDSKSS 94

>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 = 72.0 bits (177), Expect = 5e-16
 Identities = 21/93 (22%), Positives = 39/93 (41%), Gaps = 5/93 (5%)

Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPE 254
           G K      ++I     + +++ LK +FE +G I    V+     G  +G  F+ Y   E
Sbjct: 7   GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERE 66

Query: 255 FAEKAVQAWNGKEV---DGKILYVGRAQKKAER 284
            A KA  A + ++      + + V  A  ++  
Sbjct: 67  SALKAQSALHEQKTLPGMNRPIQVKPADSESRG 99

>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 = 65.0 bits (159), Expect = 2e-13
 Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 98  WSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFV 156
              +D    K     +FI  + +++D K +   F  FG I    V +D   G  KG  F+
Sbjct: 6   SGMKDHDAIK-----LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60

Query: 157 HFETEEAANKSIEKVNGM 174
            +   E+A K+   ++  
Sbjct: 61  TYCERESALKAQSALHEQ 78

>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 = 71.8 bits (176), Expect = 7e-16
 Identities = 15/87 (17%), Positives = 29/87 (33%), Gaps = 4/87 (4%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           T +  KN        +++E F  +G++    +     +      V +  P  A KA +  
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLL----PEGGITAIVEFLEPLEARKAFRHL 66

Query: 264 NGKEVDGKILYVGRAQKKAERTQELKR 290
              +     LY+  A          K+
Sbjct: 67  AYSKFHHVPLYLEWAPIGVFGAAPQKK 93

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 50.2 bits (120), Expect = 3e-08
 Identities = 16/94 (17%), Positives = 31/94 (32%), Gaps = 10/94 (10%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +  KNL        + +TFS FGS+    +             V F     A K+   + 
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPLEARKAFRHLA 67

Query: 173 GMLLNSKIVFV-----GKFIPRKEREKELGEKAK 201
               +   +++     G F    +++    E+  
Sbjct: 68  YSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPA 101

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 72.2 bits (177), Expect = 8e-16
 Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 5/88 (5%)

Query: 204 TNVYIKNFGEDFNDEKLKE----MFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKA 259
             V I N   +   EKL+     +    G I    V  +   + G  ++ + + E A+  
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLS-DDNSGKAYIVFATQESAQAF 88

Query: 260 VQAWNGKEVDGKILYVGRAQKKAERTQE 287
           V+A+ G    G  L +  ++    +  E
Sbjct: 89  VEAFQGYPFQGNPLVITFSETPQSQVAE 116

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 60.3 bits (146), Expect = 1e-11
 Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 6/76 (7%)

Query: 112 NVFIKNLDKSIDN----KAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
            V I N++  +        +Y   S+ G IL   V      ++ G  ++ F T+E+A   
Sbjct: 31  VVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLS--DDNSGKAYIVFATQESAQAF 88

Query: 168 IEKVNGMLLNSKIVFV 183
           +E   G       + +
Sbjct: 89  VEAFQGYPFQGNPLVI 104

>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 = 71.2 bits (175), Expect = 9e-16
 Identities = 22/81 (27%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             +Y+ N   D   + ++++F  YG I    + N       F FV +E P  AE AV   
Sbjct: 23  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN-RRGGPPFAFVEFEDPRDAEDAVYGR 81

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           +G + DG  L V   +     
Sbjct: 82  DGYDYDGYRLRVEFPRSGRGT 102

>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 = 54.2 bits (131), Expect = 1e-09
 Identities = 16/93 (17%), Positives = 30/93 (32%), Gaps = 3/93 (3%)

Query: 91  GRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS 150
           G                +    +++ NL   I  K + D F  +G+I    +        
Sbjct: 4   GSSGMSGGGVIRGPAGNND-CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGG 60

Query: 151 KGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
             + FV FE    A  ++   +G   +   + V
Sbjct: 61  PPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV 93

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

 Score = 70.8 bits (174), Expect = 1e-15
 Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 3/80 (3%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
            VY+ N G      +L+  F  YG + +  +  N     GF FV +E P  AE AV+  +
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN---PPGFAFVEFEDPRDAEDAVRGLD 58

Query: 265 GKEVDGKILYVGRAQKKAER 284
           GK + G  + V  +     R
Sbjct: 59  GKVICGSRVRVELSTGMPRR 78

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

 Score = 52.7 bits (127), Expect = 4e-09
 Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 4/62 (6%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            V++ NL        +   FS +G + +  +A++      G+ FV FE    A  ++  +
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 172 NG 173
           +G
Sbjct: 58  DG 59

>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 = 71.2 bits (175), Expect = 1e-15
 Identities = 24/78 (30%), Positives = 34/78 (43%), Gaps = 3/78 (3%)

Query: 216 NDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
            D  L++ FE +G I    V+     GKSRG+GFV       AE+A +  N   +DG+  
Sbjct: 30  TDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-PIIDGRKA 88

Query: 274 YVGRAQKKAERTQELKRR 291
            V  A   A+        
Sbjct: 89  NVNLAYLGAKPRSLQTGF 106

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 61.2 bits (149), Expect = 4e-12
 Identities = 25/103 (24%), Positives = 41/103 (39%), Gaps = 7/103 (6%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVH 157
           SQ+D +  K     +F+  L     + ++   F  FG I    V  D Q G S+GYGFV 
Sbjct: 11  SQKDTTFTK-----IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 65

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKA 200
                AA ++ +  N + ++ +   V       +        A
Sbjct: 66  MADRAAAERACKDPNPI-IDGRKANVNLAYLGAKPRSLQTGFA 107

>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 = 70.0 bits (172), Expect = 1e-15
 Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 5/74 (6%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           T +Y+   G+   +  L+  F  +G I +  V+    + +   F+ + + + AE A +  
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTITVV----QRQQCAFIQFATRQAAEVAAEKS 68

Query: 264 -NGKEVDGKILYVG 276
            N   V+G+ L V 
Sbjct: 69  FNKLIVNGRRLNVK 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 = 58.8 bits (143), Expect = 1e-11
 Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 11/87 (12%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHF 158
           S  D ++       +++  L  +I    + + F  FG I +  V Q      +   F+ F
Sbjct: 6   SGEDKTIT-----TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQF 55

Query: 159 ETEEAANKSIEKV-NGMLLNSKIVFVG 184
            T +AA  + EK  N +++N + + V 
Sbjct: 56  ATRQAAEVAAEKSFNKLIVNGRRLNVK 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 = 39.9 bits (94), Expect = 7e-05
 Identities = 12/30 (40%), Positives = 15/30 (50%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            LYV  L D+I +  LR  F  FG I +  
Sbjct: 14  TLYVGGLGDTITETDLRNHFYQFGEIRTIT 43

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 70.3 bits (173), Expect = 2e-15
 Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 3/71 (4%)

Query: 216 NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
             E L+  F  YG +    +M      +SRGFGFV ++ P      + +     +DG+ +
Sbjct: 29  TQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNI 87

Query: 274 YVGRAQKKAER 284
                  +  +
Sbjct: 88  DPKPCTPRGMQ 98

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 51.5 bits (124), Expect = 9e-09
 Identities = 19/95 (20%), Positives = 39/95 (41%), Gaps = 7/95 (7%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVH 157
           +     + K     +F+  LD S   + +   FS +G ++ C + +D+    S+G+GFV 
Sbjct: 10  NSGADEIGK-----LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVK 64

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
           F+        +       L+ + +      PR  +
Sbjct: 65  FKDPNCVGTVLA-SRPHTLDGRNIDPKPCTPRGMQ 98

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 70.0 bits (172), Expect = 2e-15
 Identities = 24/103 (23%), Positives = 38/103 (36%), Gaps = 9/103 (8%)

Query: 184 GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGK 241
              +PR           K+F    I         E L+E F  +G +    VM      +
Sbjct: 12  SGLVPRGSHMGS--SGCKMF----IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKR 65

Query: 242 SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
           SRGFGFV +      +K +   +  E+D K +    A  +  +
Sbjct: 66  SRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTIDPKVAFPRRAQ 107

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 55.7 bits (135), Expect = 3e-10
 Identities = 25/97 (25%), Positives = 41/97 (42%), Gaps = 7/97 (7%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVH 157
           S    S  K     +FI  L      + + + F  FG +  C V +D     S+G+GFV 
Sbjct: 19  SHMGSSGCK-----MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVT 73

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
           F  +   +K +   +   L+SK +      PR+ + K
Sbjct: 74  FMDQAGVDKVLA-QSRHELDSKTIDPKVAFPRRAQPK 109

>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 = 69.3 bits (170), Expect = 3e-15
 Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFG-SILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIE 169
           ++++ +L+  +D   +   F+  G +++S K+ ++   G   GY FV F     A K + 
Sbjct: 11  SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 170 KVNGMLLN 177
           K+NG  L 
Sbjct: 71  KINGKPLP 78

>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 = 60.0 bits (146), Expect = 7e-12
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYG-TITSYRVMNND--GKSRGFGFVAYESPEFAEKAV 260
            ++++ +     ++  +   F   G T+ S +++ N   G   G+ FV +     AEK +
Sbjct: 10  ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69

Query: 261 QAWNGKEVDGKILYV 275
              NGK + G     
Sbjct: 70  HKINGKPLPGATPAK 84

>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 = 70.0 bits (172), Expect = 3e-15
 Identities = 18/101 (17%), Positives = 38/101 (37%), Gaps = 3/101 (2%)

Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGF 245
           P +E    L  + +    V+            L++ F   G +   R++   N  +S+G 
Sbjct: 10  PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI 69

Query: 246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQ 286
            +V +   +    A+    G+ + G  + V  +Q +  R  
Sbjct: 70  AYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNRLS 109

>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 = 63.5 bits (155), Expect = 6e-13
 Identities = 21/82 (25%), Positives = 31/82 (37%), Gaps = 2/82 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
           VF   L   I  + + D FSA G +   ++  D     SKG  +V F   ++   +I   
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGL- 86

Query: 172 NGMLLNSKIVFVGKFIPRKERE 193
            G  L    + V      K R 
Sbjct: 87  TGQRLLGVPIIVQASQAEKNRL 108

>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 = 70.3 bits (172), Expect = 5e-15
 Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             VY+ N G + N  +L+  F  YG + S  V  N     GF FV +E P  A  AV+  
Sbjct: 74  CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN---PPGFAFVEFEDPRDAADAVREL 130

Query: 264 NGKEVDGKILYVGRAQKK 281
           +G+ + G  + V  +  +
Sbjct: 131 DGRTLCGCRVRVELSNGE 148

>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 = 52.2 bits (125), Expect = 1e-08
 Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 6/97 (6%)

Query: 83  TMNFDALKGRPIRIMWSQRDPSLRKSGVGN--VFIKNLDKSIDNKAMYDTFSAFGSILSC 140
           T +                    R S   +  V++ NL  + +   +   F  +G + S 
Sbjct: 44  TYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSV 103

Query: 141 KVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLN 177
            VA++      G+ FV FE    A  ++ +++G  L 
Sbjct: 104 WVARN----PPGFAFVEFEDPRDAADAVRELDGRTLC 136

>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 = 48.0 bits (114), Expect = 5e-07
 Identities = 21/105 (20%), Positives = 37/105 (35%), Gaps = 4/105 (3%)

Query: 233 YRVMNNDGKSRGFGFVAYESPEFAEKAVQAW-NGKEVDGKILYVGRAQKKAERTQELKRR 291
           Y+++ N    +G           AEK  + + N   VDG+  Y    +            
Sbjct: 3   YKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHH 62

Query: 292 FEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
             M    R +      +YV NL ++ +   L + F  +G + S  
Sbjct: 63  HHM---HRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVW 104

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 68.5 bits (168), Expect = 7e-15
 Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 10/85 (11%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN----------DGKSRGFGFVAYESP 253
             ++++  GE+   E + + F+  G I + +               GK +G   V+++ P
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 254 EFAEKAVQAWNGKEVDGKILYVGRA 278
             A+ A+  ++GKE  G  + V  A
Sbjct: 74  PSAKAAIDWFDGKEFSGNPIKVSFA 98

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 55.4 bits (134), Expect = 3e-10
 Identities = 18/93 (19%), Positives = 36/93 (38%), Gaps = 9/93 (9%)

Query: 100 QRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILS--------CKVAQD-EQGNS 150
                   S    +F++ L +++  +++ D F   G I +          +  D E G  
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 151 KGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
           KG   V F+   +A  +I+  +G   +   + V
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKV 95

>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 = 67.7 bits (166), Expect = 1e-14
 Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 2/81 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSY--RVMNNDGKSRGFGFVAYESPEFAEKAVQ 261
           T + ++N     + +++ + F  Y  I        N  G   G   VA+ES + A  AV 
Sbjct: 16  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 262 AWNGKEVDGKILYVGRAQKKA 282
             N + +  + + +      +
Sbjct: 76  DLNDRPIGSRKVKLVLGSGPS 96

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 18/82 (21%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 103 PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSI-LSCKVAQDEQGNSKGYGFVHFETE 161
            S  K G   + ++N+  ++    + D F  +  I  S  +  +E+G   G   V FE+ 
Sbjct: 8   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 67

Query: 162 EAANKSIEKVNGMLLNSKIVFV 183
           + A  ++  +N   + S+ V +
Sbjct: 68  DEATAAVIDLNDRPIGSRKVKL 89

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 67.6 bits (166), Expect = 1e-14
 Identities = 19/93 (20%), Positives = 36/93 (38%), Gaps = 8/93 (8%)

Query: 194 KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYE 251
           + + + + L     +        ++ LKE F  +G +   +V      G S+GFGFV + 
Sbjct: 10  RAVQKTSDLI----VLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT 65

Query: 252 SPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
             E   K +   +   +DG+         K  +
Sbjct: 66  EYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQ 96

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 18/85 (21%), Positives = 41/85 (48%), Gaps = 3/85 (3%)

Query: 110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSI 168
             ++ +  L      + + + FS FG +L  +V +D + G+SKG+GFV F   E   K +
Sbjct: 15  TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74

Query: 169 EKVNGMLLNSKIVFVGKFIPRKERE 193
            + +  +++ +         ++ ++
Sbjct: 75  SQRH--MIDGRWCDCKLPNSKQSQD 97

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 66.7 bits (164), Expect = 2e-14
 Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 3/65 (4%)

Query: 216 NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
             E L+E F  +G +    VM      +SRGFGFV +      +K +   +  E+D K +
Sbjct: 13  TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTI 71

Query: 274 YVGRA 278
               A
Sbjct: 72  DPKVA 76

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 49.0 bits (118), Expect = 3e-08
 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIE 169
           +FI  L      + + + F  FG +  C V +D     S+G+GFV F  +   +K + 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 67.0 bits (164), Expect = 2e-14
 Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 8/85 (9%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGT--ITSYRVMNN--DGKSRGFGFVAYESPEFAEKA 259
             + ++N       + +     PY +  + + R++ +    ++RGF FV   S   A + 
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 260 VQAWNGKE----VDGKILYVGRAQK 280
           +Q          +DGK + V  A+ 
Sbjct: 70  LQILQSLHPPLKIDGKTIGVDFAKS 94

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 58.9 bits (143), Expect = 2e-11
 Identities = 10/72 (13%), Positives = 34/72 (47%), Gaps = 3/72 (4%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFG--SILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSI 168
            + ++N+       ++    S +   ++ + ++ +D+Q   ++G+ FV   +   A++ +
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 169 EKVNGMLLNSKI 180
           + +  +    KI
Sbjct: 71  QILQSLHPPLKI 82

>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 = 66.6 bits (163), Expect = 3e-14
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
           T + ++N     + +++ + F  Y  I     +  N  G   G   VA+ES + A  AV 
Sbjct: 16  TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 262 AWNGKEVDGKILYVGRAQK 280
             N + +  + + +     
Sbjct: 76  DLNDRPIGSRKVKLSGPSS 94

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 54.6 bits (132), Expect = 6e-10
 Identities = 16/78 (20%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDEQGNSKGYGFVHFETEEAAN 165
           K G   + ++N+  ++    + D F  +  I     +  +E+G   G   V FE+ + A 
Sbjct: 12  KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71

Query: 166 KSIEKVNGMLLNSKIVFV 183
            ++  +N   + S+ V +
Sbjct: 72  AAVIDLNDRPIGSRKVKL 89

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 66.0 bits (162), Expect = 3e-14
 Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 3/68 (4%)

Query: 213 EDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
            +   E +K  FE +G +    +M      + RGFGFV +ES +  EK  +  +  E++ 
Sbjct: 9   VNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI-HFHEINN 67

Query: 271 KILYVGRA 278
           K++   +A
Sbjct: 68  KMVECKKA 75

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 51.3 bits (124), Expect = 5e-09
 Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           +F+  L  +   + +   F  FG +    +  D+     +G+GFV FE+E+   K  E  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI- 60

Query: 172 NGMLLNSKIV 181
           +   +N+K+V
Sbjct: 61  HFHEINNKMV 70

>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 = 67.2 bits (164), Expect = 4e-14
 Identities = 18/108 (16%), Positives = 40/108 (37%), Gaps = 11/108 (10%)

Query: 186 FIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGF 245
            +PR     +          ++I+    D  + ++  +  P+G +T+  ++    K +  
Sbjct: 14  LVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML----KGKNQ 69

Query: 246 GFVAYESPEFAEKAVQ--AWNGKEVDGKILYVGRAQKKAERTQELKRR 291
            F+   + E A   V         + G+ +Y+  +  K     ELK  
Sbjct: 70  AFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK-----ELKTD 112

>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 = 44.5 bits (105), Expect = 3e-06
 Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 7/73 (9%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE--K 170
           + I+ L   +    +      FG + +  + +      K   F+   TEEAAN  +    
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 88

Query: 171 VNGMLLNSKIVFV 183
               +L  + +++
Sbjct: 89  SVTPVLRGQPIYI 101

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 65.9 bits (161), Expect = 4e-14
 Identities = 17/54 (31%), Positives = 31/54 (57%)

Query: 218 EKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK 271
             + ++F  +G IT+      DGK++G+ F+ Y SP  A  AV+  +G ++D +
Sbjct: 22  NVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 49.3 bits (118), Expect = 3e-08
 Identities = 15/76 (19%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 113 VFIKNL------DKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANK 166
           + + N+              ++  FS FG I +    +++ G +KGY F+ + +   A  
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEED-GKTKGYIFLEYASPAHAVD 62

Query: 167 SIEKVNGMLLNSKIVF 182
           +++  +G  L+ +  F
Sbjct: 63  AVKNADGYKLDKQHTF 78

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 66.4 bits (162), Expect = 5e-14
 Identities = 14/84 (16%), Positives = 35/84 (41%), Gaps = 6/84 (7%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA--W 263
           ++I+    D  + ++  +  P+G +T+  ++    K +   F+   + E A   V     
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLML----KGKNQAFIEMNTEEAANTMVNYYTS 74

Query: 264 NGKEVDGKILYVGRAQKKAERTQE 287
               + G+ +Y+  +  K  +T  
Sbjct: 75  VTPVLRGQPIYIQFSNHKELKTDS 98

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 44.8 bits (106), Expect = 2e-06
 Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 8/81 (9%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE--K 170
           + I+ L   +    +      FG + +  + +      K   F+   TEEAAN  +    
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 73

Query: 171 VNGMLLNSKIVFVGKFIPRKE 191
               +L  + +++ +F   KE
Sbjct: 74  SVTPVLRGQPIYI-QFSNHKE 93

>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 = 66.7 bits (163), Expect = 7e-14
 Identities = 19/105 (18%), Positives = 39/105 (37%), Gaps = 7/105 (6%)

Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGF 245
           P    EK+  +K     +VY+ N       + L+  F   G+I    ++ +   G  +G+
Sbjct: 25  PLSAEEKKEIDK----RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGY 80

Query: 246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKR 290
            ++ +      + AV A +     G+ + V   +          R
Sbjct: 81  AYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMPGISSTDR 124

>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 = 55.1 bits (133), Expect = 9e-10
 Identities = 15/85 (17%), Positives = 35/85 (41%), Gaps = 2/85 (2%)

Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIE 169
            +V++ N+D     + +   FS+ GSI    +  D   G+ KGY ++ F    + + ++ 
Sbjct: 37  RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96

Query: 170 KVNGMLLNSKIVFVGKFIPRKEREK 194
            ++  +   + + V           
Sbjct: 97  -MDETVFRGRTIKVLPKRTNMPGIS 120

>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 = 64.8 bits (159), Expect = 1e-13
 Identities = 13/80 (16%), Positives = 33/80 (41%), Gaps = 3/80 (3%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
            ++Y+ N       E+L+  F   G++    ++ +   G  +GF ++ +   E    ++ 
Sbjct: 7   RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL- 65

Query: 262 AWNGKEVDGKILYVGRAQKK 281
           A +     G+ + V   +  
Sbjct: 66  ALDESLFRGRQIKVIPKRTN 85

>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 = 57.1 bits (139), Expect = 6e-11
 Identities = 14/80 (17%), Positives = 34/80 (42%), Gaps = 2/80 (2%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           ++++ N+D     + +   F   GS+    +  D   G+ KG+ ++ F  +E+   S+  
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 67

Query: 171 VNGMLLNSKIVFVGKFIPRK 190
            +  L   + + V      +
Sbjct: 68  -DESLFRGRQIKVIPKRTNR 86

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 64.9 bits (159), Expect = 1e-13
 Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 3/65 (4%)

Query: 216 NDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
           + + LK+ F  +G +    +    N G+SRGFGF+ ++     EK +       +DG+++
Sbjct: 24  SKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKE-HRLDGRVI 82

Query: 274 YVGRA 278
              +A
Sbjct: 83  DPKKA 87

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVH 157
           S+ +    K     +F+  L      K + D F+ FG ++ C +  D   G S+G+GF+ 
Sbjct: 5   SKNEEDAGK-----MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFIL 59

Query: 158 FETEEAANKSIEKVNGMLLNSKI 180
           F+   +  K +++    L    I
Sbjct: 60  FKDAASVEKVLDQKEHRLDGRVI 82

>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 = 64.7 bits (158), Expect = 1e-13
 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 5/79 (6%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           + + +KN  +D N +++ ++ + Y     Y       +++   FV   + E A+ A+Q +
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYV-----DRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 264 NGKEVDGKILYVGRAQKKA 282
           +     GK L V      A
Sbjct: 61  HQYSFRGKDLIVQLQPTDA 79

>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 = 54.0 bits (130), Expect = 7e-10
 Identities = 16/76 (21%), Positives = 30/76 (39%), Gaps = 6/76 (7%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
           SG   + +KNL +  + + ++D    +  +  C V       +K   FV     E A  +
Sbjct: 3   SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-----DRNKRTAFVTLLNGEQAQNA 56

Query: 168 IEKVNGMLLNSKIVFV 183
           I+  +      K + V
Sbjct: 57  IQMFHQYSFRGKDLIV 72

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 64.5 bits (158), Expect = 2e-13
 Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 5/81 (6%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           V++     D  +++L+E F  YG +    +       R F FV +   + A+        
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK---PFRAFAFVTFADDQIAQSLCG--ED 62

Query: 266 KEVDGKILYVGRAQKKAERTQ 286
             + G  +++  A+ K     
Sbjct: 63  LIIKGISVHISNAEPKHNSNS 83

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 11/82 (13%), Positives = 29/82 (35%), Gaps = 6/82 (7%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           VF+      +    + + FS +G ++   + +      + + FV F  ++ A        
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--E 61

Query: 173 GMLLNSKIVFVGKFIPRKEREK 194
            +++    V +    P+     
Sbjct: 62  DLIIKGISVHISNAEPKHNSNS 83

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 64.8 bits (158), Expect = 2e-13
 Identities = 17/54 (31%), Positives = 31/54 (57%)

Query: 218 EKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK 271
             + ++F  +G IT+      DGK++G+ F+ Y SP  A  AV+  +G ++D +
Sbjct: 36  NVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 49.0 bits (117), Expect = 7e-08
 Identities = 15/76 (19%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 113 VFIKNL------DKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANK 166
           + + N+              ++  FS FG I +    +++ G +KGY F+ + +   A  
Sbjct: 18  IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEED-GKTKGYIFLEYASPAHAVD 76

Query: 167 SIEKVNGMLLNSKIVF 182
           +++  +G  L+ +  F
Sbjct: 77  AVKNADGYKLDKQHTF 92

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 64.2 bits (157), Expect = 2e-13
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 5/79 (6%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           V++    ED   E+L++ F  YG +    +       R F FV +   + A+        
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK---PFRAFAFVTFADDKVAQSLCG--ED 68

Query: 266 KEVDGKILYVGRAQKKAER 284
             + G  +++  A+ K  +
Sbjct: 69  LIIKGISVHISNAEPKHNK 87

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 48.4 bits (116), Expect = 9e-08
 Identities = 10/80 (12%), Positives = 30/80 (37%), Gaps = 6/80 (7%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           VF+    + +  + +   F  +G ++   + +      + + FV F  ++ A     +  
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQSLCGEDL 69

Query: 173 GMLLNSKIVFVGKFIPRKER 192
             ++    V +    P+  +
Sbjct: 70  --IIKGISVHISNAEPKHNK 87

>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 = 64.1 bits (156), Expect = 3e-13
 Identities = 11/78 (14%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQ--AW 263
           ++I+    +  + ++  +  P+G +T+  ++    K +   F+   + E A   V   + 
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILML----KGKNQAFLELATEEAAITMVNYYSA 73

Query: 264 NGKEVDGKILYVGRAQKK 281
               +  + +Y+  +  K
Sbjct: 74  VTPHLRNQPIYIQYSNHK 91

>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 = 42.5 bits (100), Expect = 1e-05
 Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 8/81 (9%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE--K 170
           + I+ L   +    +      FG + +  +        K   F+   TEEAA   +    
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILM-----LKGKNQAFLELATEEAAITMVNYYS 72

Query: 171 VNGMLLNSKIVFVGKFIPRKE 191
                L ++ +++ ++   KE
Sbjct: 73  AVTPHLRNQPIYI-QYSNHKE 92

>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 = 63.4 bits (155), Expect = 4e-13
 Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 4/73 (5%)

Query: 199 KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEK 258
           KA   T +++   G + +   L   F+ +G+I +   +    K   F ++ YES + A+ 
Sbjct: 13  KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV----KGDSFAYIQYESLDAAQA 68

Query: 259 AVQAWNGKEVDGK 271
           A     G  + G 
Sbjct: 69  ACAKMRGFPLGGP 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 = 58.8 bits (143), Expect = 2e-11
 Identities = 17/87 (19%), Positives = 37/87 (42%), Gaps = 11/87 (12%)

Query: 91  GRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS 150
           G   +I + + +P+ R      +++  L  +    A+   F  FGSI +    +      
Sbjct: 4   GSSGKIGYGKANPTTR------LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG----- 52

Query: 151 KGYGFVHFETEEAANKSIEKVNGMLLN 177
             + ++ +E+ +AA  +  K+ G  L 
Sbjct: 53  DSFAYIQYESLDAAQAACAKMRGFPLG 79

>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 = 37.2 bits (87), Expect = 7e-04
 Identities = 9/30 (30%), Positives = 14/30 (46%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSAK 336
            L+V  L  +     L +EF  FG+I +  
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTID 48

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 62.5 bits (153), Expect = 5e-13
 Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 3/68 (4%)

Query: 213 EDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG 270
            D  +EK++E F  +G + S  +   N   K RGF F+ ++  E  +K ++      V  
Sbjct: 9   PDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGL 67

Query: 271 KILYVGRA 278
               +  A
Sbjct: 68  SKCEIKVA 75

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 48.7 bits (117), Expect = 4e-08
 Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
           +F+  L      + + + F  FG + S ++  D +    +G+ F+ F+ EE   K +EK
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 65.1 bits (158), Expect = 6e-13
 Identities = 16/102 (15%), Positives = 37/102 (36%), Gaps = 6/102 (5%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVF---IKNLDKSIDNKAMYDTFS 132
             + AL  +N        +    +  D  +  +G   V    ++NL   +    ++  FS
Sbjct: 9   SAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFS 68

Query: 133 AFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGM 174
            FG++L          N++    + +    +A  +   ++G 
Sbjct: 69  KFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQ 107

>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 = 50.9 bits (121), Expect = 5e-08
 Identities = 16/112 (14%), Positives = 40/112 (35%), Gaps = 5/112 (4%)

Query: 157 HFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFN 216
           H     +A  +++ VN +   +  +               G+   L   + ++N      
Sbjct: 3   HHHHHGSAQAALQAVNSVQSGNLAL-AASAAAVDAGMAMAGQSPVLR--IIVENLFYPVT 59

Query: 217 DEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEV 268
            + L ++F  +GT+           ++    + Y  P  A+ A  + +G+ +
Sbjct: 60  LDVLHQIFSKFGTVLKIITFTK--NNQFQALLQYADPVSAQHAKLSLDGQNI 109

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 62.5 bits (152), Expect = 1e-12
 Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 3/88 (3%)

Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFA 256
           GE A L  +VY+ N   D     LK      G++            R   F+ Y     A
Sbjct: 13  GEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQG---PRRRAFLHYPDSAAA 69

Query: 257 EKAVQAWNGKEVDGKILYVGRAQKKAER 284
           ++AV    G  +    L V  A+++ ++
Sbjct: 70  QQAVSCLQGLRLGTDTLRVALARQQRDK 97

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 46.7 bits (111), Expect = 3e-07
 Identities = 12/66 (18%), Positives = 26/66 (39%), Gaps = 4/66 (6%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           +V++ NL +      +       GS+      Q      +   F+H+    AA +++  +
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQ----GPRRRAFLHYPDSAAAQQAVSCL 76

Query: 172 NGMLLN 177
            G+ L 
Sbjct: 77  QGLRLG 82

>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 = 64.1 bits (155), Expect = 2e-12
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 2/86 (2%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQ 261
             +VYIK F  D   + +KE  E  G + + ++        +G  FV ++S E A+K V+
Sbjct: 109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE 168

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQE 287
              G++     L +        +  E
Sbjct: 169 T-PGQKYKETDLLILFKDDYFAKKNE 193

>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 = 50.6 bits (120), Expect = 1e-07
 Identities = 17/117 (14%), Positives = 41/117 (35%), Gaps = 7/117 (5%)

Query: 85  NFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQ 144
           +   ++  P + +    D         +V+IK          + +     G +L+ ++ +
Sbjct: 84  DKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRR 143

Query: 145 DEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAK 201
                 KG  FV F++ E+A K +E            +    +    ++    +K +
Sbjct: 144 TLHKAFKGSIFVVFDSIESAKKFVETPG-------QKYKETDLLILFKDDYFAKKNE 193

>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 = 61.2 bits (149), Expect = 3e-12
 Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 7/82 (8%)

Query: 204 TNVYIKNFGEDFNDEK-LKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
           + V+I N       +  ++ +F  YG +    V       +G+ FV Y +   A  AV  
Sbjct: 28  SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH------KGYAFVQYSNERHARAAVLG 81

Query: 263 WNGKEVDGKILYVGRAQKKAER 284
            NG+ + G+ L +  A +    
Sbjct: 82  ENGRVLAGQTLDINMAGEPKPD 103

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 57.0 bits (138), Expect = 1e-10
 Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 11/86 (12%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKA-MYDTFSAFGSILSCKVAQDEQGNSKGYGFVH 157
           ++ DP    S    VFI NL+ ++  K+ +   FS +G +  C V        KGY FV 
Sbjct: 19  NKNDPKSINS---RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQ 68

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFV 183
           +  E  A  ++   NG +L  + + +
Sbjct: 69  YSNERHARAAVLGENGRVLAGQTLDI 94

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

 Score = 60.3 bits (147), Expect = 5e-12
 Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 7/89 (7%)

Query: 204 TNVYIKNF-GEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
           + ++I N   ++ + E L  +F PYG I    +         FGF+ +++P+    A++ 
Sbjct: 11  SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NAFGFIQFDNPQSVRDAIEC 64

Query: 263 WNGKEVDGKILYVGRAQKKAERTQELKRR 291
            + +   GK L +  +   A    +    
Sbjct: 65  ESQEMNFGKKLILEVSSSNARPQFDHGDH 93

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 113 VFIKNLD-KSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           +FI NL  K++  + ++  FS +G I+   +          +GF+ F+  ++   +IE  
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECE 65

Query: 172 NGMLLNSKIVFV 183
           +  +   K + +
Sbjct: 66  SQEMNFGKKLIL 77

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 61.0 bits (148), Expect = 5e-12
 Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           + +KN  E  + + LK++       T++  +N      G G + + S E   +A++  N 
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR-DFDGTGALEFPSEEILVEALERLNN 89

Query: 266 KEVDGKILYV 275
            E  G ++ V
Sbjct: 90  IEFRGSVITV 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 52.5 bits (126), Expect = 5e-09
 Identities = 13/71 (18%), Positives = 30/71 (42%), Gaps = 2/71 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           + +KNL +    + + D        L    +     +  G G + F +EE   +++E++N
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENS--LETTFSSVNTRDFDGTGALEFPSEEILVEALERLN 88

Query: 173 GMLLNSKIVFV 183
            +     ++ V
Sbjct: 89  NIEFRGSVITV 99

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 60.6 bits (147), Expect = 7e-12
 Identities = 12/79 (15%), Positives = 23/79 (29%), Gaps = 5/79 (6%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           V +       + + LK+     G +    V        G G V +   E    AV+  + 
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADVY-----RDGTGVVEFVRKEDMTYAVRKLDN 72

Query: 266 KEVDGKILYVGRAQKKAER 284
            +           + K + 
Sbjct: 73  TKFRSHEGETAYIRVKVDG 91

>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 = 58.3 bits (141), Expect = 5e-11
 Identities = 13/82 (15%), Positives = 25/82 (30%), Gaps = 6/82 (7%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           V +  L  S   + + D     G +    V         G G V F  +E    ++ K++
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADV------YRDGTGVVEFVRKEDMTYAVRKLD 71

Query: 173 GMLLNSKIVFVGKFIPRKEREK 194
                S          + +  +
Sbjct: 72  NTKFRSHEGETAYIRVKVDGPR 93

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 60.1 bits (146), Expect = 9e-12
 Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 207 YIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQAWN 264
            I +       + L  +F   G + +     +   GK++GF FV   S   A+K +++++
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 265 GKEVDGK 271
           GK +D K
Sbjct: 76  GKRLDLK 82

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 52.8 bits (127), Expect = 3e-09
 Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 3/80 (3%)

Query: 110 VGNV-FIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKS 167
           V     I +    +  KA+   FS  G +++ +   DE  G +KG+ FV   +   A K 
Sbjct: 11  VNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKI 70

Query: 168 IEKVNGMLLNSKIVF-VGKF 186
           I+  +G  L+ K    +   
Sbjct: 71  IKSFHGKRLDLKHRLFLYTM 90

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 60.3 bits (146), Expect = 9e-12
 Identities = 20/84 (23%), Positives = 30/84 (35%), Gaps = 8/84 (9%)

Query: 206 VYIKNFGEDFNDE---KLKEMFEPYGTITSYRVMNNDG-----KSRGFGFVAYESPEFAE 257
           V++    +   D    K  E F  +G I    + N+             +V Y   E A 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 258 KAVQAWNGKEVDGKILYVGRAQKK 281
           +A+Q  N   VDG+ L       K
Sbjct: 78  RAIQCVNNVVVDGRTLKASLGTTK 101

>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 = 49.9 bits (119), Expect = 4e-08
 Identities = 13/78 (16%), Positives = 31/78 (39%), Gaps = 7/78 (8%)

Query: 113 VFIKNLDKSIDNKAM---YDTFSAFGSILSCKVAQD----EQGNSKGYGFVHFETEEAAN 165
           VF+  L + + +  +    + F  FG I    +                +V +   E A 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 166 KSIEKVNGMLLNSKIVFV 183
           ++I+ VN ++++ + +  
Sbjct: 78  RAIQCVNNVVVDGRTLKA 95

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 59.0 bits (143), Expect = 2e-11
 Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 6/72 (8%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQ--AW 263
           V+I+   +   +  L E  + +G I+   VM      +    V +E    A  AV   A 
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVM----PKKRQALVEFEDVLGACNAVNYAAD 79

Query: 264 NGKEVDGKILYV 275
           N   + G   +V
Sbjct: 80  NQIYIAGHPAFV 91

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 45.1 bits (107), Expect = 1e-06
 Identities = 15/73 (20%), Positives = 23/73 (31%), Gaps = 7/73 (9%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE--K 170
           V I+ L   +    + +    FG I    V        K    V FE    A  ++    
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVM-----PKKRQALVEFEDVLGACNAVNYAA 78

Query: 171 VNGMLLNSKIVFV 183
            N + +     FV
Sbjct: 79  DNQIYIAGHPAFV 91

>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 = 59.0 bits (143), Expect = 2e-11
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 6/79 (7%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA-- 262
            V+++   E   +  L E  E +GTI    +M      +    V +E+ + A++ V    
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMM----PFKRQALVEFENIDSAKECVTFAA 72

Query: 263 WNGKEVDGKILYVGRAQKK 281
                + G+  +   +  K
Sbjct: 73  DVPVYIAGQQAFFNYSTSK 91

>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 = 46.7 bits (111), Expect = 4e-07
 Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 7/74 (9%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE-- 169
            V ++ L +S+    + +    FG+I    +        K    V FE  ++A + +   
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFA 71

Query: 170 KVNGMLLNSKIVFV 183
               + +  +  F 
Sbjct: 72  ADVPVYIAGQQAFF 85

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 58.8 bits (143), Expect = 3e-11
 Identities = 15/81 (18%), Positives = 38/81 (46%), Gaps = 4/81 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW 263
            Y+ N   +     +  +F+    I S R++   +  K +GF +V ++  +  ++A+  +
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TY 75

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           +G  +  + L V  A+ + + 
Sbjct: 76  DGALLGDRSLRVDIAEGRKQD 96

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKV 171
            ++ NL  +     +   F     I S ++ +D +    KG+ +V F+  ++  +++   
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY- 75

Query: 172 NGMLLNSKIVFVGKFIPRKERE 193
           +G LL  + + V     RK+ +
Sbjct: 76  DGALLGDRSLRVDIAEGRKQDK 97

>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 = 58.8 bits (143), Expect = 3e-11
 Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 5/82 (6%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRV---MNNDGKSRGFGFVAYESPEFAEKAVQA 262
            ++ N   D  +E +KE F     I++ R+    +N  + +GFG+  +E  +    A+  
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76

Query: 263 WNGKEVDGKILYVGRAQKKAER 284
            N + +  K + V  A +  ++
Sbjct: 77  -NEESLGNKRIRVDVADQAQDK 97

>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 = 50.7 bits (122), Expect = 2e-08
 Identities = 14/84 (16%), Positives = 37/84 (44%), Gaps = 4/84 (4%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD--EQGNSKGYGFVHFETEEAANKSIEK 170
            F+ NL   +  +++ + F     I + ++ ++       KG+G+  FE  ++   ++  
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76

Query: 171 VNGMLLNSKIVFVGKFIPRKEREK 194
            N   L +K + V      ++++ 
Sbjct: 77  -NEESLGNKRIRVDVADQAQDKDS 99

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 58.1 bits (141), Expect = 3e-11
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 4/82 (4%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           +V++  F    +  +L E F  +G + S  +  + G    F  V        E  +   +
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV---FAIVEMGDVGAREAVLSQ-S 65

Query: 265 GKEVDGKILYVGRAQKKAERTQ 286
              + G  L V   ++K  ++ 
Sbjct: 66  QHSLGGHRLRVRPREQKEFQSP 87

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 50.4 bits (121), Expect = 2e-08
 Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 8/87 (9%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
           SG+ +VF+    + +D+  + + F AFG + S  + +D       +  V      A    
Sbjct: 6   SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD----KGVFAIVEMGDVGAREAV 61

Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREK 194
           + + +   L    + V    PR+++E 
Sbjct: 62  LSQ-SQHSLGGHRLRVR---PREQKEF 84

>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 = 58.1 bits (141), Expect = 4e-11
 Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 7/73 (9%)

Query: 204 TNVYIKNF-GEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
           + ++I N   ++ + E L  +F PYG I    +         FGF+ +++P+    A++ 
Sbjct: 23  SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NAFGFIQFDNPQSVRDAIEX 76

Query: 263 WNGKEVDGKILYV 275
            + +   GK L +
Sbjct: 77  ESQEMNFGKKLIL 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 = 50.4 bits (121), Expect = 2e-08
 Identities = 15/72 (20%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 113 VFIKNLD-KSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           +FI NL  K++  + ++  FS +G I+   +          +GF+ F+  ++   +IE  
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXE 77

Query: 172 NGMLLNSKIVFV 183
           +  +   K + +
Sbjct: 78  SQEMNFGKKLIL 89

>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 = 58.7 bits (142), Expect = 4e-11
 Identities = 20/100 (20%), Positives = 37/100 (37%), Gaps = 10/100 (10%)

Query: 198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGT----ITSYRVMNNDGKSRGFGFVAYESP 253
              +LF    I    +    E++ E           +  Y    +  K+RGF FV YES 
Sbjct: 7   GNCRLF----IGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESH 62

Query: 254 EFAEKAVQA--WNGKEVDGKILYVGRAQKKAERTQELKRR 291
             A  A +       ++ G  + V  A+ + +  +++   
Sbjct: 63  RAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 102

>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 = 52.5 bits (126), Expect = 4e-09
 Identities = 16/94 (17%), Positives = 39/94 (41%), Gaps = 5/94 (5%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFG-SILSCKVAQD--EQGNSKGYGFVHFETEEAANKSIE 169
           +FI  + K    + + +  +     +L   V     ++  ++G+ FV +E+  AA  +  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 170 KVN--GMLLNSKIVFVGKFIPRKEREKELGEKAK 201
           K+    + L    + V    P  + ++++ E   
Sbjct: 71  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVS 104

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 17/81 (20%), Positives = 37/81 (45%), Gaps = 5/81 (6%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM---NNDGKSRGFGFVAYESPEFAEKAVQA 262
            ++ N   D  +E +KE F     I++ R+    +N  + +GFG+  +E  +    A+  
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 80

Query: 263 WNGKEVDGKILYVGRAQKKAE 283
            N + +  + + V  A +  +
Sbjct: 81  -NEESLGNRRIRVDVADQAQD 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 = 48.8 bits (117), Expect = 7e-08
 Identities = 13/81 (16%), Positives = 35/81 (43%), Gaps = 4/81 (4%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD--EQGNSKGYGFVHFETEEAANKSIEK 170
            F+ NL   +  +++ + F     I + ++ ++       KG+G+  FE  ++   ++  
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 80

Query: 171 VNGMLLNSKIVFVGKFIPRKE 191
            N   L ++ + V      ++
Sbjct: 81  -NEESLGNRRIRVDVADQAQD 100

>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 = 56.8 bits (137), Expect = 2e-10
 Identities = 12/79 (15%), Positives = 23/79 (29%), Gaps = 5/79 (6%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           V +       + + LK+     G +    V        G G V +   E    AV+  + 
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADVY-----RDGTGVVEFVRKEDMTYAVRKLDN 73

Query: 266 KEVDGKILYVGRAQKKAER 284
            +           + K + 
Sbjct: 74  TKFRSHEGETAYIRVKVDG 92

>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 = 54.1 bits (130), Expect = 1e-09
 Identities = 13/82 (15%), Positives = 25/82 (30%), Gaps = 6/82 (7%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           V +  L  S   + + D     G +    V         G G V F  +E    ++ K++
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADV------YRDGTGVVEFVRKEDMTYAVRKLD 72

Query: 173 GMLLNSKIVFVGKFIPRKEREK 194
                S          + +  +
Sbjct: 73  NTKFRSHEGETAYIRVKVDGPR 94

>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 = 55.1 bits (133), Expect = 5e-10
 Identities = 13/81 (16%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYR--VMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
            +I N         + +  E      +    +++N+G+  G   V +++ + A K+ +  
Sbjct: 18  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL- 76

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           + K+++G+  +V     +  R
Sbjct: 77  HRKKLNGREAFVHVVTLEDMR 97

>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 = 52.8 bits (127), Expect = 4e-09
 Identities = 22/94 (23%), Positives = 29/94 (30%), Gaps = 2/94 (2%)

Query: 103 PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSIL-SCKVAQDEQGNSKGYGFVHFETE 161
                S      I N+  SI    +            +  V  D  G   G   V F+ E
Sbjct: 8   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 67

Query: 162 EAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKE 195
           + A KS    +   LN +  FV        RE E
Sbjct: 68  DDARKSERL-HRKKLNGREAFVHVVTLEDMREIE 100

>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 = 54.5 bits (131), Expect = 1e-09
 Identities = 15/96 (15%), Positives = 37/96 (38%), Gaps = 3/96 (3%)

Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYR--VMNNDGKSRGF 245
           P  ++        +    VY+K    +  ++ + + F+    +          +GK+ G 
Sbjct: 10  PSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGE 69

Query: 246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK 281
           GFV + +    + A+   + + +  + + V    KK
Sbjct: 70  GFVEFRNEADYKAALCR-HKQYMGNRFIQVHPITKK 104

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 52.1 bits (125), Expect = 8e-09
 Identities = 19/90 (21%), Positives = 38/90 (42%), Gaps = 3/90 (3%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           V++K L    +NK + D F     +     +A    G + G GFV F  E     ++ + 
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR- 86

Query: 172 NGMLLNSKIVFVGKFIPRKEREKELGEKAK 201
           +   + ++ + V   I +K   +++    K
Sbjct: 87  HKQYMGNRFIQV-HPITKKGMLEKIDMIRK 115

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 55.9 bits (134), Expect = 3e-09
 Identities = 13/83 (15%), Positives = 33/83 (39%), Gaps = 4/83 (4%)

Query: 202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQ 261
           +   +  K+      + +++ +F   G I   R +    +S+  GFV ++    AE A +
Sbjct: 142 IDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV----ESKNCGFVKFKYQANAEFAKE 197

Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
           A + + +          +++   
Sbjct: 198 AMSNQTLLLPSDKEWDDRREGTG 220

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 46.3 bits (109), Expect = 5e-06
 Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 14/74 (18%)

Query: 112 NVFIKNLDKSIDNKA---------MYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEE 162
            +++  +D ++++K          +   FS  G I   +  +     SK  GFV F+ + 
Sbjct: 136 TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQA 190

Query: 163 AANKSIEKVNGMLL 176
            A  + E ++   L
Sbjct: 191 NAEFAKEAMSNQTL 204

>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 = 53.4 bits (128), Expect = 3e-09
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 11/83 (13%)

Query: 205 NVYIKNFG--EDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
           ++ + N G     +  +L  + E  G + +  +  N    + + F  Y + E +++A   
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN----KPYSFARYRTTEESKRAYVT 82

Query: 263 WNGKEVDGK-----ILYVGRAQK 280
            NGKEV         LY+   +K
Sbjct: 83  LNGKEVVDDLGQKITLYLNFVEK 105

>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 = 47.2 bits (112), Expect = 4e-07
 Identities = 10/64 (15%), Positives = 24/64 (37%), Gaps = 7/64 (10%)

Query: 112 NVFIKN--LDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
           ++ + N  L   +    +       G + +  +  +     K Y F  + T E + ++  
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYV 81

Query: 170 KVNG 173
            +NG
Sbjct: 82  TLNG 85

>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 = 53.0 bits (127), Expect = 3e-09
 Identities = 19/102 (18%), Positives = 43/102 (42%), Gaps = 7/102 (6%)

Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEK-LKEMFEPYGTITSYRVMNNDGKSRGFG 246
           P  + +++  +K +L   +++ N       +  + ++ EPYG I +Y +M    + +   
Sbjct: 10  PEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM----RMKSQA 65

Query: 247 FVAYESPEFAEKAVQ--AWNGKEVDGKILYVGRAQKKAERTQ 286
           F+  E+ E A   V           G+ + V  ++K  +   
Sbjct: 66  FIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVS 107

>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 = 51.8 bits (124), Expect = 8e-09
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQ 261
            ++V ++   ++F +E   EM E YG +    V  N      G  +V +   E AEKAV 
Sbjct: 27  VSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVI 86

Query: 262 AWNGKEVDGKILYV 275
             N +  +G+ ++ 
Sbjct: 87  DLNNRWFNGQPIHA 100

>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 = 37.9 bits (88), Expect = 6e-04
 Identities = 10/40 (25%), Positives = 18/40 (45%)

Query: 134 FGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG 173
           +G +    V  +   +  G  +V F  EE A K++  +N 
Sbjct: 51  YGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNN 90

>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 = 51.1 bits (123), Expect = 1e-08
 Identities = 13/71 (18%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           V ++    ++  K + +  +     ++ ++ ++  GN  GY FV F  EE   ++++  N
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKC-N 70

Query: 173 GMLLNSKIVFV 183
              +  + + V
Sbjct: 71  REYMGGRYIEV 81

>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 = 44.6 bits (106), Expect = 2e-06
 Identities = 16/80 (20%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           V ++    +  ++ + E   P   +    V N  G   G+ FV + + E  ++A++  N 
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKC-NR 71

Query: 266 KEVDGKILYVGRAQKKAERT 285
           + + G+ + V R  K    +
Sbjct: 72  EYMGGRYIEVFRE-KSGPSS 90

>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 = 50.1 bits (120), Expect = 2e-08
 Identities = 12/79 (15%), Positives = 30/79 (37%), Gaps = 8/79 (10%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-------GKSRGFGFVAYESPEFAEK 258
           +Y+ N      +E + + F     +        +        + + F F+ + S +   +
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 259 AVQAWNGKEVDGKILYVGR 277
           A+  ++G    G+ L + R
Sbjct: 69  AMA-FDGIIFQGQSLKIRR 86

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 43.6 bits (103), Expect = 4e-06
 Identities = 12/71 (16%), Positives = 30/71 (42%), Gaps = 7/71 (9%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCK------VAQDEQGNSKGYGFVHFETEEAANK 166
           +++ N+   I  +AM D F+A   +          V   +    K + F+ F + +   +
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 167 SIEKVNGMLLN 177
           ++   +G++  
Sbjct: 69  AMA-FDGIIFQ 78

>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 = 51.4 bits (123), Expect = 2e-08
 Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 1/87 (1%)

Query: 184 GKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSR 243
           G+ + R   + E   ++     V+++       +  +   F P   +  +  +  DG+  
Sbjct: 27  GQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVT 86

Query: 244 GFGFVAYESPEFAEKAVQAWNGKEVDG 270
           G   V + + E A  A+   +   +  
Sbjct: 87  GEADVEFATHEEAVAAMSK-DRANMQH 112

>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 = 50.6 bits (121), Expect = 4e-08
 Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 2/71 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           V ++ L        +Y+ FS     +   +     G   G   V F T E A  ++ K +
Sbjct: 49  VHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSK-D 106

Query: 173 GMLLNSKIVFV 183
              +  + + +
Sbjct: 107 RANMQHRYIEL 117

>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 = 50.1 bits (120), Expect = 4e-08
 Identities = 15/71 (21%), Positives = 32/71 (45%), Gaps = 2/71 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           V +  +  S     + D F     + +  + +D  G + G G V F + +   +++++ N
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKR-N 76

Query: 173 GMLLNSKIVFV 183
            ML+  + V V
Sbjct: 77  RMLMIQRYVEV 87

>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 = 45.1 bits (107), Expect = 2e-06
 Identities = 12/76 (15%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           V +        +  +++ F        + + ++ G++ G G V + SP+   +A++  N 
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKR-NR 77

Query: 266 KEVDGKILYVGRAQKK 281
             +  + + V  A ++
Sbjct: 78  MLMIQRYVEVSPATER 93

>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 = 53.3 bits (127), Expect = 5e-08
 Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 2/85 (2%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAV 260
           F  +++     D  + KL+  FE YG I    ++ +   GK RG+ F+ YE       A 
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161

Query: 261 QAWNGKEVDGKILYVGRAQKKAERT 285
           +  +GK++DG+ + V   + +  + 
Sbjct: 162 KHADGKKIDGRRVLVDVERGRTVKG 186

>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 = 47.2 bits (111), Expect = 4e-06
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 102 DPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFET 160
           DP+ +      +F+  ++       +   F  +G I    +      G  +GY F+ +E 
Sbjct: 94  DPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEH 153

Query: 161 EEAANKSIEKVNGMLLNSKIVFV 183
           E   + + +  +G  ++ + V V
Sbjct: 154 ERDMHSAYKHADGKKIDGRRVLV 176

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 53.3 bits (127), Expect = 6e-08
 Identities = 46/306 (15%), Positives = 90/306 (29%), Gaps = 80/306 (26%)

Query: 50  DWDSGYTCHQLGSGAILVQLGQPYM--LDTERALDTMNFDALKGRPIRIMWSQRDPSLRK 107
           D+++G   HQ     IL      ++   D +   D      L    I  +   +D     
Sbjct: 8   DFETGE--HQYQYKDILSVFEDAFVDNFDCKDVQDMPK-SILSKEEIDHIIMSKD---AV 61

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGF----VHFETEEA 163
           SG   +F   L K    + M   F     +L              Y F    +  E  + 
Sbjct: 62  SGTLRLFWTLLSK---QEEMVQKF--VEEVLR-----------INYKFLMSPIKTEQRQP 105

Query: 164 ANKS---IEKVNGMLLNSKIVFVGKFIPRKEREKELGEKA-KLFTNVYI-----KNFG-- 212
           +  +   IE+ +  L N   VF    + R +   +L +   +L     +        G  
Sbjct: 106 SMMTRMYIEQRD-RLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT 164

Query: 213 ----EDFNDEKLKEMFEPYGTITSYRV--MNNDGKSRGFGFVAYESPEFAEKAVQAWNGK 266
               +     K++   +       +++  +N              SPE   + +Q     
Sbjct: 165 WVALDVCLSYKVQCKMD-------FKIFWLN-------LK--NCNSPETVLEMLQK---- 204

Query: 267 EVDGKILYV---GRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNL---DDSIDDE 320
                 L          +++ +  +K R   ++   L R      Y   L    + + + 
Sbjct: 205 ------LLYQIDPNWTSRSDHSSNIKLRIHSIQ-AELRRLLKSKPYENCLLVLLN-VQNA 256

Query: 321 RLRKEF 326
           +    F
Sbjct: 257 KAWNAF 262

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 49.5 bits (117), Expect = 1e-06
 Identities = 58/402 (14%), Positives = 110/402 (27%), Gaps = 124/402 (30%)

Query: 1   MYTAQTVQLSEEGIIIPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCH-Q 59
           MY  Q  +L  +  +  K+NV +R    +    + ++L  L     V             
Sbjct: 111 MYIEQRDRLYNDNQVFAKYNV-SRL---QPYLKLRQALLELRPAKNV--------LIDGV 158

Query: 60  LGSG----AILVQLGQPYMLDTERALDTMNFD------ALKGRPIRIM------WSQRDP 103
           LGSG    A+ V         + +    M+F            P  ++        Q DP
Sbjct: 159 LGSGKTWVALDV-------CLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP 211

Query: 104 SL--RKSGVGNVF-----IKNLDKSIDNKAMY-------------DTFSAFGSILSCK-- 141
           +   R     N+      I+   + +     Y               ++AF   LSCK  
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN--LSCKIL 269

Query: 142 -------VAQDEQGNSKGY--------GFVHFETEE----AANKSIE-------KVNGML 175
                  V       +  +             E +       +   +         N   
Sbjct: 270 LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRR 329

Query: 176 LNSKIV-FVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFE-----PYGT 229
           L S I   +   +   +  K +       T + I++        + ++MF+     P   
Sbjct: 330 L-SIIAESIRDGLATWDNWKHVNCDK--LTTI-IESSLNVLEPAEYRKMFDRLSVFPPSA 385

Query: 230 ITSYRVMN---NDGKSRGFGFVAYESPEFAEK-----AVQAWNGKEVDGKI--LYVGRAQ 279
                +++    D           +      K      V+    KE    I  +Y+   +
Sbjct: 386 HIPTILLSLIWFDVIK-------SDVMVVVNKLHKYSLVEKQP-KESTISIPSIYL-ELK 436

Query: 280 KKAERTQELKRRFEMLKIERLNRYQGVNLYVKN--LDDSIDD 319
            K E    L R         ++ Y     +  +  +   +D 
Sbjct: 437 VKLENEYALHRSI-------VDHYNIPKTFDSDDLIPPYLDQ 471

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 48.7 bits (116), Expect = 1e-07
 Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           V ++ L      + +   FS    + +   +  D +G   G  FV F ++E A K++ K 
Sbjct: 45  VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK- 103

Query: 172 NGMLLNSKIVFV 183
           +   +  + + V
Sbjct: 104 HKERIGHRYIEV 115

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 48.7 bits (116), Expect = 2e-07
 Identities = 15/78 (19%), Positives = 36/78 (46%), Gaps = 3/78 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAW 263
           V ++        E++ + F     + +   +  + +GK  G  FV + S E AEKA+   
Sbjct: 45  VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK- 103

Query: 264 NGKEVDGKILYVGRAQKK 281
           + + +  + + V ++ ++
Sbjct: 104 HKERIGHRYIEVFKSSQE 121

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 2/71 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           V ++ L        +Y+ FS     +   +     G   G   V F T E A  ++ K +
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAK-D 75

Query: 173 GMLLNSKIVFV 183
              +  + V +
Sbjct: 76  KANMQHRYVEL 86

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 45.9 bits (109), Expect = 8e-07
 Identities = 10/56 (17%), Positives = 22/56 (39%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQ 261
           V+++       +  +   F P   +  +  +  DG+  G   V + + E A  A+ 
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA 73

>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 = 47.0 bits (112), Expect = 3e-07
 Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 4/86 (4%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDEQGNSKGYGFVH 157
           S   P     G   V ++ L      + +   FS    + +   +  D QG S G  FV 
Sbjct: 6   SGNSPDTANDGF--VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQ 63

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFV 183
           F ++E A K+++K +   +  + + +
Sbjct: 64  FASQEIAEKALKK-HKERIGHRYIEI 88

>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 = 45.1 bits (107), Expect = 2e-06
 Identities = 16/82 (19%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAW 263
           V ++      + E++ + F     + +   +  +  G+S G  FV + S E AEKA++  
Sbjct: 18  VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK- 76

Query: 264 NGKEVDGKILYVGRAQKKAERT 285
           + + +  + + + ++ +   RT
Sbjct: 77  HKERIGHRYIEIFKSSRAEVRT 98

>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 Length = 104

 Score = 46.5 bits (110), Expect = 6e-07
 Identities = 15/87 (17%), Positives = 29/87 (33%), Gaps = 1/87 (1%)

Query: 204 TNVYIKNFGED-FNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
           + +      +D F++ + +  FE               KS     + + +P  A  A   
Sbjct: 6   SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAADARLR 65

Query: 263 WNGKEVDGKILYVGRAQKKAERTQELK 289
            +  E  GK + +  AQ     +  L 
Sbjct: 66  LHKTEFLGKEMKLYFAQTLHIGSSHLA 92

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 46.2 bits (109), Expect = 1e-06
 Identities = 13/87 (14%), Positives = 32/87 (36%), Gaps = 6/87 (6%)

Query: 91  GRPIRIMWSQRDPSLRKSGVGNV---FIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ 147
              +    +  D  +  +G   V    ++NL   +    ++  FS FG++L         
Sbjct: 6   NLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-- 63

Query: 148 GNSKGYGFVHFETEEAANKSIEKVNGM 174
            N++    + +    +A  +   ++G 
Sbjct: 64  -NNQFQALLQYADPVSAQHAKLSLDGQ 89

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 45.4 bits (107), Expect = 2e-06
 Identities = 10/63 (15%), Positives = 26/63 (41%), Gaps = 2/63 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           + ++N       + L ++F  +GT+           ++    + Y  P  A+ A  + +G
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK--NNQFQALLQYADPVSAQHAKLSLDG 88

Query: 266 KEV 268
           + +
Sbjct: 89  QNI 91

>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 = 45.2 bits (107), Expect = 1e-06
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 7/81 (8%)

Query: 206 VYIKNFGEDFNDEK-LKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           V+I +F    N    L ++ EP+G I+++ ++          F+   + E A+ AV  + 
Sbjct: 18  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL----NKINEAFIEMATTEDAQAAVDYYT 73

Query: 265 GK--EVDGKILYVGRAQKKAE 283
                V GK + V  +QK   
Sbjct: 74  TTPALVFGKPVRVHLSQKYKR 94

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 44.9 bits (106), Expect = 3e-06
 Identities = 20/91 (21%), Positives = 38/91 (41%), Gaps = 7/91 (7%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYR-----VMNNDGKSRGFGFVAYESPEFAEKAV 260
           V ++        E++   F  +  IT  +     V   DG+  G  FV +   E+A+ A+
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85

Query: 261 QAWNGKEVDGKILYVGRAQKKAERTQELKRR 291
           +  +   +  + + + R+   AE  Q L R 
Sbjct: 86  RK-HKDLLGKRYIELFRS-TAAEVQQVLNRF 114

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 19/103 (18%), Positives = 32/103 (31%), Gaps = 10/103 (9%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSIL----SCKVAQDEQGNSKGYG 154
             +  S     +  V ++ L  +   + +   F     I              G   G  
Sbjct: 14  VAQFLSKENQVI--VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDA 71

Query: 155 FVHFETEEAANKSIEKVNGMLLNSKI-VFVGKFIPRKEREKEL 196
           FV F  EE A  ++ K   +L    I +F        E ++ L
Sbjct: 72  FVLFACEEYAQNALRKHKDLLGKRYIELFRST---AAEVQQVL 111

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 43.0 bits (101), Expect = 1e-05
 Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 3/71 (4%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAF---GSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
           V ++ L  S   + + +  S       +         +G   G  FV  E+E+    +++
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79

Query: 170 KVNGMLLNSKI 180
           K    + +  I
Sbjct: 80  KDRESMGHRYI 90

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 13/90 (14%), Positives = 33/90 (36%), Gaps = 6/90 (6%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYR----VMNNDGKSRGFGFVAYESPEFAEKAVQ 261
           V ++      + E ++                 +   +G+  G  FV  ES +  + A++
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKRR 291
             + + +  + + V ++  + E    LK  
Sbjct: 80  -KDRESMGHRYIEVFKS-HRTEMDWVLKHS 107

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 3/66 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           + I+N       + L  +  P G +    +     ++     V +ES   A+KA  A NG
Sbjct: 28  LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK---RNGIQAMVEFESVLCAQKAKAALNG 84

Query: 266 KEVDGK 271
            ++   
Sbjct: 85  ADIYAG 90

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 12/67 (17%), Positives = 25/67 (37%), Gaps = 4/67 (5%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           + I+N    I    +Y   +  G +    + +     +     V FE+   A K+   +N
Sbjct: 28  LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK----RNGIQAMVEFESVLCAQKAKAALN 83

Query: 173 GMLLNSK 179
           G  + + 
Sbjct: 84  GADIYAG 90

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 15/88 (17%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAF---GSILSCKVAQDEQGNSKGYGF 155
           S+ +  +    +  +  + L  S   + + + FS               +  G  +G   
Sbjct: 2   SKLEEEVDDVFL--IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDAL 59

Query: 156 VHFETEEAANKSIEKVNGMLLNSKIVFV 183
           +  E+E+   K++EK + M +  + V V
Sbjct: 60  IEMESEQDVQKALEK-HRMYMGQRYVEV 86

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 16/101 (15%), Positives = 34/101 (33%), Gaps = 6/101 (5%)

Query: 194 KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYR----VMNNDGKSRGFGFVA 249
            +L E+      +  +        E +   F              ++N DGK RG   + 
Sbjct: 2   SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIE 61

Query: 250 YESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKR 290
            ES +  +KA++  +   +  + + V       +    +K 
Sbjct: 62  MESEQDVQKALE-KHRMYMGQRYVEVYEI-NNEDVDALMKS 100

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 13/76 (17%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 112 NVFIKNLDKSIDNKAM----YDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
           +V + N+D  +  K +     + F+  G + S +++            V  E  + A  +
Sbjct: 11  DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQ--LKAVVQMENLQDAIGA 68

Query: 168 IEKVNGMLLNSKIVFV 183
           +  ++   + SK + V
Sbjct: 69  VNSLHRYKIGSKKILV 84

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 8/71 (11%), Positives = 26/71 (36%), Gaps = 5/71 (7%)

Query: 197 GEKAKLFTN-VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM----NNDGKSRGFGFVAYE 251
           G      +  V++     D +++++   F  +G +           +    +G+ F+ ++
Sbjct: 1   GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60

Query: 252 SPEFAEKAVQA 262
                +  + A
Sbjct: 61  EESSVQALIDA 71

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 41.1 bits (96), Expect = 5e-05
 Identities = 18/82 (21%), Positives = 29/82 (35%), Gaps = 3/82 (3%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ---GNSKGYGFVHFETEEAANKSIE 169
           VF+  L   ID   +  +F  FG ++     + E       KGY F+ F+ E +    I+
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 170 KVNGMLLNSKIVFVGKFIPRKE 191
                     +      I  K 
Sbjct: 71  ACLEEDGKLYLCVSSPTIKDKP 92

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 11/66 (16%), Positives = 26/66 (39%), Gaps = 3/66 (4%)

Query: 210 NFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD 269
               +  ++ L+     +G I    + +      G   V++  PE A+  +Q  +G+   
Sbjct: 34  LVLNEIRED-LRVECSKFGQIRKLLLFDRH--PDGVASVSFRDPEEADYCIQTLDGRWFG 90

Query: 270 GKILYV 275
           G+ +  
Sbjct: 91  GRQITA 96

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 3/66 (4%)

Query: 213 EDFNDEKLKEMFEPYGTITS---YRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD 269
           ++  + + KE  E YG +     + +           F+ +E  E A KAV   NG+   
Sbjct: 23  DEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFG 82

Query: 270 GKILYV 275
           G+++  
Sbjct: 83  GRVVKA 88

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 12/68 (17%), Positives = 29/68 (42%), Gaps = 5/68 (7%)

Query: 210 NFGEDFNDEKLKEMFEPYGTITSYRVM----NNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
              E+  ++ +++    YG + S  +       +    G  FV + S    +KA+Q   G
Sbjct: 23  EEYEEIVED-VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 81

Query: 266 KEVDGKIL 273
           ++   +++
Sbjct: 82  RKFANRVV 89

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 39.2 bits (91), Expect = 4e-04
 Identities = 11/71 (15%), Positives = 24/71 (33%), Gaps = 3/71 (4%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAF---GSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE 169
           V ++ L  S   + + +  S                 +G   G  FV   +E+    +++
Sbjct: 47  VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK 106

Query: 170 KVNGMLLNSKI 180
           K    + +  I
Sbjct: 107 KDRESMGHRYI 117

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 38.8 bits (90), Expect = 5e-04
 Identities = 14/107 (13%), Positives = 35/107 (32%), Gaps = 6/107 (5%)

Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYR----VMNNDGKSR 243
                   LG +      V ++      + E ++                 +   +G+  
Sbjct: 29  QMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQS 88

Query: 244 GFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKR 290
           G  FV   S +  + A++  + + +  + + V ++  + E    LK 
Sbjct: 89  GEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKS-HRTEMDWVLKH 133

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114

 Score = 37.7 bits (88), Expect = 7e-04
 Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 3/66 (4%)

Query: 210 NFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD 269
            +  +  D+ + E    +G +    V  N    +G  +V   S   A  AV A +G+   
Sbjct: 25  GWDTEIKDD-VIEECNKHGGVIHIYVDKNSA--QGNVYVKCPSIAAAIAAVNALHGRWFA 81

Query: 270 GKILYV 275
           GK++  
Sbjct: 82  GKMITA 87

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	336
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.98
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.97
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.97
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.97
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.97
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.97
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.97
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.97
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.97
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.97
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.97
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.96
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.96
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.96
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.96
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.96
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.96
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.89
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.89
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.87
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.87
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.85
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.84
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.82
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.81
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.77
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.77
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.77
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.76
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.75
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.75
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.75
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.75
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.75
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.75
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.75
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.75
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.75
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.74
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.74
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.74
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.74
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.73
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.73
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.73
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.73
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.73
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.73
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.73
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.73
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.73
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.73
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.73
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.73
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.73
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.73
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.72
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.72
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.72
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.72
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.72
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.72
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.72
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.72
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.72
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.72
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.72
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.72
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.72
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.72
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.72
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.71
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.71
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.71
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.71
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.71
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.71
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.71
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.71
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.71
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.71
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.71
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.71
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.71
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.71
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.71
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.71
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.71
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.71
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.71
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.71
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.71
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.71
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.71
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.71
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.71
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.7
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.7
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.7
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.7
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.7
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.7
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.7
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.7
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.7
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.7
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.7
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.7
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.7
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.7
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.7
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.7
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.7
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.7
2div_A	99	TRNA selenocysteine associated protein; structural	99.7
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.7
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.7
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.69
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.69
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.69
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.69
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.69
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.69
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.69
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.69
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.69
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.69
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.69
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.69
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.69
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.69
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.69
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.69
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.69
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.69
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.69
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.69
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.69
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.68
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.68
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.68
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.68
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.68
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.68
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.68
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.68
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.68
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.68
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.68
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.68
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.68
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.68
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.68
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.68
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.68
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.68
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.68
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.68
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.68
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.68
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.68
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.68
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.68
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.67
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.67
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.67
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.67
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.67
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.67
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.67
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.67
2div_A	99	TRNA selenocysteine associated protein; structural	99.67
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.67
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.67
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.67
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.67
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.67
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.67
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.67
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.67
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.67
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.67
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.67
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.67
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.67
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.67
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.66
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.66
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.66
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.66
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.66
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.66
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.66
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.66
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.66
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.66
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.66
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.66
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.66
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.66
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.66
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.66
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.66
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.66
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.65
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.65
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.65
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.65
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.65
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.65
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.65
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.65
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.65
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.65
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.65
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.65
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.65
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.65
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.65
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.65
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.65
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.65
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.65
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.65
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.64
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.64
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.64
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.64
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.64
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.64
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.64
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.64
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.64
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.64
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.64
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.64
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.64
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.64
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.64
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.64
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.64
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.64
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.64
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.63
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.63
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.63
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.63
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.63
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.63
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.63
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.63
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.63
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.63
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.63
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.63
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.63
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.63
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.63
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.63
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.63
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.63
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.63
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.63
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.63
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.62
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.62
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.62
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.62
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.62
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.62
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.62
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.62
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.62
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.62
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.61
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.61
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.6
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.6
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.6
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.6
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.6
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.6
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.6
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.6
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.6
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.59
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.59
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.59
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.59
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.59
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.59
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.59
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.59
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.59
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.59
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.59
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.58
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.58
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.58
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.58
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.58
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.36
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.58
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.58
1x5p_A	97	Negative elongation factor E; structure genomics,	99.58
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.57
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.57
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.57
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.35
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.57
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.57
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.57
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.57
1x5p_A	97	Negative elongation factor E; structure genomics,	99.56
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.56
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.56
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.56
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.56
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.56
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.56
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.55
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.55
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.54
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.54
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.54
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.54
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.54
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.53
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.52
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.52
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.52
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.5
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.49
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.49
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.49
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.49
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.48
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.47
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.46
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.44
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.42
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.42
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.42
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.41
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.4
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.34
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.33
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.27
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.24
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.23
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.21
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.19
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.05
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.04
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.92
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.87
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.81
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.8
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.71
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.67
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.63
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.48
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.35
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.09
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.01
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.76
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.7
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.46
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.46
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.45
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.19
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.98
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.91
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.84
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.75
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.37
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.29
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.67
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.52
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.14
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	86.07
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	81.94

>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=100.00  E-value=1.1e-46  Score=330.60  Aligned_cols=253  Identities=20%  Similarity=0.273  Sum_probs=226.3

Q ss_pred             cccCceeeeecCchhhhhhhHHhhhcccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeee
Q psy12549         15 IIPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPI   94 (336)
Q Consensus        15 ~~p~~~v~v~~lp~~~~e~~l~~~f~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i   94 (336)
                      ..++++|||+|||+++|+++|+++|+..++.++.+         +.++|||||+|.++  ++|++|++.+++..+.|++|
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~Gi~~~~~---------~~~~g~afV~f~~~--~~A~~A~~~l~~~~~~g~~i   87 (284)
T 3smz_A           19 FRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFV---------DKYKGTAFVTLLNG--EQAEAAINAFHQSRLREREL   87 (284)
T ss_dssp             HHCCCEEEEECCCTTCCHHHHHHHTTTSCEEEEEE---------ETTTTEEEEEESSH--HHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCEEEEE---------ecCCCEEEEEeCCH--HHHHHHHHHcCCCeeCCeEE
Confidence            45788999999999999999999995555777766         34678999999999  99999999999999999999


Q ss_pred             EEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCC
Q psy12549         95 RIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNG  173 (336)
Q Consensus        95 ~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~  173 (336)
                      .|.++..        .++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|+..|+|
T Consensus        88 ~v~~~~~--------~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~  159 (284)
T 3smz_A           88 SVQLQPT--------DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLG  159 (284)
T ss_dssp             EEEECCC--------SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             EEEecCC--------CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCC
Confidence            9999643        3689999999999999999999999999999999987 889999999999999999999999999


Q ss_pred             ceeCCeEEEEeeccCchhhhHhhhccccccceEEEcCCCCCC-cHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeC
Q psy12549        174 MLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDF-NDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYE  251 (336)
Q Consensus       174 ~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~-t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~  251 (336)
                      ..+.|+.|.|.++.+....     ......++|||+|||..+ ++++|+++|+.||.|..+.+.. .+|.++|+|||+|.
T Consensus       160 ~~~~g~~i~v~~a~~~~~~-----~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~  234 (284)
T 3smz_A          160 KPLGPRTLYVHWTDAGQLT-----PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYE  234 (284)
T ss_dssp             CEETTEECEEEECCGGGCC-----TTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECS
T ss_pred             CEeCCcEEEEEECCCCCCC-----cccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeC
Confidence            9999999999998765432     122345789999999995 9999999999999999999887 77889999999999


Q ss_pred             CHHHHHHHHHHhCCceecCEEEEEeecccchhhHHHHHHH
Q psy12549        252 SPEFAEKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRR  291 (336)
Q Consensus       252 ~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~  291 (336)
                      +.++|.+|+..|||..++|+.|.|.|+.++..........
T Consensus       235 ~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~  274 (284)
T 3smz_A          235 TAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAAL  274 (284)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEECCSSSCHHHHHHHH
T ss_pred             CHHHHHHHHHHhCCCccCCeEEEEEEecCCCcccchhhhh
Confidence            9999999999999999999999999999887765554443

>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=100.00  E-value=1.7e-46  Score=330.71  Aligned_cols=249  Identities=14%  Similarity=0.181  Sum_probs=212.8

Q ss_pred             ccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCe
Q psy12549         14 IIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGR   92 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~   92 (336)
                      ...+.++|||+|||+++|+++|+++| .+|.+.++++.++.+     .++|||||+|.++  ++|++|++ +++..+.|+
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~~~g~afV~f~~~--~~A~~A~~-~~~~~~~g~  108 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-----KNFRFARIEFARY--DGALAAIT-KTHKVVGQN  108 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT-----SSSEEEEEEESSH--HHHHHHHT-TTTCEETTE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC-----CCcEEEEEEECCH--HHHHHHHH-hCCcEeCCc
Confidence            45678999999999999999999999 777888999998773     3689999999999  99999996 999999999


Q ss_pred             eeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccC-CeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHh
Q psy12549         93 PIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFG-SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV  171 (336)
Q Consensus        93 ~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G-~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l  171 (336)
                      +|.|.++.         .++|||+|||..+++++|+++|+.|| .|..+.++.++.|.++|||||+|.+.++|.+|+..|
T Consensus       109 ~i~v~~~~---------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l  179 (292)
T 2ghp_A          109 EIIVSHLT---------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL  179 (292)
T ss_dssp             ECEEEECC---------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHH
T ss_pred             EEEEEECC---------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHh
Confidence            99999863         47899999999999999999999999 999999999888889999999999999999999999


Q ss_pred             CCceeCCeEEEEeeccCchhhhHhhhccccccceEEEcCCCCC-CcHHHHHHhhccCCceeEEEEeC-CC--CccceEEE
Q psy12549        172 NGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGED-FNDEKLKEMFEPYGTITSYRVMN-ND--GKSRGFGF  247 (336)
Q Consensus       172 ~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~-~t~~~l~~~f~~~g~i~~~~i~~-~~--~~~~g~af  247 (336)
                      +|..+.|+.|.|.++.+....... .......++|||+|||.. +++++|+++|+.||.|..+.++. ..  |.++|+||
T Consensus       180 ~g~~~~g~~l~v~~a~~~~~~~~~-~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~af  258 (292)
T 2ghp_A          180 NGLKIEGYTLVTKVSNPLEKSKRT-DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAF  258 (292)
T ss_dssp             TTCEETTEECEEEECCCC----------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEE
T ss_pred             CCCEeCCcEEEEEECCCCcccccc-cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEE
Confidence            999999999999998876543322 123334588999999999 99999999999999999999988 33  88999999


Q ss_pred             EEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        248 VAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       248 V~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      |+|.+.++|.+|+ .|||..++|+.|.|.|+.++
T Consensus       259 V~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          259 MVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             EEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             EEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            9999999999999 99999999999999999876

>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=100.00  E-value=1e-36  Score=267.19  Aligned_cols=192  Identities=20%  Similarity=0.329  Sum_probs=173.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      .++|||+|||.++|+++|+++|+.|| |..+.+     +.++|||||+|.+.++|.+|+..|++..+.|+.|.+.+..+ 
T Consensus        22 ~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~-----~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~~-   94 (284)
T 3smz_A           22 RRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT-   94 (284)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC-
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE-----ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecCC-
Confidence            47899999999999999999999999 998888     34688999999999999999999999999999999987542 


Q ss_pred             hhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCce
Q psy12549        190 KEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKE  267 (336)
Q Consensus       190 ~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~  267 (336)
                                   .++|||+|||..+++++|+++|+.||.|..+.++.  .+|.++|+|||+|.+.++|.+|+..++|..
T Consensus        95 -------------~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~  161 (284)
T 3smz_A           95 -------------DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKP  161 (284)
T ss_dssp             -------------SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             -------------CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCE
Confidence                         27899999999999999999999999999998876  578899999999999999999999999999


Q ss_pred             ecCEEEEEeecccchhhHHHHHHHHHHHHHHhhcCCCCceEEEecCCCCC-CHHHHHHhcCCCCCeeecC
Q psy12549        268 VDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSI-DDERLRKEFTPFGTITSAK  336 (336)
Q Consensus       268 ~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~-t~~~l~~~F~~~G~V~~vk  336 (336)
                      +.|+.|.|.++.++...               ....++++|+|+|||..+ ++++|+++|++||.|.+|+
T Consensus       162 ~~g~~i~v~~a~~~~~~---------------~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~  216 (284)
T 3smz_A          162 LGPRTLYVHWTDAGQLT---------------PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQ  216 (284)
T ss_dssp             ETTEECEEEECCGGGCC---------------TTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEE
T ss_pred             eCCcEEEEEECCCCCCC---------------cccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEE
Confidence            99999999999875322               123466899999999995 9999999999999998764

>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=100.00  E-value=4.4e-37  Score=270.61  Aligned_cols=201  Identities=20%  Similarity=0.380  Sum_probs=172.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||.++|+++|+++|+.||.|..|.++.++.+ ++|||||+|.+.++|.+|++ +++..+.|+.|.+.++.
T Consensus        39 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~~~  116 (292)
T 2ghp_A           39 RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK-NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHLT  116 (292)
T ss_dssp             ---CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS-SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC-CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEECC
Confidence            44689999999999999999999999999999999998765 58999999999999999996 99999999999998752


Q ss_pred             CchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCC-ceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCC
Q psy12549        188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYG-TITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNG  265 (336)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g-~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g  265 (336)
                                     .++|||+|||..+++++|+++|+.|| .|..+.++. ..|.++|+|||+|.+.++|.+|+..|+|
T Consensus       117 ---------------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g  181 (292)
T 2ghp_A          117 ---------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNG  181 (292)
T ss_dssp             ---------------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTT
T ss_pred             ---------------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCC
Confidence                           37899999999999999999999999 999999987 5577899999999999999999999999


Q ss_pred             ceecCEEEEEeecccchhhHHHHHHHHHHHHHHhhcCCCCceEEEecCCCC-CCHHHHHHhcCCCCCeeecC
Q psy12549        266 KEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDS-IDDERLRKEFTPFGTITSAK  336 (336)
Q Consensus       266 ~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~-~t~~~l~~~F~~~G~V~~vk  336 (336)
                      ..+.|+.|.|.++.+.......           .....++++|+|+|||.. +++++|+++|++||.|.+|+
T Consensus       182 ~~~~g~~l~v~~a~~~~~~~~~-----------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~  242 (292)
T 2ghp_A          182 LKIEGYTLVTKVSNPLEKSKRT-----------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKIN  242 (292)
T ss_dssp             CEETTEECEEEECCCC--------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEE
T ss_pred             CEeCCcEEEEEECCCCcccccc-----------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEE
Confidence            9999999999999876433221           123456789999999999 99999999999999999874

>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=5e-35  Score=245.39  Aligned_cols=171  Identities=27%  Similarity=0.534  Sum_probs=155.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+|||.++|+++|+++|++||.|.+|++++++ +|.++|||||+|.+.++|.+|++.+++..+.|+.+.+.++.
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            35789999999999999999999999999999999987 78999999999999999999999999999999999999887


Q ss_pred             CchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCce
Q psy12549        188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKE  267 (336)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~  267 (336)
                      ........      ...+|||+|||..+++++|+++|+.||.|..++++...+.++|||||+|.+.++|.+|++.|||..
T Consensus        94 ~~~~~~~~------~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~~lng~~  167 (213)
T 4f02_A           94 RDPSLRKS------GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGML  167 (213)
T ss_dssp             CCTHHHHH------CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             cccccccc------ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHHHhCCCE
Confidence            66543322      236799999999999999999999999999999988667789999999999999999999999999


Q ss_pred             ecCEEEEEeecccchhhH
Q psy12549        268 VDGKILYVGRAQKKAERT  285 (336)
Q Consensus       268 ~~g~~l~v~~~~~~~~~~  285 (336)
                      ++|+.|.|.++.++.+..
T Consensus       168 ~~g~~i~V~~a~~~~~~~  185 (213)
T 4f02_A          168 LNDRKVFVGRFKSRKERE  185 (213)
T ss_dssp             ETTEECEEEECCCHHHHH
T ss_pred             ECCEEEEEEEcCCCcccc
Confidence            999999999998875443

>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=3e-35  Score=246.76  Aligned_cols=180  Identities=58%  Similarity=0.877  Sum_probs=158.2

Q ss_pred             CCCCccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccc
Q psy12549         10 SEEGIIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDA   88 (336)
Q Consensus        10 ~~~~~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~   88 (336)
                      +|..-..|.++|||+|||+++||++|+++| .+|.+.++++++++   .+|+++|||||+|.+.  ++|++|++.+++..
T Consensus         7 ~p~~p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~---~tg~~~G~afV~F~~~--~~A~~Ai~~~~~~~   81 (213)
T 4f02_A            7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDM---ITRRSLGYAYVNFQQP--ADAERALDTMNFDV   81 (213)
T ss_dssp             --------CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSH--HHHHHHHHHHTTCE
T ss_pred             CCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeccc---CCCCccccccceeCCH--HHHHHHHHHhhhhh
Confidence            344445788999999999999999999999 77788999999987   4789999999999999  99999999999999


Q ss_pred             cCCeeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHH
Q psy12549         89 LKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSI  168 (336)
Q Consensus        89 ~~g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~  168 (336)
                      +.|+.+++.++............+|||+|||.++++++|+++|+.||.|..+.++.++.+ ++|||||+|.+.++|.+|+
T Consensus        82 ~~g~~i~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~-~~g~~fV~f~~~~~a~~Ai  160 (213)
T 4f02_A           82 IKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAI  160 (213)
T ss_dssp             ETTEECEEEECCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTE-EEEEEEEEESSHHHHHHHH
T ss_pred             cCCcccccccccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCC-CceEEEEEeCCHHHHHHHH
Confidence            999999999987766655556689999999999999999999999999999999998643 7999999999999999999


Q ss_pred             HHhCCceeCCeEEEEeeccCchhhhHh
Q psy12549        169 EKVNGMLLNSKIVFVGKFIPRKEREKE  195 (336)
Q Consensus       169 ~~l~~~~~~~~~i~v~~~~~~~~~~~~  195 (336)
                      +.|||..+.|+.|.|.++.++..+...
T Consensus       161 ~~lng~~~~g~~i~V~~a~~~~~~~~~  187 (213)
T 4f02_A          161 EKMNGMLLNDRKVFVGRFKSRKEREAE  187 (213)
T ss_dssp             HHHTTCEETTEECEEEECCCHHHHHHH
T ss_pred             HHhCCCEECCEEEEEEEcCCCcccchh
Confidence            999999999999999999887665443

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=7.3e-34  Score=228.86  Aligned_cols=164  Identities=26%  Similarity=0.484  Sum_probs=150.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCch
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRK  190 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~  190 (336)
                      ++|||+|||.++++++|+++|+.||.|.++.++.++.+.++|||||+|.+.++|.+|+..+++..+.|+.+.+.++.+..
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            57999999999999999999999999999999999988899999999999999999999999999999999999987654


Q ss_pred             hhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCcee
Q psy12549        191 EREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEV  268 (336)
Q Consensus       191 ~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~  268 (336)
                      .      ......++|+|+|||..+++++|+++|+.||.|..+.+..  .+|.++|+|||+|.+.++|.+|+..|||..+
T Consensus        81 ~------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  154 (166)
T 3md3_A           81 Q------SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL  154 (166)
T ss_dssp             C------CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             C------CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Confidence            3      2233447899999999999999999999999999999986  6788999999999999999999999999999


Q ss_pred             cCEEEEEeeccc
Q psy12549        269 DGKILYVGRAQK  280 (336)
Q Consensus       269 ~g~~l~v~~~~~  280 (336)
                      +|+.|+|.|+.+
T Consensus       155 ~g~~i~v~~a~~  166 (166)
T 3md3_A          155 NGRPLRINWAAK  166 (166)
T ss_dssp             TTEECEEEESCC
T ss_pred             CCcEEEEEecCC
Confidence            999999999863

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=3.5e-33  Score=224.85  Aligned_cols=163  Identities=22%  Similarity=0.347  Sum_probs=152.6

Q ss_pred             ceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEE
Q psy12549         19 HNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRIM   97 (336)
Q Consensus        19 ~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~   97 (336)
                      |+|||+|||+++++++|+++| .+|.+.++++.+++.    |.++|||||+|.+.  ++|++|+..+++..+.|+++.|.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~----~~~~g~afV~f~~~--~~a~~A~~~l~~~~~~g~~i~v~   74 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN----NKNVNYAFVEYHQS--HDANIALQTLNGKQIENNIVKIN   74 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-----CCEEEEEEEESSH--HHHHHHHHHHTTCEETTEECEEE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC----CCCCCEEEEEeCCH--HHHHHHHHHcCCCccCCCeeEEE
Confidence            689999999999999999999 777888999998873    77999999999999  99999999999999999999999


Q ss_pred             eccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcee
Q psy12549         98 WSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLL  176 (336)
Q Consensus        98 ~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~  176 (336)
                      ++...........++|||+|||..+++++|+++|+.||.|..+.+..++ +|.++|+|||+|.+.++|.+|+..|||..+
T Consensus        75 ~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  154 (166)
T 3md3_A           75 WAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL  154 (166)
T ss_dssp             ECCCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             EcCCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Confidence            9988777777778899999999999999999999999999999999985 788999999999999999999999999999


Q ss_pred             CCeEEEEeecc
Q psy12549        177 NSKIVFVGKFI  187 (336)
Q Consensus       177 ~~~~i~v~~~~  187 (336)
                      .|+.|.|.++.
T Consensus       155 ~g~~i~v~~a~  165 (166)
T 3md3_A          155 NGRPLRINWAA  165 (166)
T ss_dssp             TTEECEEEESC
T ss_pred             CCcEEEEEecC
Confidence            99999999875

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=100.00  E-value=7.5e-33  Score=229.22  Aligned_cols=175  Identities=23%  Similarity=0.486  Sum_probs=147.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++|+++|+++|+.||.|.++.++.++ +|.++|||||+|.+.++|.+|++. ++..+.|+.|.+.++
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            456899999999999999999999999999999999997 688999999999999999999985 999999999999998


Q ss_pred             cCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhC
Q psy12549        187 IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWN  264 (336)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~  264 (336)
                      .+.......  ......++|||+|||..+++++|+++|+.||.|..+.+..  .+|.++|+|||+|.+.++|.+|+.. +
T Consensus        90 ~~~~~~~~~--~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~  166 (196)
T 1l3k_A           90 VSREDSQRP--GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-K  166 (196)
T ss_dssp             CC-------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-S
T ss_pred             cCccccccc--ccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-C
Confidence            766443221  1223347899999999999999999999999999999987  4788999999999999999999986 8


Q ss_pred             CceecCEEEEEeecccchhhHH
Q psy12549        265 GKEVDGKILYVGRAQKKAERTQ  286 (336)
Q Consensus       265 g~~~~g~~l~v~~~~~~~~~~~  286 (336)
                      |..++|+.|.|.++.++.+...
T Consensus       167 ~~~~~G~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          167 YHTVNGHNCEVRKALSKQEMAS  188 (196)
T ss_dssp             CCEETTEECEEEECC-------
T ss_pred             CcEECCEEEEEEecCChhHhcc
Confidence            9999999999999998865543

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=100.00  E-value=3.6e-33  Score=225.32  Aligned_cols=161  Identities=30%  Similarity=0.540  Sum_probs=149.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||.++++++|+++|+.||.|.++.++.++ +|.++|||||+|.+.++|.+|++.+++..+.|+.|.+.++.+
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            5789999999999999999999999999999999986 788999999999999999999999999999999999999876


Q ss_pred             chhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCc
Q psy12549        189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGK  266 (336)
Q Consensus       189 ~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~  266 (336)
                      ....        ...++|+|+|||..+++++|+++|++||.|..+.+..  .++.++|+|||+|.+.++|.+|+..|||.
T Consensus        83 ~~~~--------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~  154 (168)
T 1b7f_A           83 GGES--------IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNV  154 (168)
T ss_dssp             CSST--------TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             Cccc--------CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCC
Confidence            5432        2347899999999999999999999999999999887  47888999999999999999999999999


Q ss_pred             eecC--EEEEEeec
Q psy12549        267 EVDG--KILYVGRA  278 (336)
Q Consensus       267 ~~~g--~~l~v~~~  278 (336)
                      .+.|  ++|+|.||
T Consensus       155 ~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          155 IPEGGSQPLSVRLA  168 (168)
T ss_dssp             CCTTCSSCCEEEEC
T ss_pred             EecCCCeEEEEEeC
Confidence            9988  99999886

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=100.00  E-value=8.5e-33  Score=222.81  Aligned_cols=161  Identities=29%  Similarity=0.549  Sum_probs=148.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||+++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|++.|++..+.|+.|.+.++.+
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            4789999999999999999999999999999999998 899999999999999999999999999999999999999876


Q ss_pred             chhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCc
Q psy12549        189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGK  266 (336)
Q Consensus       189 ~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~  266 (336)
                      ....        ...++|+|+|||..+++++|+++|+.||.|..+.+..  .+|.++|+|||+|.+.++|.+|++.|||.
T Consensus        82 ~~~~--------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~  153 (167)
T 1fxl_A           82 SSAS--------IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ  153 (167)
T ss_dssp             CCGG--------GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             Cccc--------CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCC
Confidence            5432        2237899999999999999999999999999999887  47888999999999999999999999999


Q ss_pred             eecCEE--EEEeec
Q psy12549        267 EVDGKI--LYVGRA  278 (336)
Q Consensus       267 ~~~g~~--l~v~~~  278 (336)
                      .+.|+.  |+|.||
T Consensus       154 ~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          154 KPSGATEPITVKFA  167 (167)
T ss_dssp             CCTTCSSCCEEEEC
T ss_pred             ccCCCccceEEEeC
Confidence            999965  888875

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=100.00  E-value=1.7e-32  Score=230.56  Aligned_cols=173  Identities=28%  Similarity=0.552  Sum_probs=153.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||.++|+++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|++.|++..+.|+.|.|.++..
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            4689999999999999999999999999999999987 788999999999999999999999999999999999998876


Q ss_pred             chhhhHh---hhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHh
Q psy12549        189 RKEREKE---LGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW  263 (336)
Q Consensus       189 ~~~~~~~---~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l  263 (336)
                      .......   ........++|||+|||.++++++|+++|+.||.|..+.+..  .+|.++|+|||+|.+.++|.+|+..|
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l  187 (216)
T 2qfj_A          108 IGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM  187 (216)
T ss_dssp             CGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHH
T ss_pred             ccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHc
Confidence            6543221   112234458999999999999999999999999999999987  57889999999999999999999999


Q ss_pred             CCceecCEEEEEeecccch
Q psy12549        264 NGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       264 ~g~~~~g~~l~v~~~~~~~  282 (336)
                      ||..++|+.|+|.++.++.
T Consensus       188 ~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          188 NLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             TTCBCSSSBCEEEECSSCS
T ss_pred             cCCEeCCcEEEEEEecCCC
Confidence            9999999999999998764

>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=100.00  E-value=7.3e-33  Score=223.36  Aligned_cols=161  Identities=25%  Similarity=0.561  Sum_probs=148.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||.++|+++|+++|+.||.|.++.++.++ +|.++|||||+|.+.++|.+|+..  +..+.|+.+.+.++.+
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            5789999999999999999999999999999999986 789999999999999999999994  6789999999998876


Q ss_pred             chhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCc
Q psy12549        189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGK  266 (336)
Q Consensus       189 ~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~  266 (336)
                      .....        ..++|||+|||.++++++|+++|+.||.|..+.+..  .+|.++|+|||+|.+.++|.+|++ ++|.
T Consensus        81 ~~~~~--------~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~  151 (167)
T 2cjk_A           81 RDEQD--------KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFI  151 (167)
T ss_dssp             HHHHH--------HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEE
T ss_pred             hhhcc--------CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCE
Confidence            54432        236899999999999999999999999999999987  468899999999999999999998 8999


Q ss_pred             eecCEEEEEeecccc
Q psy12549        267 EVDGKILYVGRAQKK  281 (336)
Q Consensus       267 ~~~g~~l~v~~~~~~  281 (336)
                      .++|+.|.|.++.++
T Consensus       152 ~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          152 DFKDRKIEIKRAEPR  166 (167)
T ss_dssp             CSSSSCEEEEECCCC
T ss_pred             EeCCeEEEEeecCCC
Confidence            999999999999876

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=100.00  E-value=2.6e-32  Score=220.29  Aligned_cols=163  Identities=18%  Similarity=0.331  Sum_probs=149.8

Q ss_pred             cCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeE
Q psy12549         17 PKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIR   95 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~   95 (336)
                      |+++|+|+|||+++++++|+++| .+|.+.++++.+++   .+|.++|||||+|.++  ++|++|++.+++..+.|++|.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~--~~A~~a~~~l~~~~~~g~~l~   76 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY---KTGYSYGYAFVDFTSE--MDSQRAIKVLNGITVRNKRLK   76 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEET---TTTEECSEEEEEESSH--HHHHHHHHHHTTCEETTEECE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeC---CCCccceEEEEEECCH--HHHHHHHHhcCCCEeCCcEEE
Confidence            68899999999999999999999 66788899998876   3688999999999999  999999999999999999999


Q ss_pred             EEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCc
Q psy12549         96 IMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGM  174 (336)
Q Consensus        96 v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~  174 (336)
                      |.|+.+...  ....++|+|+|||..+++++|+++|++||.|..+.+++++ +|.++|+|||+|.+.++|.+|+..|||.
T Consensus        77 v~~~~~~~~--~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~  154 (168)
T 1b7f_A           77 VSYARPGGE--SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNV  154 (168)
T ss_dssp             EEECCCCSS--TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEecCCCcc--cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCC
Confidence            999876543  3456899999999999999999999999999999999997 8889999999999999999999999999


Q ss_pred             eeCC--eEEEEeec
Q psy12549        175 LLNS--KIVFVGKF  186 (336)
Q Consensus       175 ~~~~--~~i~v~~~  186 (336)
                      .+.|  ++|.|.++
T Consensus       155 ~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          155 IPEGGSQPLSVRLA  168 (168)
T ss_dssp             CCTTCSSCCEEEEC
T ss_pred             EecCCCeEEEEEeC
Confidence            9977  99998764

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=100.00  E-value=4.3e-32  Score=218.67  Aligned_cols=163  Identities=24%  Similarity=0.371  Sum_probs=148.5

Q ss_pred             cCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeE
Q psy12549         17 PKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIR   95 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~   95 (336)
                      |+++|||+|||+++++++|+++| .+|.+.++++.+++   .+|.++|||||+|.++  ++|++|++.+++..+.|++|.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~---~~~~~~g~afV~f~~~--~~A~~a~~~l~~~~~~g~~l~   75 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK---ITGQSLGYGFVNYIDP--KDAEKAINTLNGLRLQTKTIK   75 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT---TTCCEEEEEEEEESSH--HHHHHHHHHHTTCEETTEECE
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC---CCCcceeEEEEEECCH--HHHHHHHHHcCCCccCCceEE
Confidence            57899999999999999999999 77788899999877   4689999999999999  999999999999999999999


Q ss_pred             EEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCc
Q psy12549         96 IMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGM  174 (336)
Q Consensus        96 v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~  174 (336)
                      |.++.+...  ....++|||+|||.++++++|+++|+.||.|..+.+..++ +|.++|+|||+|.+.++|.+|++.|||.
T Consensus        76 v~~~~~~~~--~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~  153 (167)
T 1fxl_A           76 VSYARPSSA--SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ  153 (167)
T ss_dssp             EEECCCCCG--GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             EEecCCCcc--cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCC
Confidence            999876543  3345789999999999999999999999999999999987 7889999999999999999999999999


Q ss_pred             eeCCeE--EEEeec
Q psy12549        175 LLNSKI--VFVGKF  186 (336)
Q Consensus       175 ~~~~~~--i~v~~~  186 (336)
                      .+.|+.  |.|.|+
T Consensus       154 ~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          154 KPSGATEPITVKFA  167 (167)
T ss_dssp             CCTTCSSCCEEEEC
T ss_pred             ccCCCccceEEEeC
Confidence            999965  777664

>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=100.00  E-value=5e-32  Score=220.03  Aligned_cols=164  Identities=22%  Similarity=0.378  Sum_probs=145.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCC---CcccEEEEEeCCHHHHHHHHHHhCCceeC---CeEEE
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQG---NSKGYGFVHFETEEAANKSIEKVNGMLLN---SKIVF  182 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~---~~~g~afV~F~~~~~a~~a~~~l~~~~~~---~~~i~  182 (336)
                      +.++|||+|||.++|+++|+++|++||.|.++.+++++.+   .++|||||+|.+.++|.+|++.|++..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            4578999999999999999999999999999999999844   79999999999999999999999998765   67777


Q ss_pred             EeeccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHH
Q psy12549        183 VGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQ  261 (336)
Q Consensus       183 v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~  261 (336)
                      +.++.+...       .....++|||+|||..+++++|+++|+.||.|.++.+.. .+|.++|+|||+|.+.++|.+|++
T Consensus        82 ~~~~~~~~~-------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~  154 (175)
T 3nmr_A           82 MKPADSEKN-------NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK  154 (175)
T ss_dssp             EEECGGGCC-------SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHH
T ss_pred             Ecccccccc-------ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHH
Confidence            776554332       122347899999999999999999999999999999987 678889999999999999999999


Q ss_pred             HhCCceec---CEEEEEeecc
Q psy12549        262 AWNGKEVD---GKILYVGRAQ  279 (336)
Q Consensus       262 ~l~g~~~~---g~~l~v~~~~  279 (336)
                      .|||..+.   |++|+|.||.
T Consensus       155 ~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          155 AMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HHTTSCCCTTCSSCCEEEECC
T ss_pred             HhcCCcccCCCCCCeEEEecC
Confidence            99998876   4999999873

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=100.00  E-value=1e-31  Score=222.42  Aligned_cols=173  Identities=16%  Similarity=0.212  Sum_probs=148.5

Q ss_pred             ccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCe
Q psy12549         14 IIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGR   92 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~   92 (336)
                      ...+.++|||+|||+++|+++|+++| .+|.+.++++++++   .+|.++|||||+|.+.  ++|++|++. ++..+.|+
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~--~~A~~A~~~-~~~~~~g~   82 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP---NTKRSRGFGFVTYATV--EEVDAAMNA-RPHKVDGR   82 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSH--HHHHHHHHT-CSCEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcC---CCCCccceEEEEeCCH--HHHHHHHhc-CCCEECCE
Confidence            44678899999999999999999999 77788899999887   3688999999999999  999999985 89999999


Q ss_pred             eeEEEeccCCCCcC----CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHH
Q psy12549         93 PIRIMWSQRDPSLR----KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKS  167 (336)
Q Consensus        93 ~i~v~~~~~~~~~~----~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a  167 (336)
                      .|.|.++.......    ....++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|
T Consensus        83 ~l~v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A  162 (196)
T 1l3k_A           83 VVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI  162 (196)
T ss_dssp             ECEEEECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH
T ss_pred             EeeeecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHH
Confidence            99999976643322    2234799999999999999999999999999999999997 788999999999999999999


Q ss_pred             HHHhCCceeCCeEEEEeeccCchhhh
Q psy12549        168 IEKVNGMLLNSKIVFVGKFIPRKERE  193 (336)
Q Consensus       168 ~~~l~~~~~~~~~i~v~~~~~~~~~~  193 (336)
                      +.. ++..+.|+.|.|.++.++....
T Consensus       163 ~~~-~~~~~~G~~i~v~~a~~k~~~~  187 (196)
T 1l3k_A          163 VIQ-KYHTVNGHNCEVRKALSKQEMA  187 (196)
T ss_dssp             HHC-SCCEETTEECEEEECC------
T ss_pred             HHh-CCcEECCEEEEEEecCChhHhc
Confidence            996 8999999999999998876543

>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=99.98  E-value=3e-32  Score=221.48  Aligned_cols=165  Identities=25%  Similarity=0.382  Sum_probs=145.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ....++|||+|||.++++++|+++|+.||.+..+.+....+|.++|||||+|.+.++|.+|++ |++..+.|+.|.|.++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecC
Confidence            345689999999999999999999999998766333333467889999999999999999995 9999999999999998


Q ss_pred             cCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCc
Q psy12549        187 IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGK  266 (336)
Q Consensus       187 ~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~  266 (336)
                      .+....      .....++|||+|||..+++++|+++|+.||.|..+   ..++.++|+|||+|.+.++|.+|+..|||.
T Consensus        89 ~~~~~~------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~---~~~~~~~g~afV~f~~~~~A~~A~~~l~g~  159 (175)
T 1fje_B           89 KGRDSK------KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV---SQDGKSKGIAYIEFKSEADAEKNLEEKQGA  159 (175)
T ss_dssp             CCSSCS------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE---CSSSSCCSEEEEECSSHHHHHHHHHHHTEE
T ss_pred             CCcccc------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe---cCCCCCceEEEEEECCHHHHHHHHHHhCCC
Confidence            765432      22344789999999999999999999999998777   677888999999999999999999999999


Q ss_pred             eecCEEEEEeecccc
Q psy12549        267 EVDGKILYVGRAQKK  281 (336)
Q Consensus       267 ~~~g~~l~v~~~~~~  281 (336)
                      .++|+.|+|.|+.++
T Consensus       160 ~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          160 EIDGRSVSLYYTGEK  174 (175)
T ss_dssp             EETTEEEEEEECSSC
T ss_pred             EECCeEEEEEecCCC
Confidence            999999999999876

>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=1.2e-31  Score=225.38  Aligned_cols=173  Identities=21%  Similarity=0.359  Sum_probs=153.0

Q ss_pred             ccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCe
Q psy12549         14 IIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGR   92 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~   92 (336)
                      ...+.++|||+|||.++++++|+++| .+|.+.++++++++   .+|.++|||||+|.+.  ++|.+|++.+++..+.|+
T Consensus        24 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~--~~A~~A~~~l~~~~~~g~   98 (216)
T 2qfj_A           24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDS---VTMKHKGFAFVEYEVP--EAAQLALEQMNSVMLGGR   98 (216)
T ss_dssp             HHHHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC----CC-CCCSEEEEEESSH--HHHHHHHHHHSSCCCC-C
T ss_pred             ccCcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecC---CCCccCceEEEEeCCH--HHHHHHHHHccCCeeCCe
Confidence            34567899999999999999999999 77788899999887   3688999999999999  999999999999999999


Q ss_pred             eeEEEeccCCCCc---------CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHH
Q psy12549         93 PIRIMWSQRDPSL---------RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEE  162 (336)
Q Consensus        93 ~i~v~~~~~~~~~---------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~  162 (336)
                      .|.|.++......         .....++|||+|||.++++++|+++|+.||.|..+.+..++ +|.++|||||+|.+.+
T Consensus        99 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~  178 (216)
T 2qfj_A           99 NIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQ  178 (216)
T ss_dssp             CCEEECCSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHH
T ss_pred             eEEEecCCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHH
Confidence            9999887654321         12345799999999999999999999999999999999996 7889999999999999


Q ss_pred             HHHHHHHHhCCceeCCeEEEEeeccCchh
Q psy12549        163 AANKSIEKVNGMLLNSKIVFVGKFIPRKE  191 (336)
Q Consensus       163 ~a~~a~~~l~~~~~~~~~i~v~~~~~~~~  191 (336)
                      +|.+|+..||+..+.|+.|.|.++.+...
T Consensus       179 ~A~~A~~~l~g~~~~g~~i~V~~a~~~~~  207 (216)
T 2qfj_A          179 SSQDAVSSMNLFDLGGQYLRVGKAVTPPM  207 (216)
T ss_dssp             HHHHHHHHHTTCBCSSSBCEEEECSSCSS
T ss_pred             HHHHHHHHccCCEeCCcEEEEEEecCCCC
Confidence            99999999999999999999999887643

>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=7.4e-32  Score=219.18  Aligned_cols=166  Identities=18%  Similarity=0.180  Sum_probs=145.5

Q ss_pred             CccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCC
Q psy12549         13 GIIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKG   91 (336)
Q Consensus        13 ~~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g   91 (336)
                      ....+.++|||+|||.++++++|+++| .++.+.. .++.+.   .+|.++|||||+|.++  ++|++|++ +++..+.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~---~~~~~~g~afV~f~~~--~~a~~A~~-l~g~~~~g   80 (175)
T 1fje_B            8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDV---RTGTNRKFGYVDFESA--EDLEKALE-LTGLKVFG   80 (175)
T ss_dssp             SSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEE---EEETTTTEEEEEESSH--HHHHHHHH-GGGEEETT
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEEC---CCCccccEEEEEECCH--HHHHHHHh-cCCCEeCC
Confidence            455788999999999999999999999 5555444 222322   4688999999999999  99999995 99999999


Q ss_pred             eeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHh
Q psy12549         92 RPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV  171 (336)
Q Consensus        92 ~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l  171 (336)
                      ++|.|.++...........++|||+|||.++++++|+++|+.||.|..+    ..+|.++|||||+|.+.++|.+|+..|
T Consensus        81 ~~l~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l  156 (175)
T 1fje_B           81 NEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEK  156 (175)
T ss_dssp             EEEEEECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHHHHHHHH
T ss_pred             eEEEEecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHHHHHHHh
Confidence            9999999987766666677899999999999999999999999988765    557889999999999999999999999


Q ss_pred             CCceeCCeEEEEeeccCc
Q psy12549        172 NGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       172 ~~~~~~~~~i~v~~~~~~  189 (336)
                      ||..+.|+.|.|.++.++
T Consensus       157 ~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          157 QGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             TEEEETTEEEEEEECSSC
T ss_pred             CCCEECCeEEEEEecCCC
Confidence            999999999999998765

>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=3.6e-31  Score=214.96  Aligned_cols=164  Identities=18%  Similarity=0.207  Sum_probs=146.0

Q ss_pred             cCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCccccc--CCceEEEEEeCCcchhhHHHHHhhcCccccC---
Q psy12549         17 PKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQ--LGSGAILVQLGQPYMLDTERALDTMNFDALK---   90 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g--~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~---   90 (336)
                      ..++|||+|||+++++++|+++| .+|.+.++++++++.   +|  .++|||||+|.++  ++|++|++.+++..+.   
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~---~~~~~~~g~afV~f~~~--~~A~~A~~~l~~~~~~~~~   76 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRS---QNPPQSKGCCFVTFYTR--KAALEAQNALHNMKVLPGM   76 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECS---SSSCEEEEEEEEEESSH--HHHHHHHHHHTTTCCCTTC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCC---CCCCCcceEEEEEECCH--HHHHHHHHHhcCcEEccCC
Confidence            46789999999999999999999 777888999998873   34  7999999999999  9999999999998775   


Q ss_pred             CeeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHH
Q psy12549         91 GRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK  170 (336)
Q Consensus        91 g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~  170 (336)
                      ++++.+.++..... .....++|||+|||.++++++|+++|+.||.|..+.++.+++|.++|||||+|.+.++|.+|+..
T Consensus        77 ~~~~~~~~~~~~~~-~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~  155 (175)
T 3nmr_A           77 HHPIQMKPADSEKN-NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA  155 (175)
T ss_dssp             SSCCEEEECGGGCC-SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHH
T ss_pred             ccceEEcccccccc-ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHH
Confidence            68888888665433 23356799999999999999999999999999999999998899999999999999999999999


Q ss_pred             hCCceeC---CeEEEEeec
Q psy12549        171 VNGMLLN---SKIVFVGKF  186 (336)
Q Consensus       171 l~~~~~~---~~~i~v~~~  186 (336)
                      |||..+.   +++|.|.++
T Consensus       156 l~g~~~~~g~~~~l~V~~a  174 (175)
T 3nmr_A          156 MHQAQTMEGCSSPMVVKFA  174 (175)
T ss_dssp             HTTSCCCTTCSSCCEEEEC
T ss_pred             hcCCcccCCCCCCeEEEec
Confidence            9998775   499999886

>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=7.4e-31  Score=212.58  Aligned_cols=156  Identities=21%  Similarity=0.487  Sum_probs=140.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhcc----C-------CeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAF----G-------SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNS  178 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~----G-------~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~  178 (336)
                      .++|||+|||.++|+++|+++|+.|    |       .|..+.+..     ++|||||+|.++++|.+|+ .+++..+.|
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~-----~~g~afV~f~~~~~A~~A~-~~~~~~~~g   77 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ-----DKNFAFLEFRSVDETTQAM-AFDGIIFQG   77 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET-----TTTEEEEEESSHHHHHHHG-GGTTCEETT
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC-----CCCEEEEEeCCHHHHHHHH-HhCCcEecC
Confidence            4789999999999999999999999    6       677777654     4789999999999999999 799999999


Q ss_pred             eEEEEeeccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHH
Q psy12549        179 KIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFA  256 (336)
Q Consensus       179 ~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a  256 (336)
                      +.|.+.++.+....        ...++|+|+|||..+++++|+++|++||.|..+.+..  .+|.++|+|||+|.+.++|
T Consensus        78 ~~i~v~~~~~~~~~--------~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A  149 (172)
T 2g4b_A           78 QSLKIRRPHDYQPL--------PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT  149 (172)
T ss_dssp             EECEEECCSSCCCC--------TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHH
T ss_pred             ceeeecCCcccCCC--------CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHH
Confidence            99999887654321        2247899999999999999999999999999999987  4888999999999999999


Q ss_pred             HHHHHHhCCceecCEEEEEeecc
Q psy12549        257 EKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       257 ~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      .+|++.|||..++|+.|.|.+|.
T Consensus       150 ~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          150 DQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             HHHHHHHTTCEETTEECEEEECC
T ss_pred             HHHHHHcCCCEECCeEEEEEeCC
Confidence            99999999999999999999874

>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=5e-32  Score=218.43  Aligned_cols=164  Identities=17%  Similarity=0.297  Sum_probs=147.6

Q ss_pred             ccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeee
Q psy12549         16 IPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPI   94 (336)
Q Consensus        16 ~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i   94 (336)
                      .+.++|||+|||+++|+++|+++| .+|.+.++++.+++   .+|.++|||||+|.+.  ++|++|++.  +..+.|+.|
T Consensus         1 k~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~--~~a~~A~~~--~~~~~g~~i   73 (167)
T 2cjk_A            1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDP---ATGRSRGFGFLSFEKP--SSVDEVVKT--QHILDGKVI   73 (167)
T ss_dssp             CGGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCT---TTSSCCSCEEEEESST--HHHHHHHHS--CCEETTEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECC---CCCCccceEEEEEccH--HHHHHHHhc--ccccCCeEc
Confidence            367899999999999999999999 77788899999887   3789999999999999  999999994  568899999


Q ss_pred             EEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCC
Q psy12549         95 RIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNG  173 (336)
Q Consensus        95 ~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~  173 (336)
                      .+.++.....  ....++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|++ +++
T Consensus        74 ~v~~~~~~~~--~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~  150 (167)
T 2cjk_A           74 DPKRAIPRDE--QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKF  150 (167)
T ss_dssp             CCEECCCHHH--HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSE
T ss_pred             ccccccchhh--ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCC
Confidence            9988755432  2235689999999999999999999999999999999986 78999999999999999999998 899


Q ss_pred             ceeCCeEEEEeeccCc
Q psy12549        174 MLLNSKIVFVGKFIPR  189 (336)
Q Consensus       174 ~~~~~~~i~v~~~~~~  189 (336)
                      ..+.|+.|.|.++.++
T Consensus       151 ~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          151 IDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             ECSSSSCEEEEECCCC
T ss_pred             EEeCCeEEEEeecCCC
Confidence            9999999999998775

>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=1.1e-30  Score=216.78  Aligned_cols=166  Identities=13%  Similarity=0.176  Sum_probs=140.7

Q ss_pred             CCceEEEcCCC-CCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLD-KSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp-~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+||| ..+++++|+++|+.||.|.+|+++.+    ++|||||+|.+.++|++|++.|||..+.|+.|.|.++.
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~   78 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSK   78 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcc
Confidence            45789999999 89999999999999999999999875    47899999999999999999999999999999999875


Q ss_pred             Cchhhh-----------------------------HhhhccccccceEEEcCCCCCCcHHHHHHhhccCCce--eEEEEe
Q psy12549        188 PRKERE-----------------------------KELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTI--TSYRVM  236 (336)
Q Consensus       188 ~~~~~~-----------------------------~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i--~~~~i~  236 (336)
                      ......                             ........+.++|||+|||.++++++|+++|++||.|  ..+++.
T Consensus        79 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~  158 (205)
T 3tyt_A           79 QPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVF  158 (205)
T ss_dssp             CSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEEC
T ss_pred             CCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEE
Confidence            321100                             0000011334689999999999999999999999999  899998


Q ss_pred             CCCCccceEEEEEeCCHHHHHHHHHHhCCceecCE----EEEEeec
Q psy12549        237 NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK----ILYVGRA  278 (336)
Q Consensus       237 ~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~----~l~v~~~  278 (336)
                      ...+..+|+|||+|.+.++|.+|+..|||..+.|+    ++.|.++
T Consensus       159 ~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          159 SGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             SCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             cCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            86566679999999999999999999999999885    5666654

>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=2e-30  Score=210.09  Aligned_cols=157  Identities=17%  Similarity=0.306  Sum_probs=139.5

Q ss_pred             ccCceeeeecCchhhhhhhHHhhh-ccc-----------CCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhh
Q psy12549         16 IPKHNVATRELSAKVVEGVSRSLS-SLI-----------DGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDT   83 (336)
Q Consensus        16 ~p~~~v~v~~lp~~~~e~~l~~~f-~~~-----------~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~   83 (336)
                      ++.++|||+|||+++|+++|+++| .++           .+.++++         +.++|||||+|.++  ++|++|+ .
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~---------~~~~g~afV~f~~~--~~A~~A~-~   69 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI---------NQDKNFAFLEFRSV--DETTQAM-A   69 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE---------ETTTTEEEEEESSH--HHHHHHG-G
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEe---------cCCCCEEEEEeCCH--HHHHHHH-H
Confidence            578999999999999999999999 442           2233333         45679999999999  9999999 7


Q ss_pred             cCccccCCeeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHH
Q psy12549         84 MNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEE  162 (336)
Q Consensus        84 ~~~~~~~g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~  162 (336)
                      +++..+.|+++.|.++.....  ....++|||+|||.++++++|+++|++||.|..+.+..++ +|.++|+|||+|.+.+
T Consensus        70 ~~~~~~~g~~i~v~~~~~~~~--~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~  147 (172)
T 2g4b_A           70 FDGIIFQGQSLKIRRPHDYQP--LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDIN  147 (172)
T ss_dssp             GTTCEETTEECEEECCSSCCC--CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTT
T ss_pred             hCCcEecCceeeecCCcccCC--CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHH
Confidence            999999999999998765432  3446889999999999999999999999999999999996 8899999999999999


Q ss_pred             HHHHHHHHhCCceeCCeEEEEeec
Q psy12549        163 AANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       163 ~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      +|.+|++.|||..+.|+.|.|.++
T Consensus       148 ~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          148 VTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             HHHHHHHHHTTCEETTEECEEEEC
T ss_pred             HHHHHHHHcCCCEECCeEEEEEeC
Confidence            999999999999999999999886

>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=2.8e-30  Score=214.01  Aligned_cols=168  Identities=20%  Similarity=0.437  Sum_probs=144.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhcc----C-------CeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAF----G-------SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNS  178 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~----G-------~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~  178 (336)
                      .++|||+|||.++++++|+++|+.|    |       .|..+.+.     .++|||||+|.+.++|.+|+ .|++..+.|
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~-----~~~g~afV~F~~~~~A~~Al-~l~g~~~~g   77 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-----QDKNFAFLEFRSVDETTQAM-AFDGIIFQG   77 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE-----TTTTEEEEEESCSHHHHHHG-GGTTEEETT
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec-----CCCCEEEEEeCCHHHHHHHH-HhcCCEEcC
Confidence            5789999999999999999999999    5       56666554     45899999999999999999 799999999


Q ss_pred             eEEEEeeccCchhhhHh------------hhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccce
Q psy12549        179 KIVFVGKFIPRKEREKE------------LGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRG  244 (336)
Q Consensus       179 ~~i~v~~~~~~~~~~~~------------~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g  244 (336)
                      +.|.|.++.+.......            ........++|||+|||..+++++|+++|+.||.|..+.+..  .+|.++|
T Consensus        78 ~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g  157 (198)
T 2yh0_A           78 QSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG  157 (198)
T ss_dssp             EEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEE
T ss_pred             ceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcce
Confidence            99999988765321110            011123458999999999999999999999999999999987  4888999


Q ss_pred             EEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchh
Q psy12549        245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAE  283 (336)
Q Consensus       245 ~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~  283 (336)
                      +|||+|.+.++|.+|++.|||..++|+.|.|.++.++..
T Consensus       158 ~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          158 YAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             EEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999999999999999999987643

>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=9.6e-30  Score=210.82  Aligned_cols=169  Identities=15%  Similarity=0.246  Sum_probs=141.1

Q ss_pred             ccCceeeeecCchhhhhhhHHhhh-cccCCceEE-----EeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCcccc
Q psy12549         16 IPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVK-----YDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDAL   89 (336)
Q Consensus        16 ~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~-----~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~   89 (336)
                      ...++|||+|||+++++++|+++| .+|.+..+.     .+.+   ..++.++|||||+|.++  ++|++|+ .+++..+
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~---~~~~~~~g~afV~F~~~--~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLA---VQINQDKNFAFLEFRSV--DETTQAM-AFDGIIF   75 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEE---EEEETTTTEEEEEESCS--HHHHHHG-GGTTEEE
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEE---eEecCCCCEEEEEeCCH--HHHHHHH-HhcCCEE
Confidence            457899999999999999999999 443221110     0000   12356789999999999  9999999 6999999


Q ss_pred             CCeeeEEEeccCCCCc------------------CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCc
Q psy12549         90 KGRPIRIMWSQRDPSL------------------RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNS  150 (336)
Q Consensus        90 ~g~~i~v~~~~~~~~~------------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~  150 (336)
                      .|++|.|.++......                  .....++|||+|||..+++++|+++|+.||.|..+.+..++ +|.+
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~  155 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLS  155 (198)
T ss_dssp             TTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSE
T ss_pred             cCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCc
Confidence            9999999987654211                  11345899999999999999999999999999999999997 8889


Q ss_pred             ccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCch
Q psy12549        151 KGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRK  190 (336)
Q Consensus       151 ~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~  190 (336)
                      +|||||+|.+.++|.+|+..|||..+.|+.|.|.++.++.
T Consensus       156 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  195 (198)
T 2yh0_A          156 KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA  195 (198)
T ss_dssp             EEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             ceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            9999999999999999999999999999999999988764

>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=1.8e-29  Score=213.86  Aligned_cols=170  Identities=16%  Similarity=0.289  Sum_probs=146.6

Q ss_pred             cCCCCCceEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        105 LRKSGVGNVFIKNLDK-SIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       105 ~~~~~~~~l~v~nlp~-~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      ......++|||+|||. ++++++|+++|+.||.|..+.++.++    +|||||+|.+.++|.+|++.|++..+.|+.|.|
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 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI  104 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            3345668999999999 99999999999999999999999875    679999999999999999999999999999999


Q ss_pred             eeccCchhhhH---------------------------hhhccccccceEEEcCCCCCCcHHHHHHhhccCC-ceeEEEE
Q psy12549        184 GKFIPRKEREK---------------------------ELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYG-TITSYRV  235 (336)
Q Consensus       184 ~~~~~~~~~~~---------------------------~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g-~i~~~~i  235 (336)
                      .++.+......                           .......+.++|||+|||..+++++|+++|+.|| .|..+.+
T Consensus       105 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i  184 (229)
T 2adc_A          105 TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF  184 (229)
T ss_dssp             ECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEE
T ss_pred             EEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEE
Confidence            98875421000                           0001123357899999999999999999999999 9999999


Q ss_pred             eCCCCccceEEEEEeCCHHHHHHHHHHhCCceec-CEEEEEeecccc
Q psy12549        236 MNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD-GKILYVGRAQKK  281 (336)
Q Consensus       236 ~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~-g~~l~v~~~~~~  281 (336)
                      ...   ++|+|||+|.+.++|.+|+..|+|..+. |+.|+|.|+.++
T Consensus       185 ~~~---~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          185 FQK---DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CSS---STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EEC---CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            652   3789999999999999999999999999 999999999864

>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=4.8e-29  Score=218.14  Aligned_cols=167  Identities=19%  Similarity=0.302  Sum_probs=144.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMY----DTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~----~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      ...++|||+|||.++++++|+    ++|+.||.|..|.+.+  +|.++|||||+|.+.++|.+|++.|||..+.|+.|.|
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   84 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   84 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEEE
Confidence            446899999999999999966    8999999999999886  6778999999999999999999999999999999999


Q ss_pred             eeccCchhhhHh--------------------------------------------------------------------
Q psy12549        184 GKFIPRKEREKE--------------------------------------------------------------------  195 (336)
Q Consensus       184 ~~~~~~~~~~~~--------------------------------------------------------------------  195 (336)
                      .++.........                                                                    
T Consensus        85 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~  164 (282)
T 3pgw_A           85 QYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYM  164 (282)
T ss_pred             EEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCCC
Confidence            998654421000                                                                    


Q ss_pred             -----------------------------------hhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCC
Q psy12549        196 -----------------------------------LGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG  240 (336)
Q Consensus       196 -----------------------------------~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~  240 (336)
                                                         ........++|||+|||..+++++|+++|+.||.|.++.+.... 
T Consensus       165 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-  243 (282)
T 3pgw_A          165 PPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-  243 (282)
T ss_pred             CCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-
Confidence                                               00111234779999999999999999999999999999998531 


Q ss_pred             ccceEEEEEeCCHHHHHHHHHHhCCceec-CEEEEEeecc
Q psy12549        241 KSRGFGFVAYESPEFAEKAVQAWNGKEVD-GKILYVGRAQ  279 (336)
Q Consensus       241 ~~~g~afV~F~~~~~a~~a~~~l~g~~~~-g~~l~v~~~~  279 (336)
                        +|+|||+|.+.++|.+|+..|||..+. |+.|+|.|++
T Consensus       244 --~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          244 --HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             --CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence              589999999999999999999999999 9999999986

>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=99.97  E-value=1.6e-29  Score=218.42  Aligned_cols=156  Identities=19%  Similarity=0.352  Sum_probs=142.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||.++|+++|+++|+.||.|..+.+.+     ++|||||+|.+.++|.+|+..++|..+.|+.|.|.++.
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~   94 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR-----DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT   94 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeecc
Confidence            4557999999999999999999999999999999965     37899999999999999999999999999999999986


Q ss_pred             CchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCc
Q psy12549        188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGK  266 (336)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~  266 (336)
                      +.              ++|||+|||..+++++|+++|+.||.|..+.++. .+|.++|+|||+|.+.++|.+|+..||+.
T Consensus        95 ~~--------------~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~  160 (261)
T 3sde_A           95 HG--------------AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDG  160 (261)
T ss_dssp             CS--------------SEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHS
T ss_pred             cC--------------CcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCC
Confidence            42              6899999999999999999999999999999887 78889999999999999999999999554


Q ss_pred             -eec---CEEEEEeecccch
Q psy12549        267 -EVD---GKILYVGRAQKKA  282 (336)
Q Consensus       267 -~~~---g~~l~v~~~~~~~  282 (336)
                       .+.   |++|.|.++.+..
T Consensus       161 ~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          161 AFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             CEESSSSCCBCEEEECCCEE
T ss_pred             eEEecCCCceEEEeeccccC
Confidence             444   8999999987653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.96  E-value=5.6e-30  Score=212.30  Aligned_cols=166  Identities=16%  Similarity=0.288  Sum_probs=144.3

Q ss_pred             CCceEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDK-SIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~-~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      +.++|||+|||. ++++++|+++|+.||.|..+.++.++    +|||||+|.+.++|.+|+..|++..+.|+.|.|.++.
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 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            357899999999 99999999999999999999999875    6799999999999999999999999999999999887


Q ss_pred             CchhhhHh---------------------------hhccccccceEEEcCCCCCCcHHHHHHhhccCC-ceeEEEEeCCC
Q psy12549        188 PRKEREKE---------------------------LGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYG-TITSYRVMNND  239 (336)
Q Consensus       188 ~~~~~~~~---------------------------~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g-~i~~~~i~~~~  239 (336)
                      +.......                           ......+.++|+|+|||..+++++|+++|+.|| .|..+.+.+. 
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-  156 (198)
T 1qm9_A           78 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-  156 (198)
T ss_dssp             CCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-
T ss_pred             CCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-
Confidence            54211000                           001113357899999999999999999999999 9999999763 


Q ss_pred             CccceEEEEEeCCHHHHHHHHHHhCCceec-CEEEEEeecccc
Q psy12549        240 GKSRGFGFVAYESPEFAEKAVQAWNGKEVD-GKILYVGRAQKK  281 (336)
Q Consensus       240 ~~~~g~afV~F~~~~~a~~a~~~l~g~~~~-g~~l~v~~~~~~  281 (336)
                        .+|+|||+|.+.++|.+|+..|||..+. |+.|+|.|+.++
T Consensus       157 --~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          157 --DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             --TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             --CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence              2789999999999999999999999999 999999998764

>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=99.96  E-value=1e-28  Score=216.09  Aligned_cols=162  Identities=15%  Similarity=0.223  Sum_probs=143.4

Q ss_pred             ccccCceeeeecCchhhhhhhHH----hhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccc
Q psy12549         14 IIIPKHNVATRELSAKVVEGVSR----SLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDA   88 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~~~e~~l~----~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~   88 (336)
                      ...|+++|||+|||.++++++|+    ++| .+|.+.++++.+      +|+++|||||+|.+.  ++|++|++.+||..
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~------~~~~~g~afV~f~~~--~~a~~A~~~l~g~~   76 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR------SLKMRGQAFVIFKEV--SSATNALRSMQGFP   76 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC------CCCcceEEEEEECCH--HHHHHHHHHhcCCe
Confidence            45789999999999999999977    888 777888888876      467999999999999  99999999999999


Q ss_pred             cCCeeeEEEeccCCCC----------------------------------------------------------------
Q psy12549         89 LKGRPIRIMWSQRDPS----------------------------------------------------------------  104 (336)
Q Consensus        89 ~~g~~i~v~~~~~~~~----------------------------------------------------------------  104 (336)
                      +.|+.|+|.|+.....                                                                
T Consensus        77 ~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (282)
T 3pgw_A           77 FYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHH  156 (282)
T ss_pred             eCCcEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCccccccccccc
Confidence            9999999998765431                                                                


Q ss_pred             ---------------------------------------------cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeE
Q psy12549        105 ---------------------------------------------LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILS  139 (336)
Q Consensus       105 ---------------------------------------------~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~  139 (336)
                                                                   ......++|||+|||..+++++|+++|+.||.|.+
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                                                         01113467999999999999999999999999999


Q ss_pred             EEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEeecc
Q psy12549        140 CKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLN-SKIVFVGKFI  187 (336)
Q Consensus       140 ~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~-~~~i~v~~~~  187 (336)
                      +.+..++    +|||||+|.+.++|.+|+..|||..+. |+.|.|.|++
T Consensus       237 v~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          237 VRLVPGR----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             EEEecCC----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            9999764    579999999999999999999999999 9999999875

>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=99.96  E-value=3.1e-29  Score=208.04  Aligned_cols=159  Identities=13%  Similarity=0.171  Sum_probs=136.2

Q ss_pred             ccCceeeeecCc-hhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCee
Q psy12549         16 IPKHNVATRELS-AKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRP   93 (336)
Q Consensus        16 ~p~~~v~v~~lp-~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~   93 (336)
                      .+.++|||+||| .++++++|+++| .+|.+.+++++++        ++|||||+|.++  ++|+.|++.|||..+.|++
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~--------~~g~afV~f~~~--~~A~~Ai~~lng~~~~g~~   71 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS--------KPGAAMVEMADG--YAVDRAITHLNNNFMFGQK   71 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT--------STTCEEEEESSH--HHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC--------CCCEEEEEECCH--HHHHHHHHHhCCCEECCce
Confidence            367899999999 799999999999 7778889999874        368999999999  9999999999999999999


Q ss_pred             eEEEeccCCCCcC-----------------------------------CCCCceEEEcCCCCCCCHHHHHHHhhccCCe-
Q psy12549         94 IRIMWSQRDPSLR-----------------------------------KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSI-  137 (336)
Q Consensus        94 i~v~~~~~~~~~~-----------------------------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v-  137 (336)
                      |+|.++.......                                   ....++|||+|||+++|+++|+++|++||.| 
T Consensus        72 l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~  151 (205)
T 3tyt_A           72 MNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKR  151 (205)
T ss_dssp             CEEEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCC
T ss_pred             EEEEEccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcc
Confidence            9999875321100                                   0123579999999999999999999999998 


Q ss_pred             -eEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCe----EEEEee
Q psy12549        138 -LSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSK----IVFVGK  185 (336)
Q Consensus       138 -~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~----~i~v~~  185 (336)
                       .+++++.+. +.++|+|||+|.+.++|.+|+..|||..+.|.    ++.|.+
T Consensus       152 ~~~v~~~~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~  203 (205)
T 3tyt_A          152 PTSVKVFSGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKL  203 (205)
T ss_dssp             CSEEEECSCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEE
T ss_pred             eEEEEEEcCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEe
Confidence             899998876 44679999999999999999999999999875    455544

>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=99.96  E-value=1.2e-28  Score=213.00  Aligned_cols=162  Identities=23%  Similarity=0.346  Sum_probs=145.5

Q ss_pred             CCCccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCcccc
Q psy12549         11 EEGIIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDAL   89 (336)
Q Consensus        11 ~~~~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~   89 (336)
                      ......+.++|||+|||+++|+++|+++| .+|.+..+.+.+         ++|||||+|.+.  ++|.+|+..++|..+
T Consensus        15 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~---------~kg~afV~f~~~--~~A~~A~~~l~g~~i   83 (261)
T 3sde_A           15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR---------DRGFGFIRLESR--TLAEIAKAELDGTIL   83 (261)
T ss_dssp             TCCSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET---------TTTEEEEECSSH--HHHHHHHHHHTTCEE
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC---------CCcEEEEEECCH--HHHHHHHHHcCCcEE
Confidence            34455777899999999999999999999 777888998865         458999999999  999999999999999


Q ss_pred             CCeeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHH
Q psy12549         90 KGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE  169 (336)
Q Consensus        90 ~g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~  169 (336)
                      .|+.|.|.++..        .++|||+|||..+|+++|+++|+.||.|..+.++.+++|.++|||||+|.+.++|.+|+.
T Consensus        84 ~g~~l~v~~a~~--------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~  155 (261)
T 3sde_A           84 KSRPLRIRFATH--------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALE  155 (261)
T ss_dssp             TTEECEEEECCC--------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCceeEeeeccc--------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHH
Confidence            999999999854        367999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhC-CceeC---CeEEEEeeccCchh
Q psy12549        170 KVN-GMLLN---SKIVFVGKFIPRKE  191 (336)
Q Consensus       170 ~l~-~~~~~---~~~i~v~~~~~~~~  191 (336)
                      .|+ +..+.   +++|.|.++.+...
T Consensus       156 ~l~~~~~~~~~~~r~i~v~~~~~~~~  181 (261)
T 3sde_A          156 RCGDGAFLLTTTPRPVIVEPMEQFDD  181 (261)
T ss_dssp             HHHHSCEESSSSCCBCEEEECCCEES
T ss_pred             HhcCCeEEecCCCceEEEeeccccCc
Confidence            994 55554   99999999876543

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.96  E-value=1.6e-28  Score=208.10  Aligned_cols=164  Identities=18%  Similarity=0.166  Sum_probs=143.6

Q ss_pred             CCccccCceeeeecCch-hhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCcccc
Q psy12549         12 EGIIIPKHNVATRELSA-KVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDAL   89 (336)
Q Consensus        12 ~~~~~p~~~v~v~~lp~-~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~   89 (336)
                      .....|.++|||+|||+ ++++++|+++| .+|.+.++++.+++        +|||||+|.+.  ++|++|++.+++..+
T Consensus        28 ~~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~--------~g~afV~F~~~--~~A~~Ai~~l~g~~~   97 (229)
T 2adc_A           28 GLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--------KENALVQMADG--NQAQLAMSHLNGHKL   97 (229)
T ss_dssp             GGGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT--------SCCEEEEESCH--HHHHHHHHHHTTCBC
T ss_pred             CCCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC--------CCEEEEEECCH--HHHHHHHHHhCCCeE
Confidence            33456788999999999 99999999999 77788899998855        58999999999  999999999999999


Q ss_pred             CCeeeEEEeccCCC----Cc-----------------------------CCCCCceEEEcCCCCCCCHHHHHHHhhccC-
Q psy12549         90 KGRPIRIMWSQRDP----SL-----------------------------RKSGVGNVFIKNLDKSIDNKAMYDTFSAFG-  135 (336)
Q Consensus        90 ~g~~i~v~~~~~~~----~~-----------------------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G-  135 (336)
                      .|+.|.|.++....    ..                             .....++|||+|||..+++++|+++|+.|| 
T Consensus        98 ~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~  177 (229)
T 2adc_A           98 HGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGG  177 (229)
T ss_dssp             SSSBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSC
T ss_pred             CCeEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCC
Confidence            99999999876441    10                             011257899999999999999999999999 


Q ss_pred             CeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEeeccCc
Q psy12549        136 SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLN-SKIVFVGKFIPR  189 (336)
Q Consensus       136 ~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~-~~~i~v~~~~~~  189 (336)
                      .|..+.+..+    ++|+|||+|.+.++|.+|+..|+|..+. |+.|.|.++.+.
T Consensus       178 ~i~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          178 VVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             CEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             CeeEEEEEEC----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            9999999764    3689999999999999999999999999 999999998764

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.96  E-value=3.3e-28  Score=201.60  Aligned_cols=158  Identities=18%  Similarity=0.200  Sum_probs=139.9

Q ss_pred             CceeeeecCch-hhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeE
Q psy12549         18 KHNVATRELSA-KVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIR   95 (336)
Q Consensus        18 ~~~v~v~~lp~-~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~   95 (336)
                      +++|||+|||+ ++++++|+++| .+|.+..+++.+++        +|||||+|.+.  ++|++|++.+++..+.|++|.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~--------~g~afV~f~~~--~~a~~A~~~l~~~~~~g~~l~   72 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--------KENALVQMADG--NQAQLAMSHLNGHKLHGKPIR   72 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC--------SSCCEEECTTT--HHHHHHHHHHTTCCCSSCCCE
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC--------CCEEEEEECCH--HHHHHHHHHhCCCeecCeEEE
Confidence            57899999999 99999999999 77788899998854        57999999999  999999999999999999999


Q ss_pred             EEeccCCCCc---------------------------------CCCCCceEEEcCCCCCCCHHHHHHHhhccC-CeeEEE
Q psy12549         96 IMWSQRDPSL---------------------------------RKSGVGNVFIKNLDKSIDNKAMYDTFSAFG-SILSCK  141 (336)
Q Consensus        96 v~~~~~~~~~---------------------------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G-~v~~~~  141 (336)
                      |.++......                                 .....++|||+|||..+++++|+++|+.|| .|..+.
T Consensus        73 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~  152 (198)
T 1qm9_A           73 ITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFK  152 (198)
T ss_dssp             EEECCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEE
T ss_pred             EEEecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEE
Confidence            9997654210                                 012257899999999999999999999999 999999


Q ss_pred             EeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeC-CeEEEEeeccCc
Q psy12549        142 VAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLN-SKIVFVGKFIPR  189 (336)
Q Consensus       142 ~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~-~~~i~v~~~~~~  189 (336)
                      +..+    .+|+|||+|.+.++|.+|+..|||..+. |+.|.|.++.+.
T Consensus       153 i~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          153 FFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             ESST----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             EEeC----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            9764    3689999999999999999999999999 999999998764

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.89  E-value=4.7e-23  Score=154.92  Aligned_cols=110  Identities=73%  Similarity=1.127  Sum_probs=76.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      +.++|||+|||+++|+++|+++|+.||.|.+|+++.++. .++|||||+|.+.++|++|++.|++..+.|+.|.|.++.+
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~-~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC-CCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            357899999999999999999999999999999999864 4899999999999999999999999999999999999988


Q ss_pred             chhhhHhhhccccccceEEEcCCCCCCcHHH
Q psy12549        189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEK  219 (336)
Q Consensus       189 ~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~  219 (336)
                      ...............++|||+|||+++|++.
T Consensus        83 ~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           83 RKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CCC----------------------------
T ss_pred             ccccccccccccCCCCceEeCCCCCCccccc
Confidence            7766655555555667899999999998763

>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=99.89  E-value=1.2e-22  Score=161.88  Aligned_cols=139  Identities=14%  Similarity=0.237  Sum_probs=111.2

Q ss_pred             eEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeee-------EEEeccCC----CCcCCCCCceEE
Q psy12549         46 TVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPI-------RIMWSQRD----PSLRKSGVGNVF  114 (336)
Q Consensus        46 ~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i-------~v~~~~~~----~~~~~~~~~~l~  114 (336)
                      +++++.+.     .+++|||||+|.+.  ++|++|++.+++....+...       ........    ........++||
T Consensus         2 ~~kl~ln~-----~~~~G~~fV~f~~~--~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~   74 (158)
T 2kn4_A            2 QYKLILNG-----KTLKGETTTEAVDA--ATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLK   74 (158)
T ss_dssp             EEEEEEEC-----SSCEEEEEEECSSH--HHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEE
T ss_pred             cEEEEecC-----ccccchhHHHHHHH--HhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEE
Confidence            45666655     36899999999999  99999998877643322222       22211111    112223457999


Q ss_pred             EcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchh
Q psy12549        115 IKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKE  191 (336)
Q Consensus       115 v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~  191 (336)
                      |+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|+..|||..+.|+.|.|.++.+...
T Consensus        75 v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A           75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             EESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             EeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            99999999999999999999999999999996 789999999999999999999999999999999999999887643

>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=99.87  E-value=2.2e-22  Score=151.20  Aligned_cols=108  Identities=31%  Similarity=0.597  Sum_probs=75.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchh
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAE  283 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~  283 (336)
                      .+|||+|||.++++++|+++|+.||.|.+++++...+.++|||||+|.+.++|.+|++.|+|..+.|+.|+|.++.++..
T Consensus         6 ~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~   85 (115)
T 4f25_A            6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE   85 (115)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCCC
T ss_pred             CEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCccc
Confidence            67999999999999999999999999999999986677899999999999999999999999999999999999987654


Q ss_pred             hHHHHHHHHHHHHHHhhcCCCCceEEEecCCCCCCHHH
Q psy12549        284 RTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDER  321 (336)
Q Consensus       284 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~  321 (336)
                      .......          .....++|||+|||+.+|++.
T Consensus        86 ~~~~~~~----------~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           86 REAELGA----------RAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             --------------------------------------
T ss_pred             ccccccc----------ccCCCCceEeCCCCCCccccc
Confidence            3322111          112335799999999998863

>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=99.87  E-value=8.5e-22  Score=156.89  Aligned_cols=143  Identities=20%  Similarity=0.209  Sum_probs=109.8

Q ss_pred             EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchh-----hhHhhhccccccceEEEcCCCC
Q psy12549        139 SCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKE-----REKELGEKAKLFTNVYIKNFGE  213 (336)
Q Consensus       139 ~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~-----~~~~~~~~~~~~~~l~V~nlp~  213 (336)
                      ++++..+.. .++|||||+|.+.++|++|+..+++....+....+........     ............++|||+|||.
T Consensus         2 ~~kl~ln~~-~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~   80 (158)
T 2kn4_A            2 QYKLILNGK-TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTY   80 (158)
T ss_dssp             EEEEEEECS-SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCT
T ss_pred             cEEEEecCc-cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCC
Confidence            345566543 5899999999999999999988776433222222221111100     0001112223458899999999


Q ss_pred             CCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        214 DFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       214 ~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      .+++++|+++|+.||.|..+.++.  .+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.++.
T Consensus        81 ~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  151 (158)
T 2kn4_A           81 RTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  151 (158)
T ss_dssp             TCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSS
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            999999999999999999999987  478899999999999999999999999999999999999998763

>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=99.85  E-value=2.1e-21  Score=153.14  Aligned_cols=123  Identities=18%  Similarity=0.213  Sum_probs=110.2

Q ss_pred             CCceEEEEEeCCcchhhHHHHHhhc-CccccCCeeeEEEeccCC--------------CCcCCCCCceEEEcCCCCCCCH
Q psy12549         60 LGSGAILVQLGQPYMLDTERALDTM-NFDALKGRPIRIMWSQRD--------------PSLRKSGVGNVFIKNLDKSIDN  124 (336)
Q Consensus        60 ~~~g~afV~f~~~~~~~A~~A~~~~-~~~~~~g~~i~v~~~~~~--------------~~~~~~~~~~l~v~nlp~~~t~  124 (336)
                      .-+|+++|+|.+.  ++|++|++.+ |+..+.| ++.+.++...              ........++|||+|||+++++
T Consensus        11 ~l~G~~~ve~~~~--~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~   87 (150)
T 2i2y_A           11 TLKGETTTEAVDA--ATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNK   87 (150)
T ss_dssp             SSCEEEEEECSSH--HHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSC
T ss_pred             cccccceeeecCH--HHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCH
Confidence            4689999999999  9999999999 9999999 9999886542              1233345689999999999999


Q ss_pred             HHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        125 KAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       125 ~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      ++|+++|+.||.|..+.++.+    ++|||||+|.+.++|.+|+..|||..+.|+.|.|.++.++
T Consensus        88 ~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           88 TELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             HHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            999999999999999999886    5789999999999999999999999999999999998765

>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=99.84  E-value=2.3e-21  Score=152.92  Aligned_cols=129  Identities=23%  Similarity=0.286  Sum_probs=111.2

Q ss_pred             CcccEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEEeeccCchhhh--------HhhhccccccceEEEcCCCCCCcHHH
Q psy12549        149 NSKGYGFVHFETEEAANKSIEKV-NGMLLNSKIVFVGKFIPRKERE--------KELGEKAKLFTNVYIKNFGEDFNDEK  219 (336)
Q Consensus       149 ~~~g~afV~F~~~~~a~~a~~~l-~~~~~~~~~i~v~~~~~~~~~~--------~~~~~~~~~~~~l~V~nlp~~~t~~~  219 (336)
                      ..+|+++++|.+.++|++|++.+ |+..++| .+.+.++.......        ..........++|||+|||..+++++
T Consensus        11 ~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~~   89 (150)
T 2i2y_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTE   89 (150)
T ss_dssp             SSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCHH
T ss_pred             cccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHH
Confidence            46789999999999999999999 9999999 99998876532211        01122334458999999999999999


Q ss_pred             HHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        220 LKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       220 l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      |+++|+.||.|.++.++..   ++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.++
T Consensus        90 l~~~F~~~G~i~~v~i~~~---~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           90 LERAFGYYGPLRSVWVARN---PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             HHHHHHHHSCEEEEEECSS---SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             HHHHHHhhCCEEEEEEeeC---CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            9999999999999999864   5899999999999999999999999999999999999875

>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=99.82  E-value=7.2e-20  Score=133.37  Aligned_cols=80  Identities=31%  Similarity=0.549  Sum_probs=76.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+|||.++|+++|+++|++||.|.++.+++++ +|.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            45789999999999999999999999999999999987 78999999999999999999999999999999999999986


Q ss_pred             C
Q psy12549        188 P  188 (336)
Q Consensus       188 ~  188 (336)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            5

>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=99.81  E-value=1.8e-19  Score=131.27  Aligned_cols=78  Identities=27%  Similarity=0.522  Sum_probs=74.2

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||.++|+++|+++|++||+|.++.++.  .+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.||+|
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            37899999999999999999999999999999987  6788999999999999999999999999999999999999976

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.77  E-value=3.3e-18  Score=126.92  Aligned_cols=86  Identities=14%  Similarity=0.231  Sum_probs=79.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+|||.++++++|+++|++||.|.++.++.++ +|.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            35789999999999999999999999999999999998 69999999999999999999999999999999999999987


Q ss_pred             CchhhhH
Q psy12549        188 PRKEREK  194 (336)
Q Consensus       188 ~~~~~~~  194 (336)
                      .......
T Consensus        85 ~~~~~~~   91 (110)
T 3s8s_A           85 KGQQRMK   91 (110)
T ss_dssp             TTHHHHH
T ss_pred             CCcHHHH
Confidence            7655443

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.77  E-value=3.5e-18  Score=126.81  Aligned_cols=83  Identities=20%  Similarity=0.305  Sum_probs=76.8

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      +.++|||+|||+.+++++|+++|++||.|.++.++.  .++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            347899999999999999999999999999999987  568899999999999999999999999999999999999997


Q ss_pred             cchhh
Q psy12549        280 KKAER  284 (336)
Q Consensus       280 ~~~~~  284 (336)
                      .....
T Consensus        85 ~~~~~   89 (110)
T 3s8s_A           85 KGQQR   89 (110)
T ss_dssp             TTHHH
T ss_pred             CCcHH
Confidence            66443

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.77  E-value=4.5e-19  Score=127.12  Aligned_cols=80  Identities=16%  Similarity=0.328  Sum_probs=73.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccC-CeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEEeecc
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFG-SILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV-NGMLLNSKIVFVGKFI  187 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G-~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l-~~~~~~~~~i~v~~~~  187 (336)
                      .+|||+|||+++|+++|+++|++|| .|.+|++++++ +|.++|||||+|.+.++|.+|++.+ ++..+.|++|.|.++.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            5799999999999999999999999 89999999987 7899999999999999999999977 4567999999999988


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      ++.
T Consensus        82 ~~~   84 (91)
T 2lxi_A           82 PKP   84 (91)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            764

>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=99.76  E-value=9e-19  Score=131.57  Aligned_cols=103  Identities=26%  Similarity=0.387  Sum_probs=91.3

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ..++|||+|||..+++++|+++|+.||.|..+.++. ++.++|+|||+|.+.++|.+|+..|||..+.|+.|.|.++.++
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   85 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN-TPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNAN   85 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC-STTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEee-CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            347899999999999999999999999999999986 3556999999999999999999999999999999999999865


Q ss_pred             hhhHHHHHHHHHHHHHHhhcCCCCceEEEecCCCCCCHHHHHHhcCCCCC
Q psy12549        282 AERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLRKEFTPFGT  331 (336)
Q Consensus       282 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~  331 (336)
                      ...                          ++++...++++|.++|++||.
T Consensus        86 ~~~--------------------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           86 RAF--------------------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HHT--------------------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             hhh--------------------------hhhhHhHhHHHHHHHHHHhCC
Confidence            322                          466777888999999999884

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.75  E-value=5.9e-19  Score=126.50  Aligned_cols=80  Identities=19%  Similarity=0.357  Sum_probs=73.1

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCC-ceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhC-CceecCEEEEEeecc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYG-TITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWN-GKEVDGKILYVGRAQ  279 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g-~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~-g~~~~g~~l~v~~~~  279 (336)
                      ++|||+|||.++|+++|+++|++|| .|.++++++  .+|.++|||||+|.+.++|.+|++.++ +..++|++|+|.++.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            6899999999999999999999999 799999887  678899999999999999999999874 567999999999998


Q ss_pred             cchh
Q psy12549        280 KKAE  283 (336)
Q Consensus       280 ~~~~  283 (336)
                      ++.+
T Consensus        82 ~~~~   85 (91)
T 2lxi_A           82 PKPK   85 (91)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7754

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.75  E-value=6.6e-19  Score=135.88  Aligned_cols=124  Identities=15%  Similarity=0.266  Sum_probs=81.6

Q ss_pred             eEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEE
Q psy12549         63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKV  142 (336)
Q Consensus        63 g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~  142 (336)
                      -++|.+|...  ..|..|+..+++....|+. .+.  ...+.......++|||+|||.++++++|+++|+.||.|..+.+
T Consensus         5 ~~~~~~~~~~--~~~~~a~~~~~g~~~~g~~-~~~--~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i   79 (135)
T 2lea_A            5 HHHHHHSSGL--VPRGSHMASMTGGQQMGRG-SMS--YGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYI   79 (135)
T ss_dssp             ---------------------------------CC--SCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEEC
T ss_pred             ccccccccCC--CchhhhhhhccCCCCCCCC-CCC--cCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE
Confidence            3578888888  8888899888887665543 112  2233334455689999999999999999999999999999999


Q ss_pred             eeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchh
Q psy12549        143 AQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKE  191 (336)
Q Consensus       143 ~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~  191 (336)
                      +.++ ++.++|||||+|.+.++|.+|+..|++..+.|+.|.|.++.+...
T Consensus        80 ~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~  129 (135)
T 2lea_A           80 PRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  129 (135)
T ss_dssp             CCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCC
T ss_pred             EecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            9986 788999999999999999999999999999999999999887543

>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=99.75  E-value=9.8e-18  Score=118.13  Aligned_cols=79  Identities=29%  Similarity=0.529  Sum_probs=75.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      .+|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|+..|+|..+.|+.|.|.++.++
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            579999999999999999999999999999999985 7889999999999999999999999999999999999998765

>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=99.75  E-value=9.1e-18  Score=119.41  Aligned_cols=81  Identities=30%  Similarity=0.495  Sum_probs=75.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|++.|++..+.|+.|.|.++.
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            45789999999999999999999999999999999996 88899999999999999999999999999999999999987


Q ss_pred             Cc
Q psy12549        188 PR  189 (336)
Q Consensus       188 ~~  189 (336)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            64

>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=99.75  E-value=3.1e-18  Score=128.63  Aligned_cols=104  Identities=22%  Similarity=0.423  Sum_probs=92.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.+  +.++|||||+|.+.++|.+|+..|||..+.|+.|.|.++.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            34578999999999999999999999999999999875  4458999999999999999999999999999999999987


Q ss_pred             CchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCc
Q psy12549        188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGT  229 (336)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~  229 (336)
                      +....                .+++...++++|.++|++||.
T Consensus        84 ~~~~~----------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           84 ANRAF----------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HHHHT----------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             CChhh----------------hhhhHhHhHHHHHHHHHHhCC
Confidence            65432                467888899999999999984

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=1.6e-17  Score=121.47  Aligned_cols=83  Identities=22%  Similarity=0.390  Sum_probs=78.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.+++|.++|||||+|.+.++|.+|++.|++..+.|+.|.|.++.
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   94 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISN   94 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            44678999999999999999999999999999999999988999999999999999999999999999999999999988


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      +..
T Consensus        95 ~~~   97 (100)
T 2do4_A           95 SGP   97 (100)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            764

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.75  E-value=2.3e-18  Score=123.93  Aligned_cols=78  Identities=13%  Similarity=0.331  Sum_probs=72.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCC--eeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCc----eeCCeEEEE
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGS--ILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGM----LLNSKIVFV  183 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~--v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~----~~~~~~i~v  183 (336)
                      .+|||+|||+++|+++|+++|++||.  +..|++++++ +|.++|||||+|.+.++|.+|++.||+.    .++|++|.|
T Consensus        10 ~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V   89 (95)
T 2lkz_A           10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGV   89 (95)
T ss_dssp             CEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEE
Confidence            58999999999999999999999995  6689999987 7899999999999999999999999986    589999999


Q ss_pred             eeccC
Q psy12549        184 GKFIP  188 (336)
Q Consensus       184 ~~~~~  188 (336)
                      .++.+
T Consensus        90 ~~Aks   94 (95)
T 2lkz_A           90 DFAKS   94 (95)
T ss_dssp             EECCC
T ss_pred             EEccC
Confidence            99864

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.75  E-value=2.9e-18  Score=123.40  Aligned_cols=80  Identities=21%  Similarity=0.404  Sum_probs=72.4

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCc--eeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCc----eecCEE
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGT--ITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGK----EVDGKI  272 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~--i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~----~~~g~~  272 (336)
                      ....+|||+|||+.+|+++|+++|++||.  +.++++++  .+|.++|||||+|.+.++|.+|++.|||.    .++|++
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            34588999999999999999999999995  56888876  57889999999999999999999999997    589999


Q ss_pred             EEEeeccc
Q psy12549        273 LYVGRAQK  280 (336)
Q Consensus       273 l~v~~~~~  280 (336)
                      |.|+||+.
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999874

>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=99.75  E-value=9.9e-18  Score=118.10  Aligned_cols=79  Identities=29%  Similarity=0.571  Sum_probs=74.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      .+|||+|||.++++++|+++|+.||+|..+.++.  .++.++|+|||+|.+.++|.+|+..|||..+.|+.|+|.++.++
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            5799999999999999999999999999999886  57888999999999999999999999999999999999999876


Q ss_pred             h
Q psy12549        282 A  282 (336)
Q Consensus       282 ~  282 (336)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.74  E-value=6.8e-19  Score=135.79  Aligned_cols=123  Identities=21%  Similarity=0.263  Sum_probs=78.7

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCcee
Q psy12549        152 GYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTIT  231 (336)
Q Consensus       152 g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~  231 (336)
                      .++|++|++...+..|+..+++....|+.- ..+..+.        ......++|||+|||..+++++|+++|+.||.|.
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~~~~~--------~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~   75 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSYGRPP--------PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVG   75 (135)
T ss_dssp             -------------------------------CCSCCSC--------SSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCS
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCCC-CCcCCCC--------CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEE
Confidence            478899999999999999988876655442 2222221        2223347899999999999999999999999999


Q ss_pred             EEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchh
Q psy12549        232 SYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAE  283 (336)
Q Consensus       232 ~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~  283 (336)
                      .+.++.  .++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.+...
T Consensus        76 ~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~  129 (135)
T 2lea_A           76 DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  129 (135)
T ss_dssp             EEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCC
T ss_pred             EEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999987  4788999999999999999999999999999999999999987643

>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=99.74  E-value=1.1e-17  Score=118.91  Aligned_cols=79  Identities=28%  Similarity=0.556  Sum_probs=73.6

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||..+++++|+++|+.||.|.++.+..  .++.++|+|||+|.+.++|.+|++.|||..+.|+.|+|.++.+
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 (87)
T 3bs9_A            6 HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR   85 (87)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC-
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCC
Confidence            47899999999999999999999999999999987  5788999999999999999999999999999999999999987


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      +
T Consensus        86 k   86 (87)
T 3bs9_A           86 K   86 (87)
T ss_dssp             -
T ss_pred             C
Confidence            5

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

Probab=99.74  E-value=1.8e-18  Score=126.80  Aligned_cols=98  Identities=19%  Similarity=0.332  Sum_probs=83.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCch
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRK  190 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~  190 (336)
                      ++|||+|||.++++++|+++|++||.|..+.++.+    ++|||||+|.+.++|.+|++.|++..+.|+.|.|.++.+..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            47999999999999999999999999999999987    68899999999999999999999999999999999998765


Q ss_pred             hhhHhhhc--cccccceEEEcCCC
Q psy12549        191 EREKELGE--KAKLFTNVYIKNFG  212 (336)
Q Consensus       191 ~~~~~~~~--~~~~~~~l~V~nlp  212 (336)
                      ........  ......++||+||+
T Consensus        77 ~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           77 RRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             CcccCCCCCccccCCCceecCCCC
Confidence            43222111  12224679999986

>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=99.74  E-value=2.2e-17  Score=119.65  Aligned_cols=85  Identities=22%  Similarity=0.389  Sum_probs=79.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||.++++++|+++|+.||.|..+.+..++ +|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.+
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            4789999999999999999999999999999999986 688999999999999999999999999999999999999988


Q ss_pred             chhhhH
Q psy12549        189 RKEREK  194 (336)
Q Consensus       189 ~~~~~~  194 (336)
                      ......
T Consensus        82 ~~~~~~   87 (96)
T 2x1f_A           82 SDISGV   87 (96)
T ss_dssp             SSGGGH
T ss_pred             CCCCCc
Confidence            765543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.3e-17  Score=122.62  Aligned_cols=86  Identities=28%  Similarity=0.468  Sum_probs=80.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       106 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      .....++|||+|||.++++++|+++|+.||.|..|.++.++ ++.++|||||+|.+.++|.+|+..|++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            44557899999999999999999999999999999999996 78899999999999999999999999999999999999


Q ss_pred             eccCchh
Q psy12549        185 KFIPRKE  191 (336)
Q Consensus       185 ~~~~~~~  191 (336)
                      ++.+...
T Consensus        91 ~a~~~~~   97 (103)
T 2cq0_A           91 WAKPSTN   97 (103)
T ss_dssp             ESSCCCC
T ss_pred             ECCCCCC
Confidence            9887653

>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=99.73  E-value=1.7e-17  Score=117.50  Aligned_cols=80  Identities=24%  Similarity=0.420  Sum_probs=74.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            345899999999999999999999999999999999885 7889999999999999999999999999999999999886


Q ss_pred             c
Q psy12549        187 I  187 (336)
Q Consensus       187 ~  187 (336)
                      .
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.73  E-value=1.4e-17  Score=122.84  Aligned_cols=84  Identities=26%  Similarity=0.404  Sum_probs=78.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCC---eEEEEe
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNS---KIVFVG  184 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~---~~i~v~  184 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.+++|.++|||||+|.+.++|.+|++.||+..+.|   +.|.|.
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            45689999999999999999999999999999999999989999999999999999999999999999988   999999


Q ss_pred             eccCchh
Q psy12549        185 KFIPRKE  191 (336)
Q Consensus       185 ~~~~~~~  191 (336)
                      ++.+...
T Consensus        93 ~a~~~~~   99 (105)
T 2dnh_A           93 FADTDKE   99 (105)
T ss_dssp             ESCSSCC
T ss_pred             ECccCcc
Confidence            9887654

>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=99.73  E-value=1.2e-17  Score=118.21  Aligned_cols=79  Identities=30%  Similarity=0.499  Sum_probs=73.7

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||.++++++|+++|++||.|..+.++.  .++.++|+|||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            3458999999999999999999999999999999876  67888999999999999999999999999999999999987


Q ss_pred             c
Q psy12549        279 Q  279 (336)
Q Consensus       279 ~  279 (336)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.73  E-value=1.2e-17  Score=123.74  Aligned_cols=85  Identities=32%  Similarity=0.566  Sum_probs=78.7

Q ss_pred             cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        105 LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       105 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      ......++|||+|||..+++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  100 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV  100 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344556899999999999999999999999999999999986 7889999999999999999999999999999999999


Q ss_pred             eeccCc
Q psy12549        184 GKFIPR  189 (336)
Q Consensus       184 ~~~~~~  189 (336)
                      .++.++
T Consensus       101 ~~a~~k  106 (108)
T 2jrs_A          101 GHVTER  106 (108)
T ss_dssp             ECSCSS
T ss_pred             EEcccC
Confidence            998765

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=3.8e-17  Score=118.21  Aligned_cols=82  Identities=23%  Similarity=0.370  Sum_probs=76.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ....++|||+|||.++++++|+++|+.||.|..+.++.++ ++.++|||||+|.+.++|.+|+..||+..+.|+.|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3456789999999999999999999999999999999987 688999999999999999999999999999999999998


Q ss_pred             ccC
Q psy12549        186 FIP  188 (336)
Q Consensus       186 ~~~  188 (336)
                      +.+
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            764

>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=99.73  E-value=1.1e-17  Score=133.92  Aligned_cols=129  Identities=19%  Similarity=0.270  Sum_probs=77.1

Q ss_pred             EEeCCHHHHHHHHHHhCCceeC--CeEEEEeeccCchhh------------hHhhhccccccceEEEcCCCCCCcHHHHH
Q psy12549        156 VHFETEEAANKSIEKVNGMLLN--SKIVFVGKFIPRKER------------EKELGEKAKLFTNVYIKNFGEDFNDEKLK  221 (336)
Q Consensus       156 V~F~~~~~a~~a~~~l~~~~~~--~~~i~v~~~~~~~~~------------~~~~~~~~~~~~~l~V~nlp~~~t~~~l~  221 (336)
                      ..|.+.++|..|+..+++....  |+.....+.......            ...........++|||+|||..+++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            6789999999999988886654  555554432211100            11111223344789999999999999999


Q ss_pred             HhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchhh
Q psy12549        222 EMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER  284 (336)
Q Consensus       222 ~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~~  284 (336)
                      ++|+.||.|..+.++.  .+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+.++...
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  155 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK  155 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC--
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCC
Confidence            9999999999999987  57889999999999999999999999999999999999999876543

>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=99.73  E-value=2.3e-17  Score=120.31  Aligned_cols=85  Identities=28%  Similarity=0.482  Sum_probs=79.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.++ ++.++|||||+|.+.++|.+|+..||+..+.|+.|.|.++
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            446899999999999999999999999999999999998 8889999999999999999999999999999999999999


Q ss_pred             cCchhh
Q psy12549        187 IPRKER  192 (336)
Q Consensus       187 ~~~~~~  192 (336)
                      .+....
T Consensus        86 ~~~~~~   91 (99)
T 1whw_A           86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCccc
Confidence            887543

>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=99.73  E-value=3.3e-18  Score=122.48  Aligned_cols=81  Identities=20%  Similarity=0.286  Sum_probs=71.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccC--CeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFG--SILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G--~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      .+|||+|||.++++++|+++|+.||  .|.++.++.++ +|.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.
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            4699999999999999999999999  99999999997 88999999999999999999999999999999999999988


Q ss_pred             Cchh
Q psy12549        188 PRKE  191 (336)
Q Consensus       188 ~~~~  191 (336)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7654

>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=99.73  E-value=2.7e-17  Score=119.01  Aligned_cols=81  Identities=25%  Similarity=0.487  Sum_probs=76.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.++.|.++|||||+|.+.++|.+|++.||+..+.|+.|.|.++.
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            34589999999999999999999999999999999999888899999999999999999999999999999999998875


Q ss_pred             C
Q psy12549        188 P  188 (336)
Q Consensus       188 ~  188 (336)
                      .
T Consensus        94 ~   94 (95)
T 2ywk_A           94 S   94 (95)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.73  E-value=2.9e-17  Score=119.04  Aligned_cols=84  Identities=20%  Similarity=0.411  Sum_probs=77.4

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||..+++++|+++|+.||.|.++.+..  .+|.++|||||+|.+.++|.+|++.|+|..++|+.|+|.++.+
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            37899999999999999999999999999999987  4688899999999999999999999999999999999999988


Q ss_pred             chhhHH
Q psy12549        281 KAERTQ  286 (336)
Q Consensus       281 ~~~~~~  286 (336)
                      +.....
T Consensus        82 ~~~~~~   87 (96)
T 2x1f_A           82 SDISGV   87 (96)
T ss_dssp             SSGGGH
T ss_pred             CCCCCc
Confidence            765433

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.73  E-value=2.9e-17  Score=119.79  Aligned_cols=82  Identities=21%  Similarity=0.331  Sum_probs=76.2

Q ss_pred             cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeE--------EEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCce
Q psy12549        105 LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILS--------CKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGML  175 (336)
Q Consensus       105 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~--------~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~  175 (336)
                      ......++|||+|||.++++++|+++|++||.|..        +.++.++ +|.++|||||+|.+.++|.+|++.|||..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            34455689999999999999999999999999999        9999986 78999999999999999999999999999


Q ss_pred             eCCeEEEEeec
Q psy12549        176 LNSKIVFVGKF  186 (336)
Q Consensus       176 ~~~~~i~v~~~  186 (336)
                      +.|+.|.|.++
T Consensus        88 ~~g~~l~V~~A   98 (99)
T 2la6_A           88 FSGNPIKVSFA   98 (99)
T ss_dssp             SSSSBCEEEEC
T ss_pred             eCCcEEEEEec
Confidence            99999999886

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=4.6e-17  Score=117.54  Aligned_cols=80  Identities=24%  Similarity=0.473  Sum_probs=75.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.++ ++.++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
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            456799999999999999999999999999999999987 5889999999999999999999999999999999999886


Q ss_pred             c
Q psy12549        187 I  187 (336)
Q Consensus       187 ~  187 (336)
                      +
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.73  E-value=2.2e-17  Score=132.07  Aligned_cols=124  Identities=19%  Similarity=0.298  Sum_probs=78.0

Q ss_pred             EEeCCcchhhHHHHHhhcCccccC--CeeeEEEeccCC------------------CCcCCCCCceEEEcCCCCCCCHHH
Q psy12549         67 VQLGQPYMLDTERALDTMNFDALK--GRPIRIMWSQRD------------------PSLRKSGVGNVFIKNLDKSIDNKA  126 (336)
Q Consensus        67 V~f~~~~~~~A~~A~~~~~~~~~~--g~~i~v~~~~~~------------------~~~~~~~~~~l~v~nlp~~~t~~~  126 (336)
                      .+|...  ++|..|+..+++....  |+.....+....                  ........++|||+|||..+++++
T Consensus        11 ee~e~~--~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~   88 (165)
T 1rk8_A           11 EEFEVD--EDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDE   88 (165)
T ss_dssp             ---------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHH
T ss_pred             hhhhcc--ccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHH
Confidence            688889  9999999988887654  555554442110                  011223456899999999999999


Q ss_pred             HHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchhh
Q psy12549        127 MYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER  192 (336)
Q Consensus       127 l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~  192 (336)
                      |+++|+.||.|..|.++.++ +|.++|||||+|.+.++|.+|+..|||..+.|+.|.|.++.+....
T Consensus        89 L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~  155 (165)
T 1rk8_A           89 IQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPK  155 (165)
T ss_dssp             HHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC--
T ss_pred             HHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCC
Confidence            99999999999999999986 8889999999999999999999999999999999999998766543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.72  E-value=1.8e-17  Score=119.26  Aligned_cols=78  Identities=19%  Similarity=0.232  Sum_probs=71.4

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCce--ecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKE--VDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~--~~g~~l~v~~~  278 (336)
                      .+.++|||+|||+++++++|+++|++||.|.++.+++    .+|+|||+|.+.++|.+|++.++|..  +.|++|+|.|+
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~----~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S   94 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP----KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYS   94 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET----TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc----CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEec
Confidence            4558899999999999999999999999999999985    37899999999999999999999876  78999999999


Q ss_pred             ccch
Q psy12549        279 QKKA  282 (336)
Q Consensus       279 ~~~~  282 (336)
                      +++.
T Consensus        95 ~~k~   98 (100)
T 3r27_A           95 TSQK   98 (100)
T ss_dssp             SCSC
T ss_pred             cccc
Confidence            8763

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=2.4e-17  Score=119.23  Aligned_cols=83  Identities=30%  Similarity=0.594  Sum_probs=78.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+.++.++ ++.++|||||+|.+.++|.+|++.||+..+.|+.|.|.++.
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            45889999999999999999999999999999999987 68899999999999999999999999999999999999988


Q ss_pred             Cchh
Q psy12549        188 PRKE  191 (336)
Q Consensus       188 ~~~~  191 (336)
                      ++..
T Consensus        84 ~~~~   87 (95)
T 2dnz_A           84 ERLD   87 (95)
T ss_dssp             CCCC
T ss_pred             cccC
Confidence            7654

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=9.9e-18  Score=122.74  Aligned_cols=83  Identities=18%  Similarity=0.184  Sum_probs=76.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..++|||+|||.++|+++|+++|+.||+|.+|.++.++.|.++|||||+|.+.++|.+|+. +++..+.|+.|.|.++..
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            4578999999999999999999999999999999999888999999999999999999999 899999999999998766


Q ss_pred             chhh
Q psy12549        189 RKER  192 (336)
Q Consensus       189 ~~~~  192 (336)
                      ....
T Consensus        89 ~~~~   92 (103)
T 1s79_A           89 YFAK   92 (103)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.72  E-value=1.8e-17  Score=114.84  Aligned_cols=73  Identities=18%  Similarity=0.297  Sum_probs=69.6

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ...|+|+||++.+|+++|+++|.+||+|.++++..    ++|||||+|.++++|++|++.|||..+.|++|+|.+|.
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 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL----NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET----TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC----CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            46799999999999999999999999999999975    59999999999999999999999999999999999994

>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=6.4e-17  Score=121.36  Aligned_cols=87  Identities=28%  Similarity=0.458  Sum_probs=80.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       106 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      .....++|||+|||..+++++|+++|+.||.|..+.++.++ ++.++|||||+|.+.++|.+|++.|++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34556899999999999999999999999999999999996 88899999999999999999999999999999999999


Q ss_pred             eccCchhh
Q psy12549        185 KFIPRKER  192 (336)
Q Consensus       185 ~~~~~~~~  192 (336)
                      ++.+....
T Consensus        91 ~a~~~~~~   98 (115)
T 2dgo_A           91 WATRKPPA   98 (115)
T ss_dssp             ESSCCCCC
T ss_pred             EccCCCCC
Confidence            98876543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=2.8e-17  Score=120.80  Aligned_cols=85  Identities=38%  Similarity=0.671  Sum_probs=79.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       106 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      .....++|||+|||.++++++|+++|+.||.|..+.++.+ +|.++|||||+|.+.++|.+|+..||+..+.|+.|.|.+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3446689999999999999999999999999999999998 888999999999999999999999999999999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.+...
T Consensus        90 a~~~~~   95 (103)
T 2d9p_A           90 AQRKEE   95 (103)
T ss_dssp             CSSCCC
T ss_pred             eccccc
Confidence            887654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=3.3e-17  Score=119.72  Aligned_cols=81  Identities=23%  Similarity=0.432  Sum_probs=76.0

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ..++|||+|||..+++++|+++|+.||.|..+.+.. .++.++|+|||+|.+.++|.+|++.|||..+.|+.|+|.++.+
T Consensus        16 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   95 (100)
T 2do4_A           16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNS   95 (100)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            447899999999999999999999999999999987 6688899999999999999999999999999999999999987


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      +.
T Consensus        96 ~~   97 (100)
T 2do4_A           96 GP   97 (100)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>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=99.72  E-value=3.9e-17  Score=122.54  Aligned_cols=85  Identities=26%  Similarity=0.448  Sum_probs=79.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ....++|||+|||.++++++|+++|+.||.|..+.++.++ ++.++|||||+|.+.++|.+|++.||+..+.|+.|.|.+
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            3455899999999999999999999999999999999997 789999999999999999999999999999999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.+...
T Consensus       102 a~~~~~  107 (115)
T 2cpz_A          102 KRSKND  107 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCc
Confidence            887654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=3.8e-17  Score=117.96  Aligned_cols=79  Identities=23%  Similarity=0.450  Sum_probs=73.7

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|+.||+|..+.+..  .++.++|+|||+|.+.++|.+|++.|||..+.|+.|+|.++
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            4458899999999999999999999999999999987  55788999999999999999999999999999999999997


Q ss_pred             c
Q psy12549        279 Q  279 (336)
Q Consensus       279 ~  279 (336)
                      +
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.3e-17  Score=120.98  Aligned_cols=83  Identities=43%  Similarity=0.744  Sum_probs=77.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEE-EEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~-~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+ .++.++ +|.++|||||+|.+.++|.+|+..||+..+.|+.|.|.++
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            45889999999999999999999999999999 999985 7889999999999999999999999999999999999998


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      .+...
T Consensus        84 ~~~~~   88 (96)
T 1x5t_A           84 FKKDS   88 (96)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            87654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=2.9e-17  Score=121.42  Aligned_cols=83  Identities=24%  Similarity=0.371  Sum_probs=77.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|+..|+|..+.|+.|.|.++
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            456789999999999999999999999999999999987 6889999999999999999999999999999999999998


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .+..
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            7643

>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=2.1e-17  Score=124.04  Aligned_cols=85  Identities=24%  Similarity=0.430  Sum_probs=79.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.+..+++|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.
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            44689999999999999999999999999999999999888999999999999999999999999999999999999988


Q ss_pred             Cchhh
Q psy12549        188 PRKER  192 (336)
Q Consensus       188 ~~~~~  192 (336)
                      +....
T Consensus        85 ~~~~~   89 (116)
T 2fy1_A           85 KPSFQ   89 (116)
T ss_dssp             CSSCS
T ss_pred             CCCCC
Confidence            76543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=4.7e-17  Score=117.71  Aligned_cols=80  Identities=26%  Similarity=0.422  Sum_probs=74.4

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      .+.++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|+|||+|.+.++|.+|+..|||..+.|+.|+|.++
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            3458899999999999999999999999999999986  55788999999999999999999999999999999999998


Q ss_pred             cc
Q psy12549        279 QK  280 (336)
Q Consensus       279 ~~  280 (336)
                      ..
T Consensus        93 ~~   94 (95)
T 2cqc_A           93 SS   94 (95)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.72  E-value=9.4e-18  Score=122.52  Aligned_cols=81  Identities=20%  Similarity=0.296  Sum_probs=75.5

Q ss_pred             cceEEEcCCCC------CCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecC-EEE
Q psy12549        203 FTNVYIKNFGE------DFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG-KIL  273 (336)
Q Consensus       203 ~~~l~V~nlp~------~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g-~~l  273 (336)
                      .++|||+|||.      ++++++|+++|++||.|.++.++.  .+|.++|||||+|.+.++|.+|++.|||..+.| +.|
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            47899999999      999999999999999999999887  568999999999999999999999999999999 999


Q ss_pred             EEeecccchh
Q psy12549        274 YVGRAQKKAE  283 (336)
Q Consensus       274 ~v~~~~~~~~  283 (336)
                      +|.++.++..
T Consensus        86 ~V~~a~~~~~   95 (100)
T 3ns6_A           86 FLYTMKDVER   95 (100)
T ss_dssp             EEEESHHHHH
T ss_pred             EEEECchhhh
Confidence            9999987643

>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=3.1e-17  Score=119.65  Aligned_cols=82  Identities=27%  Similarity=0.450  Sum_probs=76.6

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ..++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   86 (99)
T 1whw_A            7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            448899999999999999999999999999999987  478899999999999999999999999999999999999998


Q ss_pred             cchh
Q psy12549        280 KKAE  283 (336)
Q Consensus       280 ~~~~  283 (336)
                      ++..
T Consensus        87 ~~~~   90 (99)
T 1whw_A           87 IKKE   90 (99)
T ss_dssp             CCST
T ss_pred             CCcc
Confidence            8754

>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=99.71  E-value=6.7e-17  Score=118.73  Aligned_cols=83  Identities=28%  Similarity=0.506  Sum_probs=76.6

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++...+.++|+|||+|.+.++|.+|+..|||..+.|+.|+|.++.+
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 (103)
T 2cq3_A           13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA   92 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccc
Confidence            34589999999999999999999999999999999986556899999999999999999999999999999999999987


Q ss_pred             chh
Q psy12549        281 KAE  283 (336)
Q Consensus       281 ~~~  283 (336)
                      +..
T Consensus        93 ~~~   95 (103)
T 2cq3_A           93 RVM   95 (103)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=3.4e-17  Score=118.49  Aligned_cols=82  Identities=27%  Similarity=0.651  Sum_probs=76.4

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ..++|||+|||..+++++|+++|+.||.|..+.+..  .++.++|+|||+|.+.++|.+|++.|||..+.|+.|+|.++.
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            347899999999999999999999999999999988  468889999999999999999999999999999999999998


Q ss_pred             cchh
Q psy12549        280 KKAE  283 (336)
Q Consensus       280 ~~~~  283 (336)
                      ++..
T Consensus        84 ~~~~   87 (95)
T 2dnz_A           84 ERLD   87 (95)
T ss_dssp             CCCC
T ss_pred             cccC
Confidence            7643

>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=99.71  E-value=3.9e-17  Score=120.46  Aligned_cols=86  Identities=24%  Similarity=0.491  Sum_probs=79.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       106 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      .....++|||+|||.++++++|+++|+.||.|..+.++.++ ++.++|||||+|.+.++|.+|+..|++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34556899999999999999999999999999999999987 78899999999999999999999999999999999999


Q ss_pred             eccCchh
Q psy12549        185 KFIPRKE  191 (336)
Q Consensus       185 ~~~~~~~  191 (336)
                      ++.+...
T Consensus        91 ~a~~~~~   97 (105)
T 1x5u_A           91 KASAHNK   97 (105)
T ss_dssp             ETTTTSC
T ss_pred             ECCCCCc
Confidence            9877643

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.71  E-value=6e-18  Score=123.57  Aligned_cols=81  Identities=22%  Similarity=0.333  Sum_probs=76.5

Q ss_pred             CceEEEcCCCC------CCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCC-eEE
Q psy12549        110 VGNVFIKNLDK------SIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNS-KIV  181 (336)
Q Consensus       110 ~~~l~v~nlp~------~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~-~~i  181 (336)
                      .++|||+|||.      ++++++|+++|++||.|.++.++.++ +|.++|||||+|.+.++|.+|++.|||..+.| +.|
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            57899999999      99999999999999999999999998 59999999999999999999999999999999 999


Q ss_pred             EEeeccCch
Q psy12549        182 FVGKFIPRK  190 (336)
Q Consensus       182 ~v~~~~~~~  190 (336)
                      .|.++.+..
T Consensus        86 ~V~~a~~~~   94 (100)
T 3ns6_A           86 FLYTMKDVE   94 (100)
T ss_dssp             EEEESHHHH
T ss_pred             EEEECchhh
Confidence            999987654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.8e-17  Score=120.54  Aligned_cols=80  Identities=15%  Similarity=0.288  Sum_probs=72.4

Q ss_pred             ccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhC--CceecCEEEEEee
Q psy12549        200 AKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN--GKEVDGKILYVGR  277 (336)
Q Consensus       200 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~--g~~~~g~~l~v~~  277 (336)
                      ....++|||+|||+++++++|+++|++||.|.++.+++.    +|||||+|.+.++|.+|++.++  +..+.|++|+|.+
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   88 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF   88 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            344589999999999999999999999999999999864    8999999999999999999886  4789999999999


Q ss_pred             cccchh
Q psy12549        278 AQKKAE  283 (336)
Q Consensus       278 ~~~~~~  283 (336)
                      +.++..
T Consensus        89 A~~~~~   94 (105)
T 1sjq_A           89 SNHKEL   94 (105)
T ss_dssp             CSSSSC
T ss_pred             cCCCCC
Confidence            987644

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=5.3e-17  Score=118.39  Aligned_cols=83  Identities=20%  Similarity=0.432  Sum_probs=77.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.++ ++.++|||||+|.+.++|.+|++ +++..+.|+.|.|.++
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            456899999999999999999999999999999999986 68899999999999999999999 9999999999999998


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      .++..
T Consensus        87 ~~~~~   91 (99)
T 2dgs_A           87 EPRDS   91 (99)
T ss_dssp             CCCCC
T ss_pred             CCCcc
Confidence            87654

>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=99.71  E-value=1.2e-16  Score=117.28  Aligned_cols=85  Identities=28%  Similarity=0.513  Sum_probs=77.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       106 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      .....++|||+|||.++++++|+++|+.||.|..+.++.++.+ ++|||||+|.+.++|.+|+..|++..+.|+.|.|.+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3445689999999999999999999999999999999998755 899999999999999999999999999999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.+...
T Consensus        90 a~~~~~   95 (103)
T 2cq3_A           90 ATARVM   95 (103)
T ss_dssp             CCSSCC
T ss_pred             cccCCC
Confidence            887643

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=4.9e-17  Score=119.47  Aligned_cols=83  Identities=28%  Similarity=0.507  Sum_probs=76.9

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (103)
T 2cq0_A           13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   92 (103)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEC
Confidence            3458899999999999999999999999999999987  57889999999999999999999999999999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus        93 ~~~~~   97 (103)
T 2cq0_A           93 KPSTN   97 (103)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87643

>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=99.71  E-value=2.3e-17  Score=122.15  Aligned_cols=83  Identities=29%  Similarity=0.634  Sum_probs=76.9

Q ss_pred             ccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEee
Q psy12549        200 AKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR  277 (336)
Q Consensus       200 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~  277 (336)
                      ....++|||+|||..+++++|+++|+.||.|..+.++.  .+|.++|||||+|.+.++|.+|++.|+|..+.|+.|+|.+
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34458999999999999999999999999999999986  6788899999999999999999999999999999999999


Q ss_pred             cccch
Q psy12549        278 AQKKA  282 (336)
Q Consensus       278 ~~~~~  282 (336)
                      +.++.
T Consensus       103 a~~k~  107 (108)
T 2jrs_A          103 VTERT  107 (108)
T ss_dssp             SCSSC
T ss_pred             cccCC
Confidence            98763

>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=99.71  E-value=4.5e-17  Score=119.65  Aligned_cols=83  Identities=20%  Similarity=0.344  Sum_probs=76.6

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.+....+.++|||||+|.+.++|.+|+..|+|..+.|+.|+|.++.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   92 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATT   92 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCC
Confidence            34589999999999999999999999999999999986666799999999999999999999999999999999999987


Q ss_pred             chh
Q psy12549        281 KAE  283 (336)
Q Consensus       281 ~~~  283 (336)
                      +..
T Consensus        93 ~~~   95 (103)
T 2cqi_A           93 PSS   95 (103)
T ss_dssp             TTC
T ss_pred             Ccc
Confidence            643

>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=99.71  E-value=9.1e-17  Score=114.17  Aligned_cols=79  Identities=24%  Similarity=0.565  Sum_probs=72.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ....++|||+|||.++++++|+++|++||.|..+.++.++ +|.++|||||+|.+.++|.+|++ +++..+.|+.|.|.+
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            3456899999999999999999999999999999999997 68999999999999999999997 588899999999976


Q ss_pred             c
Q psy12549        186 F  186 (336)
Q Consensus       186 ~  186 (336)
                      +
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=4.4e-17  Score=119.49  Aligned_cols=84  Identities=24%  Similarity=0.423  Sum_probs=78.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.++ ++.++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
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            456889999999999999999999999999999999986 7889999999999999999999999999999999999998


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      .+...
T Consensus        90 ~~~~~   94 (102)
T 2cqb_A           90 KPMRI   94 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>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=2.9e-17  Score=120.71  Aligned_cols=86  Identities=15%  Similarity=0.295  Sum_probs=79.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       106 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      .....++|||+|||.++++++|+++|+.||.|..+.++.++ ++.++|||||+|.+.++|.+|+..||+..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34456899999999999999999999999999999999987 68899999999999999999999999999999999999


Q ss_pred             eccCchh
Q psy12549        185 KFIPRKE  191 (336)
Q Consensus       185 ~~~~~~~  191 (336)
                      ++.+...
T Consensus        89 ~a~~~~~   95 (103)
T 2dnm_A           89 VARYGRR   95 (103)
T ss_dssp             ECSSCCS
T ss_pred             ECCcCCC
Confidence            9886543

>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=99.71  E-value=9e-17  Score=118.92  Aligned_cols=80  Identities=26%  Similarity=0.451  Sum_probs=76.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.+++|.++|||||+|.+.++|.+|++.|++..+.|+.|.|.++.
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            44689999999999999999999999999999999999999999999999999999999999999999999999998874

>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=99.71  E-value=6e-18  Score=121.11  Aligned_cols=80  Identities=25%  Similarity=0.359  Sum_probs=69.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCC--ceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYG--TITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g--~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      .+|||+|||.++++++|+++|+.||  .|.++.++.  .+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  999999887  588999999999999999999999999999999999999998


Q ss_pred             cchh
Q psy12549        280 KKAE  283 (336)
Q Consensus       280 ~~~~  283 (336)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7644

>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=99.71  E-value=3e-17  Score=116.99  Aligned_cols=82  Identities=21%  Similarity=0.437  Sum_probs=75.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCC-cccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGN-SKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~-~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+.++.++ ++. ++|||||+|.+.++|.+|+..|||..+.|+.|.|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            35789999999999999999999999999999999887 333 8899999999999999999999999999999999998


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.71  E-value=1.3e-16  Score=117.15  Aligned_cols=84  Identities=21%  Similarity=0.352  Sum_probs=77.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ....++|||+|||..+++++|+++|+.||.|..|.++.++.+ ++|||||+|.+.++|.+|+..|++..+.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            345689999999999999999999999999999999998644 6899999999999999999999999999999999998


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      .+...
T Consensus        91 ~~~~~   95 (103)
T 2cqi_A           91 TTPSS   95 (103)
T ss_dssp             CCTTC
T ss_pred             CCCcc
Confidence            87653

>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=99.71  E-value=4.6e-17  Score=121.15  Aligned_cols=83  Identities=22%  Similarity=0.368  Sum_probs=77.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|+..|+|..+.|+.|.|.++
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            456789999999999999999999999999999999986 7889999999999999999999999999999999999998


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .+..
T Consensus       104 ~~~~  107 (110)
T 1oo0_B          104 FVKG  107 (110)
T ss_dssp             EESS
T ss_pred             ccCC
Confidence            7654

>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=99.71  E-value=6.1e-17  Score=115.60  Aligned_cols=79  Identities=18%  Similarity=0.389  Sum_probs=74.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|+ .+++..+.|+.|.|.++.+
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            4789999999999999999999999999999999987 8889999999999999999999 8999999999999999876


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.71  E-value=2.7e-17  Score=118.27  Aligned_cols=81  Identities=30%  Similarity=0.500  Sum_probs=76.6

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ..++|||+|||..+++++|+++|+.||.|..+.+...++.++|+|||+|.+.++|.+|++.|||..+.|+.|+|.++.+.
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            44889999999999999999999999999999998888889999999999999999999999999999999999999876


Q ss_pred             h
Q psy12549        282 A  282 (336)
Q Consensus       282 ~  282 (336)
                      .
T Consensus        87 ~   87 (92)
T 2dgv_A           87 S   87 (92)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.71  E-value=5.2e-17  Score=117.50  Aligned_cols=80  Identities=26%  Similarity=0.483  Sum_probs=74.4

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ...++|||+|||..+++++|+++|+.||+|..+.+.. .++.++|+|||+|.+.++|.+|++.|||..+.|+.|+|.++.
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            3448899999999999999999999999999999987 558889999999999999999999999999999999999986


Q ss_pred             c
Q psy12549        280 K  280 (336)
Q Consensus       280 ~  280 (336)
                      .
T Consensus        94 ~   94 (95)
T 2ywk_A           94 S   94 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=3.3e-17  Score=120.39  Aligned_cols=82  Identities=50%  Similarity=0.831  Sum_probs=77.1

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ..++|||+|||..+++++|+++|+.||.|..+.+...++.+++||||+|.+.++|.+|+..|||..+.|+.|.|.++.++
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 (103)
T 2d9p_A           14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRK   93 (103)
T ss_dssp             SCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeccc
Confidence            45889999999999999999999999999999998878889999999999999999999999999999999999999876


Q ss_pred             hh
Q psy12549        282 AE  283 (336)
Q Consensus       282 ~~  283 (336)
                      ..
T Consensus        94 ~~   95 (103)
T 2d9p_A           94 EE   95 (103)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=3.2e-17  Score=121.68  Aligned_cols=82  Identities=28%  Similarity=0.517  Sum_probs=76.3

Q ss_pred             ccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        200 AKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       200 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ....++|||+|||..+++++|+++|+.||.|..+.+....+.++|||||+|.+.++|.+|++.|+|..+.|+.|+|.++.
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  105 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT  105 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34458999999999999999999999999999999988666789999999999999999999999999999999999998


Q ss_pred             cc
Q psy12549        280 KK  281 (336)
Q Consensus       280 ~~  281 (336)
                      ++
T Consensus       106 ~~  107 (109)
T 2err_A          106 AR  107 (109)
T ss_dssp             CS
T ss_pred             CC
Confidence            75

>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=99.71  E-value=9.3e-17  Score=119.69  Aligned_cols=84  Identities=29%  Similarity=0.460  Sum_probs=78.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhC------CceeCCeE
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVN------GMLLNSKI  180 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~------~~~~~~~~  180 (336)
                      ...++|||+|||.++++++|+++|+.||.|..|.++.++ +|.++|||||+|.+.++|.+|+..++      +..+.|+.
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            456789999999999999999999999999999999987 68899999999999999999999999      99999999


Q ss_pred             EEEeeccCchh
Q psy12549        181 VFVGKFIPRKE  191 (336)
Q Consensus       181 i~v~~~~~~~~  191 (336)
                      |.|.++.++..
T Consensus        93 l~v~~a~~~~~  103 (111)
T 1x4h_A           93 LKVDLAVTRDE  103 (111)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCcc
Confidence            99999887644

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=2.7e-17  Score=121.56  Aligned_cols=82  Identities=21%  Similarity=0.368  Sum_probs=76.0

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.+..  .+|.++|+|||+|.+.++|.+|+..|||..+.|+.|.|.++
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            3447899999999999999999999999999999986  56888999999999999999999999999999999999999


Q ss_pred             ccch
Q psy12549        279 QKKA  282 (336)
Q Consensus       279 ~~~~  282 (336)
                      .++.
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            8763

>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=3.5e-17  Score=120.08  Aligned_cols=84  Identities=25%  Similarity=0.477  Sum_probs=78.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.++ ++.++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
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            456899999999999999999999999999999999986 7789999999999999999999999999999999999998


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      .+...
T Consensus        90 ~~~~~   94 (102)
T 1x5s_A           90 GKSSD   94 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            77653

>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=99.70  E-value=7.6e-17  Score=119.32  Aligned_cols=80  Identities=24%  Similarity=0.383  Sum_probs=74.7

Q ss_pred             ccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        200 AKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       200 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ....++|||+|||..+++++|+++|+.||.|..+.++. .+|.++|+|||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            34558999999999999999999999999999999887 67888999999999999999999999999999999999997


Q ss_pred             c
Q psy12549        279 Q  279 (336)
Q Consensus       279 ~  279 (336)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=5.6e-17  Score=120.34  Aligned_cols=85  Identities=28%  Similarity=0.525  Sum_probs=77.4

Q ss_pred             CcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        104 SLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       104 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      .......++|||+|||.++++++|+++|+.||.|..+.+..++.+ ++|||||+|.+.++|.+|+..|+|..+.|+.|.|
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~-~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTB-CTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCC-CceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            344456789999999999999999999999999999999988644 8999999999999999999999999999999999


Q ss_pred             eeccCc
Q psy12549        184 GKFIPR  189 (336)
Q Consensus       184 ~~~~~~  189 (336)
                      .++.++
T Consensus       102 ~~a~~~  107 (109)
T 2err_A          102 NNATAR  107 (109)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            998764

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=7.4e-17  Score=119.37  Aligned_cols=86  Identities=19%  Similarity=0.436  Sum_probs=79.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeC-C-CCCcccEEEEEeCCHHHHHHHHHHh-CCceeCCeEEE
Q psy12549        106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-E-QGNSKGYGFVHFETEEAANKSIEKV-NGMLLNSKIVF  182 (336)
Q Consensus       106 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~-~-~~~~~g~afV~F~~~~~a~~a~~~l-~~~~~~~~~i~  182 (336)
                      .....++|||+|||..+++++|+++|+.||.|..|.++.+ + ++.++|||||+|.+.++|.+|+..| |+..+.|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3445689999999999999999999999999999999998 3 7889999999999999999999999 99999999999


Q ss_pred             EeeccCchh
Q psy12549        183 VGKFIPRKE  191 (336)
Q Consensus       183 v~~~~~~~~  191 (336)
                      |.++.+...
T Consensus        91 v~~a~~~~~   99 (107)
T 2cph_A           91 LEWADSEVT   99 (107)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999887644

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=4.5e-17  Score=119.44  Aligned_cols=83  Identities=29%  Similarity=0.454  Sum_probs=76.6

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++
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            3458899999999999999999999999999999877  56788999999999999999999999999999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus        90 ~~~~~   94 (102)
T 2cqb_A           90 KPMRI   94 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87643

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=4.9e-17  Score=118.33  Aligned_cols=82  Identities=35%  Similarity=0.528  Sum_probs=75.0

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--C---CCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEe
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--N---DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG  276 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~---~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~  276 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+.+..  .   ++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.
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            347899999999999999999999999999999987  2   34889999999999999999999999999999999999


Q ss_pred             ecccchh
Q psy12549        277 RAQKKAE  283 (336)
Q Consensus       277 ~~~~~~~  283 (336)
                      ++.++..
T Consensus        84 ~a~~~~~   90 (98)
T 2cpf_A           84 ISERATK   90 (98)
T ss_dssp             CSSCSSC
T ss_pred             EccCCCC
Confidence            9987643

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=5.1e-17  Score=118.10  Aligned_cols=79  Identities=16%  Similarity=0.233  Sum_probs=71.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCC--ceeCCeEEEEee
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG--MLLNSKIVFVGK  185 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~--~~~~~~~i~v~~  185 (336)
                      ...++|||+|||+++|+++|+++|++||.|.++.++++     +|||||+|.+.++|..|++.+++  ..+.|++|.|.+
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   88 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF   88 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            44588999999999999999999999999999999875     68999999999999999998864  789999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.++..
T Consensus        89 A~~~~~   94 (105)
T 1sjq_A           89 SNHKEL   94 (105)
T ss_dssp             CSSSSC
T ss_pred             cCCCCC
Confidence            876543

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.70  E-value=5.5e-17  Score=128.00  Aligned_cols=83  Identities=22%  Similarity=0.343  Sum_probs=77.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccC--CeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFG--SILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G--~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ..++|||+|||.++++++|+++|+.||  .|..+.++.++ +|.++|||||+|.+.++|.+|+..|||..+.|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            457999999999999999999999999  99999999997 899999999999999999999999999999999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.+...
T Consensus       134 a~~~~~  139 (156)
T 3n9u_C          134 ATRQNL  139 (156)
T ss_dssp             CCHHHH
T ss_pred             cCCCcc
Confidence            876543

>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=99.70  E-value=1.1e-16  Score=115.95  Aligned_cols=81  Identities=16%  Similarity=0.245  Sum_probs=75.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMY----DTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~----~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      ...++|||+|||.++++++|+    ++|++||.|.++.++.++.+  +|||||+|.+.++|.+|++.|||..+.|+.|.|
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            345789999999999999999    99999999999999988755  889999999999999999999999999999999


Q ss_pred             eeccCch
Q psy12549        184 GKFIPRK  190 (336)
Q Consensus       184 ~~~~~~~  190 (336)
                      .++.+..
T Consensus        85 ~~a~~~~   91 (96)
T 2dgx_A           85 SLATGAS   91 (96)
T ss_dssp             EECCCSS
T ss_pred             EEcCCCC
Confidence            9987653

>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=3.2e-17  Score=118.88  Aligned_cols=82  Identities=24%  Similarity=0.502  Sum_probs=76.1

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEE-EEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSY-RVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~-~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ..++|||+|||..+++++|+++|+.||.|..+ .++.  .++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
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            34889999999999999999999999999999 8887  67888999999999999999999999999999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus        84 ~~~~~   88 (96)
T 1x5t_A           84 FKKDS   88 (96)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            87643

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=7.2e-17  Score=117.43  Aligned_cols=83  Identities=29%  Similarity=0.532  Sum_probs=76.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCC--C--CcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ--G--NSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~--~--~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+.+..++.  |  .++|||||+|.+.++|.+|+..||+..+.|+.|.|.
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            457899999999999999999999999999999998763  3  789999999999999999999999999999999999


Q ss_pred             eccCchh
Q psy12549        185 KFIPRKE  191 (336)
Q Consensus       185 ~~~~~~~  191 (336)
                      ++.+...
T Consensus        84 ~a~~~~~   90 (98)
T 2cpf_A           84 ISERATK   90 (98)
T ss_dssp             CSSCSSC
T ss_pred             EccCCCC
Confidence            9877643

>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=6.2e-17  Score=118.01  Aligned_cols=82  Identities=22%  Similarity=0.501  Sum_probs=75.8

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|++ +++..+.|+.|.|.++
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            3458999999999999999999999999999999987  568889999999999999999998 9999999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus        87 ~~~~~   91 (99)
T 2dgs_A           87 EPRDS   91 (99)
T ss_dssp             CCCCC
T ss_pred             CCCcc
Confidence            87643

>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=99.70  E-value=5e-17  Score=120.95  Aligned_cols=82  Identities=26%  Similarity=0.389  Sum_probs=76.2

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.  .+|.++|+|||+|.+.++|.+|+..|||..+.|+.|.|.++
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            3457899999999999999999999999999999976  57888999999999999999999999999999999999999


Q ss_pred             ccch
Q psy12549        279 QKKA  282 (336)
Q Consensus       279 ~~~~  282 (336)
                      .++.
T Consensus       104 ~~~~  107 (110)
T 1oo0_B          104 FVKG  107 (110)
T ss_dssp             EESS
T ss_pred             ccCC
Confidence            8764

>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=8.2e-17  Score=111.58  Aligned_cols=73  Identities=22%  Similarity=0.328  Sum_probs=68.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..-|||+||++.+|+++|+++|.+||+|.++.+..     ++|||||+|.++++|.+|++.||+..+.|++|.|..+.
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 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            46799999999999999999999999999999875     58999999999999999999999999999999998873

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=2e-16  Score=118.49  Aligned_cols=83  Identities=29%  Similarity=0.388  Sum_probs=77.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.+++|.++|||||+|.+.++|.+|+..||+..+.|+.|.|.++.
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            34578999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      ...
T Consensus        93 ~~~   95 (114)
T 2do0_A           93 RAL   95 (114)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=1.6e-16  Score=113.95  Aligned_cols=80  Identities=16%  Similarity=0.331  Sum_probs=75.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||.++++++|+++|+.| .|..+.++.+.+|.++|||||+|.+.++|.+|+. +|+..+.|+.|.|.++.
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            456899999999999999999999999 8999999999889999999999999999999999 99999999999999987


Q ss_pred             Cc
Q psy12549        188 PR  189 (336)
Q Consensus       188 ~~  189 (336)
                      +.
T Consensus        86 ~~   87 (91)
T 2dgw_A           86 SG   87 (91)
T ss_dssp             SC
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=99.70  E-value=5.6e-17  Score=121.66  Aligned_cols=82  Identities=33%  Similarity=0.560  Sum_probs=76.4

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.
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~  103 (115)
T 2cpz_A           24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR  103 (115)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            447899999999999999999999999999999987  478899999999999999999999999999999999999998


Q ss_pred             cchh
Q psy12549        280 KKAE  283 (336)
Q Consensus       280 ~~~~  283 (336)
                      ++..
T Consensus       104 ~~~~  107 (115)
T 2cpz_A          104 SKND  107 (115)
T ss_dssp             CSCC
T ss_pred             CCCc
Confidence            7643

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.70  E-value=9.9e-17  Score=120.31  Aligned_cols=83  Identities=29%  Similarity=0.550  Sum_probs=77.0

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|++.|+|..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   92 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            3458899999999999999999999999999999987  47889999999999999999999999999999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus        93 ~~~~~   97 (115)
T 2dgo_A           93 TRKPP   97 (115)
T ss_dssp             SCCCC
T ss_pred             cCCCC
Confidence            87643

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=7e-17  Score=117.74  Aligned_cols=83  Identities=22%  Similarity=0.386  Sum_probs=77.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCee-EEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeE----E
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSIL-SCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKI----V  181 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~-~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~----i  181 (336)
                      ...++|||+|||.++++++|+++|++||.|. .+.++.++ +|.++|||||+|.+.++|.+|++.||+..+.|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            3468999999999999999999999999999 99999997 7889999999999999999999999999999999    9


Q ss_pred             EEeeccCch
Q psy12549        182 FVGKFIPRK  190 (336)
Q Consensus       182 ~v~~~~~~~  190 (336)
                      .|.++.+..
T Consensus        87 ~v~~a~~~~   95 (99)
T 2div_A           87 KLNYATYSG   95 (99)
T ss_dssp             CEEETTCCS
T ss_pred             EEeecCCCC
Confidence            999987653

>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=99.70  E-value=7e-17  Score=119.31  Aligned_cols=86  Identities=21%  Similarity=0.332  Sum_probs=78.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCcee---CCeEE
Q psy12549        106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLL---NSKIV  181 (336)
Q Consensus       106 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~---~~~~i  181 (336)
                      .....++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|++.||+..+   .|+.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            33456899999999999999999999999999999999987 688999999999999999999999999987   89999


Q ss_pred             EEeeccCchh
Q psy12549        182 FVGKFIPRKE  191 (336)
Q Consensus       182 ~v~~~~~~~~  191 (336)
                      .|.++.+...
T Consensus        89 ~v~~a~~~~~   98 (106)
T 2dgp_A           89 QVKPADSESR   98 (106)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEECCcccc
Confidence            9999877643

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=5.8e-17  Score=119.31  Aligned_cols=84  Identities=31%  Similarity=0.532  Sum_probs=78.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhc-cCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCce-eCCeEEEEee
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSA-FGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGML-LNSKIVFVGK  185 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~-~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~-~~~~~i~v~~  185 (336)
                      ...++|||+|||.++++++|+++|+. ||.|..+.++.+++|.++|||||+|.+.++|.+|++.|++.. +.|+.|.|.+
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            44588999999999999999999999 999999999999988999999999999999999999999999 9999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.+...
T Consensus        87 a~~~~~   92 (104)
T 2dhg_A           87 AIPKAS   92 (104)
T ss_dssp             CCCCCS
T ss_pred             ccCCCc
Confidence            876654

>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=99.69  E-value=7.8e-17  Score=119.98  Aligned_cols=81  Identities=23%  Similarity=0.322  Sum_probs=74.1

Q ss_pred             ccceEEEcCCCCCCcHHHHH---HhhccCCceeEEEEeCCC-----CccceEEEEEeCCHHHHHHHHHHhCCceecCEEE
Q psy12549        202 LFTNVYIKNFGEDFNDEKLK---EMFEPYGTITSYRVMNND-----GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL  273 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~---~~f~~~g~i~~~~i~~~~-----~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l  273 (336)
                      ..++|||+|||.++++++|+   ++|++||+|..+.+....     +.++|||||+|.+.++|++|++.|||..+.|+.|
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            34789999999999999999   999999999999998732     2567999999999999999999999999999999


Q ss_pred             EEeecccch
Q psy12549        274 YVGRAQKKA  282 (336)
Q Consensus       274 ~v~~~~~~~  282 (336)
                      +|.++.++.
T Consensus        94 ~V~~a~~k~  102 (111)
T 2cpi_A           94 KASLGTTKY  102 (111)
T ss_dssp             EEESCCCCS
T ss_pred             EEEeccccc
Confidence            999998774

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.69  E-value=1.2e-16  Score=114.91  Aligned_cols=77  Identities=18%  Similarity=0.227  Sum_probs=70.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCce--eCCeEEEEee
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGML--LNSKIVFVGK  185 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~--~~~~~i~v~~  185 (336)
                      ..+++|||+|||.++|+++|+++|++||.|.++.+++     ++|+|||+|.+.++|.+|++.|++..  +.|++|.|.+
T Consensus        19 ~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           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNY   93 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc-----CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEe
Confidence            4457899999999999999999999999999999985     37899999999999999999998865  7899999999


Q ss_pred             ccCc
Q psy12549        186 FIPR  189 (336)
Q Consensus       186 ~~~~  189 (336)
                      +.++
T Consensus        94 S~~k   97 (100)
T 3r27_A           94 STSQ   97 (100)
T ss_dssp             CSCS
T ss_pred             cccc
Confidence            8764

>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=99.69  E-value=6.4e-17  Score=119.07  Aligned_cols=85  Identities=26%  Similarity=0.534  Sum_probs=79.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||..+++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.+
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            4789999999999999999999999999999999986 788999999999999999999999999999999999999988


Q ss_pred             chhhhH
Q psy12549        189 RKEREK  194 (336)
Q Consensus       189 ~~~~~~  194 (336)
                      ......
T Consensus        88 ~~~~~~   93 (104)
T 1p1t_A           88 EKNKEE   93 (104)
T ss_dssp             TTHHHH
T ss_pred             ccchhh
Confidence            766543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.69  E-value=7.7e-17  Score=117.50  Aligned_cols=80  Identities=24%  Similarity=0.457  Sum_probs=73.9

Q ss_pred             ccccceEEEcCCCCCCcHHHHHHhhccCCceeE--------EEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceec
Q psy12549        200 AKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS--------YRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD  269 (336)
Q Consensus       200 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~--------~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~  269 (336)
                      ....++|||+|||.++++++|+++|+.||.|..        +.+..  .+|.++|+|||+|.+.++|.+|++.|||..+.
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            344589999999999999999999999999999        88876  57889999999999999999999999999999


Q ss_pred             CEEEEEeecc
Q psy12549        270 GKILYVGRAQ  279 (336)
Q Consensus       270 g~~l~v~~~~  279 (336)
                      |+.|+|.+|+
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999874

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=3.7e-17  Score=119.64  Aligned_cols=78  Identities=26%  Similarity=0.288  Sum_probs=72.8

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      .++|||+|||.++|+++|+++|++||+|.++.++. ..|.++|||||+|.+.++|.+|+. ++|..+.|+.|.|.++...
T Consensus        11 ~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~~   89 (103)
T 1s79_A           11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKDDY   89 (103)
T ss_dssp             GGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEchHH
Confidence            47899999999999999999999999999999988 448899999999999999999999 8999999999999987654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.69  E-value=1e-16  Score=115.17  Aligned_cols=82  Identities=30%  Similarity=0.481  Sum_probs=76.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.+..+ +|.++|||||+|.+.++|.+|+..|++..+.|+.|.|.++.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            34589999999999999999999999999999999984 77899999999999999999999999999999999999987


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      +..
T Consensus        85 ~~~   87 (92)
T 2dgv_A           85 NAS   87 (92)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            754

>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=99.69  E-value=4.4e-17  Score=125.12  Aligned_cols=83  Identities=13%  Similarity=0.101  Sum_probs=76.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCC---eeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGS---ILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~---v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      ....++|||+|||.++|+++|+++|+.||.   |..|.++.++.|.++|||||+|.+.++|++|++ +|+..+.|+.|.|
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            345689999999999999999999999999   889999999889999999999999999999999 9999999999999


Q ss_pred             eeccCch
Q psy12549        184 GKFIPRK  190 (336)
Q Consensus       184 ~~~~~~~  190 (336)
                      .++.+..
T Consensus       120 ~~a~~~e  126 (136)
T 2hgl_A          120 FKSHRTE  126 (136)
T ss_dssp             EECCHHH
T ss_pred             EECChHH
Confidence            8876443

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.69  E-value=9.3e-17  Score=121.04  Aligned_cols=80  Identities=30%  Similarity=0.470  Sum_probs=75.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ....++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|++.||+..+.|+.|.|.+
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            3456899999999999999999999999999999999986 788999999999999999999999999999999999987


Q ss_pred             c
Q psy12549        186 F  186 (336)
Q Consensus       186 ~  186 (336)
                      +
T Consensus       117 a  117 (118)
T 2khc_A          117 K  117 (118)
T ss_dssp             C
T ss_pred             c
Confidence            6

>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=99.69  E-value=7.1e-17  Score=123.34  Aligned_cols=84  Identities=24%  Similarity=0.398  Sum_probs=78.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ....++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|++.|++..+.|+.|.|.+
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            3456899999999999999999999999999999999986 688999999999999999999999999999999999999


Q ss_pred             ccCch
Q psy12549        186 FIPRK  190 (336)
Q Consensus       186 ~~~~~  190 (336)
                      +.++.
T Consensus       123 a~~~~  127 (129)
T 2kxn_B          123 SITKR  127 (129)
T ss_dssp             CSSSS
T ss_pred             ecCCC
Confidence            87654

>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=7.6e-17  Score=118.90  Aligned_cols=82  Identities=26%  Similarity=0.447  Sum_probs=76.2

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecC---EEEEEee
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG---KILYVGR  277 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g---~~l~v~~  277 (336)
                      ..++|||+|||..+++++|+++|+.||.|..+.+.. .++.++|||||+|.+.++|.+|++.|||..+.|   +.|+|.+
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~   93 (105)
T 2dnh_A           14 RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKF   93 (105)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEE
Confidence            458999999999999999999999999999999987 678889999999999999999999999999998   9999999


Q ss_pred             cccchh
Q psy12549        278 AQKKAE  283 (336)
Q Consensus       278 ~~~~~~  283 (336)
                      +.++..
T Consensus        94 a~~~~~   99 (105)
T 2dnh_A           94 ADTDKE   99 (105)
T ss_dssp             SCSSCC
T ss_pred             CccCcc
Confidence            987643

>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=99.69  E-value=7.3e-17  Score=118.76  Aligned_cols=83  Identities=30%  Similarity=0.631  Sum_probs=77.2

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||..+++++|+++|+.||.|..+.+..  .+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.+
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            37899999999999999999999999999999887  5788999999999999999999999999999999999999988


Q ss_pred             chhhH
Q psy12549        281 KAERT  285 (336)
Q Consensus       281 ~~~~~  285 (336)
                      +....
T Consensus        88 ~~~~~   92 (104)
T 1p1t_A           88 EKNKE   92 (104)
T ss_dssp             TTHHH
T ss_pred             ccchh
Confidence            75544

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

Probab=99.69  E-value=4.9e-18  Score=124.39  Aligned_cols=100  Identities=27%  Similarity=0.415  Sum_probs=82.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchh
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAE  283 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~  283 (336)
                      ++|||+|||.++++++|+++|++||+|..+.+...   ++|+|||+|.+.++|.+|++.|+|..+.|+.|+|.++.++..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   77 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN---PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPR   77 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS---SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCC
Confidence            47999999999999999999999999999999865   689999999999999999999999999999999999987743


Q ss_pred             hHHHHHHHHHHHHHHhhcCCCCceEEEecCC
Q psy12549        284 RTQELKRRFEMLKIERLNRYQGVNLYVKNLD  314 (336)
Q Consensus       284 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp  314 (336)
                      ....        ...........+|||+||+
T Consensus        78 ~~~~--------~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           78 RSRF--------DRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             SSCC--------CSCCCSCCCCSCCCSCCCC
T ss_pred             cccC--------CCCCccccCCCceecCCCC
Confidence            2110        0111112335679999987

>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=99.69  E-value=1.2e-16  Score=115.81  Aligned_cols=80  Identities=19%  Similarity=0.175  Sum_probs=73.5

Q ss_pred             ccceEEEcCCCCCCcHHHHH----HhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEee
Q psy12549        202 LFTNVYIKNFGEDFNDEKLK----EMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR  277 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~----~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~  277 (336)
                      ..++|||+|||..+++++|+    ++|++||.|.++.++..... +|||||+|.+.++|.+|++.|||..+.|+.|+|.+
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~-rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   86 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY-QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSL   86 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST-TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC-CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34789999999999999999    99999999999999874444 89999999999999999999999999999999999


Q ss_pred             cccch
Q psy12549        278 AQKKA  282 (336)
Q Consensus       278 ~~~~~  282 (336)
                      +.+..
T Consensus        87 a~~~~   91 (96)
T 2dgx_A           87 ATGAS   91 (96)
T ss_dssp             CCCSS
T ss_pred             cCCCC
Confidence            98764

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.69  E-value=2.2e-16  Score=115.90  Aligned_cols=82  Identities=20%  Similarity=0.331  Sum_probs=76.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|+.|| |..+.++.++ +|.++|||||+|.+.++|.+|+ .||+..+.|+.|.|.++
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            4468999999999999999999999997 9999999997 6889999999999999999999 79999999999999998


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      .+...
T Consensus        91 ~~~~~   95 (103)
T 2dng_A           91 EGRKQ   95 (103)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87643

>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=6.3e-17  Score=115.26  Aligned_cols=79  Identities=25%  Similarity=0.470  Sum_probs=72.4

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCc-cceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGK-SRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~-~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      .++|||+|||.++++++|+++|+.||.|..+.+..  .++. ++|+|||+|.+.++|.+|+..|||..+.|+.|+|.++.
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            37899999999999999999999999999999877  2233 79999999999999999999999999999999999987


Q ss_pred             cc
Q psy12549        280 KK  281 (336)
Q Consensus       280 ~~  281 (336)
                      +.
T Consensus        84 ~~   85 (88)
T 4a8x_A           84 AP   85 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=1.4e-16  Score=119.14  Aligned_cols=85  Identities=19%  Similarity=0.296  Sum_probs=78.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCee--------EEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeC
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSIL--------SCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLN  177 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~--------~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~  177 (336)
                      ....++|||+|||.++++++|+++|+.||.|.        .+.++.++ +|.++|||||+|.+.++|.+|++.||+..+.
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            34568999999999999999999999999999        69999985 7889999999999999999999999999999


Q ss_pred             CeEEEEeeccCchh
Q psy12549        178 SKIVFVGKFIPRKE  191 (336)
Q Consensus       178 ~~~i~v~~~~~~~~  191 (336)
                      |+.|.|.++.+...
T Consensus        92 g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           92 GSKLKVSLARKKPP  105 (113)
T ss_dssp             TEECEEECSSCCCC
T ss_pred             CCEEEEEECCCCCC
Confidence            99999999887654

>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=8.2e-17  Score=119.15  Aligned_cols=83  Identities=24%  Similarity=0.488  Sum_probs=77.0

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCC---CCccceEEEEEeCCHHHHHHHHHHh-CCceecCEEEEEe
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN---DGKSRGFGFVAYESPEFAEKAVQAW-NGKEVDGKILYVG  276 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~---~~~~~g~afV~F~~~~~a~~a~~~l-~g~~~~g~~l~v~  276 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++..   ++.++|||||+|.+.++|.+|+..| ||..+.|+.|.|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~   92 (107)
T 2cph_A           13 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   92 (107)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEE
Confidence            34588999999999999999999999999999999875   7889999999999999999999999 9999999999999


Q ss_pred             ecccchh
Q psy12549        277 RAQKKAE  283 (336)
Q Consensus       277 ~~~~~~~  283 (336)
                      ++.++..
T Consensus        93 ~a~~~~~   99 (107)
T 2cph_A           93 WADSEVT   99 (107)
T ss_dssp             ECCCCCC
T ss_pred             eCCCCCC
Confidence            9987643

>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=99.69  E-value=5.1e-17  Score=118.06  Aligned_cols=77  Identities=26%  Similarity=0.287  Sum_probs=70.0

Q ss_pred             cccceEEEcCCCC-CCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCC--ceecCEEEEEee
Q psy12549        201 KLFTNVYIKNFGE-DFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG--KEVDGKILYVGR  277 (336)
Q Consensus       201 ~~~~~l~V~nlp~-~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g--~~~~g~~l~v~~  277 (336)
                      .+.++|||+|||+ ++++++|+++|++||.|.++.+++.    +++|||+|.+.++|..|++.|++  ..+.|++|+|.+
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~   88 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHL   88 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEE
Confidence            3458899999999 9999999999999999999999864    68999999999999999999886  459999999999


Q ss_pred             cccc
Q psy12549        278 AQKK  281 (336)
Q Consensus       278 ~~~~  281 (336)
                      +...
T Consensus        89 a~~~   92 (102)
T 1x4d_A           89 SQKY   92 (102)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            9865

>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=99.69  E-value=1.1e-16  Score=114.33  Aligned_cols=77  Identities=17%  Similarity=0.387  Sum_probs=73.0

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ++|||+|||..+++++|+++|+.||.|..+.+..  .++.++|+|||+|.+.++|.+|+ .+||..+.|+.|+|.++.+.
T Consensus         7 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A            7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccCC
Confidence            7899999999999999999999999999999987  47889999999999999999999 89999999999999998764

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=3.8e-17  Score=119.83  Aligned_cols=82  Identities=34%  Similarity=0.586  Sum_probs=76.3

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++
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            3458999999999999999999999999999999987  56788999999999999999999999999999999999999


Q ss_pred             ccch
Q psy12549        279 QKKA  282 (336)
Q Consensus       279 ~~~~  282 (336)
                      .++.
T Consensus        90 ~~~~   93 (102)
T 1x5s_A           90 GKSS   93 (102)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            8764

>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=99.69  E-value=6.3e-17  Score=119.33  Aligned_cols=83  Identities=24%  Similarity=0.392  Sum_probs=76.8

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.+..  .++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   92 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   92 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            3458999999999999999999999999999999987  47889999999999999999999999999999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus        93 ~~~~~   97 (105)
T 1x5u_A           93 SAHNK   97 (105)
T ss_dssp             TTTSC
T ss_pred             CCCCc
Confidence            87643

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.4e-16  Score=117.52  Aligned_cols=84  Identities=23%  Similarity=0.510  Sum_probs=78.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ....++|||+|||..+++++|+++|+.||.|..|.++.++ ++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.+
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            3456899999999999999999999999999999999996 788999999999999999999998 99999999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.++..
T Consensus        92 a~~~~~   97 (105)
T 2dh8_A           92 CTPRGM   97 (105)
T ss_dssp             SCCSSC
T ss_pred             ccCCCC
Confidence            887654

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.68  E-value=4e-17  Score=112.59  Aligned_cols=74  Identities=26%  Similarity=0.448  Sum_probs=70.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      +|||+|||.++++++|+++|++||.|..+.++.++ +|.++|||||+|.+.++|++|++ +++..+.|+.|.|.++
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            48999999999999999999999999999999987 78899999999999999999998 9999999999999764

>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=99.68  E-value=2.4e-16  Score=114.66  Aligned_cols=78  Identities=13%  Similarity=0.258  Sum_probs=71.0

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHh--CCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW--NGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l--~g~~~~g~~l~v~~~  278 (336)
                      .+.++|||+|||.++++++|+++|++||.|..+.+++.    +|+|||+|.+.++|.+|++.+  ++..+.|++|.|.|+
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a   88 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYS   88 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEc
Confidence            34578999999999999999999999999999988864    899999999999999999976  578899999999999


Q ss_pred             ccch
Q psy12549        279 QKKA  282 (336)
Q Consensus       279 ~~~~  282 (336)
                      .++.
T Consensus        89 ~~~~   92 (101)
T 2cq1_A           89 NHKE   92 (101)
T ss_dssp             SCSS
T ss_pred             Cccc
Confidence            8764

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.68  E-value=3.9e-17  Score=120.36  Aligned_cols=80  Identities=24%  Similarity=0.370  Sum_probs=74.9

Q ss_pred             ccceEEEcCCCCCC------cHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCE-EEE
Q psy12549        202 LFTNVYIKNFGEDF------NDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK-ILY  274 (336)
Q Consensus       202 ~~~~l~V~nlp~~~------t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~-~l~  274 (336)
                      ..++|||+|||..+      ++++|+++|++||.|..+.+.+.+|.++|||||+|.+.++|.+|+..|||..+.|+ .|+
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~   93 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   93 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEE
Confidence            34789999999999      78999999999999999999887889999999999999999999999999999998 999


Q ss_pred             Eeecccc
Q psy12549        275 VGRAQKK  281 (336)
Q Consensus       275 v~~~~~~  281 (336)
                      |.++...
T Consensus        94 V~~a~~~  100 (105)
T 2nlw_A           94 VNLFTDF  100 (105)
T ss_dssp             EECSCCC
T ss_pred             EEEcchH
Confidence            9998765

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.68  E-value=2.2e-16  Score=124.55  Aligned_cols=80  Identities=21%  Similarity=0.366  Sum_probs=75.1

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCC--ceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYG--TITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g--~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      .++|||+|||.++++++|+++|+.||  .|..+.++.  .+|.++|||||+|.+.++|.+|+..|||..+.|+.|.|.++
T Consensus        55 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a  134 (156)
T 3n9u_C           55 RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPA  134 (156)
T ss_dssp             -CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEc
Confidence            37899999999999999999999999  999999986  58999999999999999999999999999999999999999


Q ss_pred             ccch
Q psy12549        279 QKKA  282 (336)
Q Consensus       279 ~~~~  282 (336)
                      .++.
T Consensus       135 ~~~~  138 (156)
T 3n9u_C          135 TRQN  138 (156)
T ss_dssp             CHHH
T ss_pred             CCCc
Confidence            8764

>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=99.68  E-value=8.7e-17  Score=120.61  Aligned_cols=81  Identities=31%  Similarity=0.548  Sum_probs=76.0

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+.+.. .+|.++|||||+|.+.++|++|++.|||..+.|+.|.|.++.+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   85 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKK   85 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            347899999999999999999999999999999988 6788899999999999999999999999999999999999987


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      +.
T Consensus        86 ~~   87 (116)
T 2fy1_A           86 PS   87 (116)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>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=99.68  E-value=1.2e-16  Score=119.06  Aligned_cols=83  Identities=29%  Similarity=0.457  Sum_probs=76.6

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhC------CceecCEE
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWN------GKEVDGKI  272 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~------g~~~~g~~  272 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|+..+|      |..+.|+.
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            3458899999999999999999999999999999987  567889999999999999999999999      99999999


Q ss_pred             EEEeecccchh
Q psy12549        273 LYVGRAQKKAE  283 (336)
Q Consensus       273 l~v~~~~~~~~  283 (336)
                      |+|.++.++..
T Consensus        93 l~v~~a~~~~~  103 (111)
T 1x4h_A           93 LKVDLAVTRDE  103 (111)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCcc
Confidence            99999987643

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.68  E-value=1.5e-16  Score=117.98  Aligned_cols=84  Identities=26%  Similarity=0.450  Sum_probs=74.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       106 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      .....++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|+..+ +..+.|+.|.|.
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            33456899999999999999999999999999999999987 6889999999999999999999975 599999999999


Q ss_pred             eccCch
Q psy12549        185 KFIPRK  190 (336)
Q Consensus       185 ~~~~~~  190 (336)
                      ++.++.
T Consensus       100 ~a~~~~  105 (109)
T 2rs2_A          100 VAFPRR  105 (109)
T ss_dssp             ECCCCC
T ss_pred             EccCCC
Confidence            987764

>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=99.68  E-value=1.8e-16  Score=116.62  Aligned_cols=82  Identities=18%  Similarity=0.329  Sum_probs=76.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-C-CCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-Q-GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~-~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ...++|||+|||.++++++|+++|+.|| |..|.++.++ + |.++|||||+|.+.++|.+|+ .|++..+.|+.|.|.+
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            4458999999999999999999999999 9999999987 3 889999999999999999999 8999999999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.++..
T Consensus        91 a~~~~~   96 (104)
T 1wi8_A           91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            887654

>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=99.68  E-value=1.6e-16  Score=118.32  Aligned_cols=83  Identities=16%  Similarity=0.282  Sum_probs=75.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHH---HHhhccCCeeEEEEeeCC-C---CCcccEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMY---DTFSAFGSILSCKVAQDE-Q---GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKI  180 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~---~~f~~~G~v~~~~~~~~~-~---~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~  180 (336)
                      ...++|||+|||+++++++|+   ++|++||.|..+.++.++ +   +.++|||||+|.+.++|.+|++.||+..+.|+.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            445789999999999999999   999999999999999886 2   356699999999999999999999999999999


Q ss_pred             EEEeeccCch
Q psy12549        181 VFVGKFIPRK  190 (336)
Q Consensus       181 i~v~~~~~~~  190 (336)
                      |.|.++.++.
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999988765

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.68  E-value=2.1e-16  Score=122.73  Aligned_cols=87  Identities=25%  Similarity=0.467  Sum_probs=79.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       106 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      .....++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|++.||+..+.|+.|.|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            33456899999999999999999999999999999999987 68899999999999999999999999999999999999


Q ss_pred             eccCchhh
Q psy12549        185 KFIPRKER  192 (336)
Q Consensus       185 ~~~~~~~~  192 (336)
                      ++.+....
T Consensus       118 ~a~~~~~~  125 (139)
T 1u6f_A          118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             ECCCCCCC
Confidence            98876543

>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=1.1e-16  Score=116.48  Aligned_cols=82  Identities=17%  Similarity=0.218  Sum_probs=74.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|++|++.||+..+.|+.|.|.++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            345789999999999999999999999999887777765 7889999999999999999999999999999999999997


Q ss_pred             cCc
Q psy12549        187 IPR  189 (336)
Q Consensus       187 ~~~  189 (336)
                      ..+
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=3.1e-17  Score=116.10  Aligned_cols=80  Identities=24%  Similarity=0.461  Sum_probs=74.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|++.|||..+.|+.+.+.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            345889999999999999999999999999999999986 7889999999999999999999999999999999888665


Q ss_pred             c
Q psy12549        187 I  187 (336)
Q Consensus       187 ~  187 (336)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.68  E-value=1.2e-16  Score=117.79  Aligned_cols=82  Identities=21%  Similarity=0.333  Sum_probs=74.5

Q ss_pred             CCCCceEEEcCCCCCC------CHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCe-
Q psy12549        107 KSGVGNVFIKNLDKSI------DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSK-  179 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~------t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~-  179 (336)
                      ....++|||+|||..+      ++++|+++|++||.|..+.++ ..+|.++|||||+|.+.++|.+|+..|||..+.|+ 
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            3446799999999999      789999999999999999988 45788999999999999999999999999999998 


Q ss_pred             EEEEeeccCc
Q psy12549        180 IVFVGKFIPR  189 (336)
Q Consensus       180 ~i~v~~~~~~  189 (336)
                      .|.|.++...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999988654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.68  E-value=3.4e-16  Score=119.02  Aligned_cols=83  Identities=23%  Similarity=0.390  Sum_probs=78.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.+..+++|.++|||||+|.+.++|.+|+..|++..+.|+.|.|.++.
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  112 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  112 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeC
Confidence            44579999999999999999999999999999999999888899999999999999999999999999999999999987


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      +..
T Consensus       113 ~~~  115 (124)
T 2kt5_A          113 SQI  115 (124)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            654

>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=99.68  E-value=2.8e-16  Score=111.66  Aligned_cols=77  Identities=23%  Similarity=0.520  Sum_probs=70.8

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|++||.|..+.++.  .+|.++|+|||+|.+.++|.+|++ +++..+.|+.|.|.+|
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEeC
Confidence            3458999999999999999999999999999999986  568899999999999999999996 5889999999999875

>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=99.68  E-value=8.1e-17  Score=116.46  Aligned_cols=80  Identities=18%  Similarity=0.261  Sum_probs=73.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+|||.++++++|+++|++||.|..+.++.++ +|.++|||||+|.+.++|.+|++.||+..+.|+.|.|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            35789999999999999999999999999988888765 78899999999999999999999999999999999998865


Q ss_pred             C
Q psy12549        188 P  188 (336)
Q Consensus       188 ~  188 (336)
                      +
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            3

>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=99.68  E-value=8.9e-17  Score=116.25  Aligned_cols=78  Identities=19%  Similarity=0.278  Sum_probs=71.6

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||.++++++|+++|+.||.|..+.++.  .++.++|+|||+|.++++|.+|++.|||..+.|+.|+|.++.+
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            47899999999999999999999999998776665  7788999999999999999999999999999999999998764

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=3.2e-16  Score=117.34  Aligned_cols=80  Identities=29%  Similarity=0.448  Sum_probs=74.8

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ..++|||+|||..+++++|+++|+.||.|..+.+.. .++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++..
T Consensus        14 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   93 (114)
T 2do0_A           14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDER   93 (114)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEccc
Confidence            447899999999999999999999999999999887 6688899999999999999999999999999999999999875


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      .
T Consensus        94 ~   94 (114)
T 2do0_A           94 A   94 (114)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.68  E-value=3.1e-17  Score=114.94  Aligned_cols=72  Identities=26%  Similarity=0.450  Sum_probs=68.1

Q ss_pred             ceEEEcCCCCCC------cHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCE-EEEE
Q psy12549        204 TNVYIKNFGEDF------NDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK-ILYV  275 (336)
Q Consensus       204 ~~l~V~nlp~~~------t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~-~l~v  275 (336)
                      ++|||+|||..+      ++++|+++|++||+|..+.+.+.+|.++|||||+|.+.++|.+|+..|||..+.|+ .|+|
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            689999999999      78999999999999999998888889999999999999999999999999999999 8876

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.68  E-value=1.5e-16  Score=119.73  Aligned_cols=82  Identities=15%  Similarity=0.140  Sum_probs=76.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCC---eeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGS---ILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~---v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      ...++|||+|||.++|+++|+++|+.||.   |..+.++.++.|.++|||||+|.+.++|.+|++ +|+..+.|+.|.|.
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            45688999999999999999999999999   899999999889999999999999999999999 99999999999999


Q ss_pred             eccCch
Q psy12549        185 KFIPRK  190 (336)
Q Consensus       185 ~~~~~~  190 (336)
                      ++.+..
T Consensus        94 ~a~~~~   99 (118)
T 2db1_A           94 KSHRTE   99 (118)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            886544

>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=99.68  E-value=3.7e-17  Score=119.37  Aligned_cols=82  Identities=18%  Similarity=0.315  Sum_probs=73.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC--CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE--QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       106 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~--~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      .....++|||+|||.++++++|+++|+.|| |.++.++.++  +|.++|||||+|.+.++|.+|+ .|+|..+.|+.|.|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            334568999999999999999999999999 9999999986  7889999999999999999999 79999999999999


Q ss_pred             eeccCc
Q psy12549        184 GKFIPR  189 (336)
Q Consensus       184 ~~~~~~  189 (336)
                      .++.++
T Consensus        93 ~~a~~~   98 (100)
T 2j76_E           93 DVADQA   98 (100)
T ss_dssp             EECCCS
T ss_pred             EeccCC
Confidence            998765

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=2.6e-16  Score=112.76  Aligned_cols=79  Identities=18%  Similarity=0.342  Sum_probs=73.9

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ..++|||+|||.++++++|+++|+.| .|..+.++. .+|.++|+|||+|.+.++|.+|+. +||..+.|+.|.|.++.+
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a~~   86 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKS   86 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEESS
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEECCc
Confidence            44889999999999999999999999 899999987 678899999999999999999999 999999999999999987


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      +.
T Consensus        87 ~~   88 (91)
T 2dgw_A           87 GP   88 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.3e-16  Score=117.79  Aligned_cols=79  Identities=22%  Similarity=0.283  Sum_probs=73.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ...+|||+|||.++++++|+++|+.| .|..|.++.++.|+++|||||+|.+.++|.+|+ .+|+..++|+.|.|..+.+
T Consensus        15 ~~~~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           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            34689999999999999999999999 899999999988999999999999999999999 5999999999999987765


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      .
T Consensus        93 ~   93 (109)
T 2dnn_A           93 R   93 (109)
T ss_dssp             H
T ss_pred             c
Confidence            4

>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=99.68  E-value=4.3e-16  Score=113.27  Aligned_cols=80  Identities=15%  Similarity=0.174  Sum_probs=71.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHh--CCceeCCeEEEEe
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV--NGMLLNSKIVFVG  184 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l--~~~~~~~~~i~v~  184 (336)
                      ....++|||+|||..+++++|+++|++||.|..+.++++     +|||||+|.+.++|..|++.|  ++..+.|++|.|.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   86 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   86 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEE
Confidence            345689999999999999999999999999999988864     789999999999999999976  5678999999999


Q ss_pred             eccCchh
Q psy12549        185 KFIPRKE  191 (336)
Q Consensus       185 ~~~~~~~  191 (336)
                      ++.+...
T Consensus        87 ~a~~~~~   93 (101)
T 2cq1_A           87 YSNHKEL   93 (101)
T ss_dssp             ECSCSSC
T ss_pred             EcCcccC
Confidence            9886543

>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=3.3e-16  Score=117.63  Aligned_cols=83  Identities=23%  Similarity=0.413  Sum_probs=76.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ....++|||+|||.++++++|+++|+.||.|..+.++.++ ++.++|||||+|.+.++|.+|+..+++ .+.|+.|.|.+
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            3456899999999999999999999999999999999986 688999999999999999999999998 89999999999


Q ss_pred             ccCch
Q psy12549        186 FIPRK  190 (336)
Q Consensus       186 ~~~~~  190 (336)
                      +.+..
T Consensus        93 a~~~~   97 (116)
T 2cqd_A           93 AYLGA   97 (116)
T ss_dssp             STTTC
T ss_pred             cccCC
Confidence            86543

>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=99.67  E-value=6.4e-17  Score=148.51  Aligned_cols=83  Identities=17%  Similarity=0.418  Sum_probs=77.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||..+|+++|.++|+.||.|..|.|+.++ +|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++
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            445799999999999999999999999999999999986 7889999999999999999999999999999999999998


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .+..
T Consensus       180 ~~~~  183 (437)
T 3pgw_S          180 RGRT  183 (437)
T ss_pred             CCCC
Confidence            7643

>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=99.67  E-value=1.8e-17  Score=127.71  Aligned_cols=124  Identities=12%  Similarity=0.103  Sum_probs=74.4

Q ss_pred             eEEEEEeCCcchhhHHHHHhhcCccccCCeeeEEEeccCCCCcCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEE
Q psy12549         63 GAILVQLGQPYMLDTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKV  142 (336)
Q Consensus        63 g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~  142 (336)
                      |+|+.+|.-+  +.+..+...... ...|....-..............++|||+|||.++|+++|+++|+.|| +..|.+
T Consensus         2 ~~~~~~~~~~--~~~~~~~~~~~~-~~gg~~~g~~~g~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i   77 (139)
T 2hgn_A            2 GSSHHHHHHS--SGLVPRGSHMAS-MTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHI   77 (139)
T ss_dssp             ----------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEEC
T ss_pred             CcccccccCc--cccchhcccchh-ccCCCCCCCCCCCcccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEE
Confidence            5688888888  666655554332 233332211111111122334457899999999999999999999999 669999


Q ss_pred             eeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchh
Q psy12549        143 AQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKE  191 (336)
Q Consensus       143 ~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~  191 (336)
                      +.++.|.++|||||+|.+.++|++|+ .+|+..+.|+.|.|..+.+...
T Consensus        78 ~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           78 EIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             CCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC
T ss_pred             EECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCC
Confidence            99988999999999999999999999 6899999999999988776543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.67  E-value=1.4e-16  Score=120.04  Aligned_cols=79  Identities=32%  Similarity=0.532  Sum_probs=73.3

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus        38 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a  117 (118)
T 2khc_A           38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK  117 (118)
T ss_dssp             CCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            3458899999999999999999999999999999987  56888999999999999999999999999999999999987


Q ss_pred             c
Q psy12549        279 Q  279 (336)
Q Consensus       279 ~  279 (336)
                      +
T Consensus       118 k  118 (118)
T 2khc_A          118 K  118 (118)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=1.9e-16  Score=116.32  Aligned_cols=89  Identities=13%  Similarity=0.095  Sum_probs=79.3

Q ss_pred             CCCccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCcccc
Q psy12549         11 EEGIIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDAL   89 (336)
Q Consensus        11 ~~~~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~   89 (336)
                      +.....+.++|||+|||.++++++|+++| .++.+..+.+..++   .+|.++|||||+|.+.  ++|++|++.+|+..+
T Consensus         6 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~---~~~~~~g~afV~f~~~--~~A~~A~~~l~g~~~   80 (103)
T 2dnm_A            6 SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREP---HTKAPRGFAFVRFHDR--RDAQDAEAAMDGAEL   80 (103)
T ss_dssp             CSSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCS---SSCSBCSCEEEEESSS--SHHHHHHHHHSSCCB
T ss_pred             CCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCCCCeEEEEEECCH--HHHHHHHHHcCCCEE
Confidence            34455778999999999999999999999 67788899999887   3688999999999999  999999999999999


Q ss_pred             CCeeeEEEeccCCCC
Q psy12549         90 KGRPIRIMWSQRDPS  104 (336)
Q Consensus        90 ~g~~i~v~~~~~~~~  104 (336)
                      .|+.|.|.++.....
T Consensus        81 ~g~~l~V~~a~~~~~   95 (103)
T 2dnm_A           81 DGRELRVQVARYGRR   95 (103)
T ss_dssp             TTBCCEEEECSSCCS
T ss_pred             CCcEEEEEECCcCCC
Confidence            999999999876543

>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=99.67  E-value=1.1e-16  Score=116.44  Aligned_cols=80  Identities=19%  Similarity=0.223  Sum_probs=72.9

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ..++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|+|||+|.+.++|++|++.|||..+.|+.|+|.++.
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            347899999999999999999999999998665554  778899999999999999999999999999999999999987


Q ss_pred             cc
Q psy12549        280 KK  281 (336)
Q Consensus       280 ~~  281 (336)
                      ..
T Consensus        94 ~~   95 (98)
T 2cqp_A           94 GP   95 (98)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

>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=2.8e-16  Score=116.62  Aligned_cols=81  Identities=27%  Similarity=0.431  Sum_probs=74.1

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.+.. ++.+++||||+|.+.++|.+|++.||+..+.|+.|+|.++.+
T Consensus        20 ~~~~~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           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN-RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   98 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC-SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE-CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEccc
Confidence            3458899999999999999999999999999999865 455799999999999999999999999999999999999987


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      +.
T Consensus        99 ~~  100 (109)
T 1x4a_A           99 GR  100 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>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=99.67  E-value=1.9e-16  Score=118.52  Aligned_cols=86  Identities=24%  Similarity=0.252  Sum_probs=78.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCe-eEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSI-LSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v-~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ....++|||+|||.++++++|+++|+.||.| ..|.++.+++|.++|||||+|.+.++|.+|+.. |+..+.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            3456899999999999999999999999999 889999999999999999999999999999996 99999999999999


Q ss_pred             ccCchhhh
Q psy12549        186 FIPRKERE  193 (336)
Q Consensus       186 ~~~~~~~~  193 (336)
                      +.+.....
T Consensus        91 a~~~~~~~   98 (114)
T 2cpy_A           91 VTLEDMRE   98 (114)
T ss_dssp             ECHHHHHH
T ss_pred             CCHHHHHH
Confidence            87665433

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=1.1e-16  Score=116.70  Aligned_cols=81  Identities=19%  Similarity=0.376  Sum_probs=75.3

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCcee-EEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEE----E
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTIT-SYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKI----L  273 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~-~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~----l  273 (336)
                      ...++|||+|||..+++++|+++|+.||.|. .+.++.  .++.++|||||+|.+.++|++|++.|||..+.|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            3458999999999999999999999999999 999887  57889999999999999999999999999999999    9


Q ss_pred             EEeecccc
Q psy12549        274 YVGRAQKK  281 (336)
Q Consensus       274 ~v~~~~~~  281 (336)
                      +|.|+.+.
T Consensus        87 ~v~~a~~~   94 (99)
T 2div_A           87 KLNYATYS   94 (99)
T ss_dssp             CEEETTCC
T ss_pred             EEeecCCC
Confidence            99999765

>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=99.67  E-value=1.6e-16  Score=118.94  Aligned_cols=81  Identities=25%  Similarity=0.345  Sum_probs=75.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|+ .||+..+.|+.|.|.++.+
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            4689999999999999999999999999999999987 5889999999999999999999 8999999999999999876


Q ss_pred             chh
Q psy12549        189 RKE  191 (336)
Q Consensus       189 ~~~  191 (336)
                      ...
T Consensus       104 ~~~  106 (114)
T 2cq4_A          104 EKN  106 (114)
T ss_dssp             HHH
T ss_pred             Ccc
Confidence            544

>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=99.67  E-value=3.9e-16  Score=116.86  Aligned_cols=82  Identities=26%  Similarity=0.504  Sum_probs=76.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcee--------CCe
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLL--------NSK  179 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~--------~~~  179 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.+++|.++|||||+|.+.++|.+|+..|||..+        .++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~  102 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE  102 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCC
Confidence            456899999999999999999999999999999999999889999999999999999999999999998        578


Q ss_pred             EEEEeeccCc
Q psy12549        180 IVFVGKFIPR  189 (336)
Q Consensus       180 ~i~v~~~~~~  189 (336)
                      +|.|.++.+.
T Consensus       103 ~l~v~~a~p~  112 (114)
T 1x5o_A          103 PLLCKFSGPS  112 (114)
T ss_dssp             CBEEEECCCS
T ss_pred             ceeEEccCCC
Confidence            8888888754

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=2e-16  Score=118.24  Aligned_cols=83  Identities=27%  Similarity=0.480  Sum_probs=76.1

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCcee--------EEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecC
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTIT--------SYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG  270 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~--------~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g  270 (336)
                      ...++|||+|||..+++++|+++|+.||.|.        .+.++.  .++.++|||||+|.+.++|.+|++.|||..+.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   92 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   92 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCC
Confidence            3458999999999999999999999999998        588876  678889999999999999999999999999999


Q ss_pred             EEEEEeecccchh
Q psy12549        271 KILYVGRAQKKAE  283 (336)
Q Consensus       271 ~~l~v~~~~~~~~  283 (336)
                      +.|+|.++.++..
T Consensus        93 ~~l~V~~a~~~~~  105 (113)
T 2cpe_A           93 SKLKVSLARKKPP  105 (113)
T ss_dssp             EECEEECSSCCCC
T ss_pred             CEEEEEECCCCCC
Confidence            9999999987644

>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=99.67  E-value=1.2e-16  Score=122.07  Aligned_cols=82  Identities=27%  Similarity=0.407  Sum_probs=76.2

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      .+.++|||+|||.++++++|+++|+.||+|..+.++.  .++.++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a  123 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS  123 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            4458899999999999999999999999999999987  56788999999999999999999999999999999999999


Q ss_pred             ccch
Q psy12549        279 QKKA  282 (336)
Q Consensus       279 ~~~~  282 (336)
                      .++.
T Consensus       124 ~~~~  127 (129)
T 2kxn_B          124 ITKR  127 (129)
T ss_dssp             SSSS
T ss_pred             cCCC
Confidence            8763

>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=99.67  E-value=1.5e-16  Score=115.58  Aligned_cols=78  Identities=18%  Similarity=0.155  Sum_probs=70.4

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCC--ceeCCeEEEEe
Q psy12549        108 SGVGNVFIKNLDK-SIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG--MLLNSKIVFVG  184 (336)
Q Consensus       108 ~~~~~l~v~nlp~-~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~--~~~~~~~i~v~  184 (336)
                      ...++|||+|||. ++++++|+++|++||.|.++.++++     ++||||+|.+.++|..|++.|++  ..+.|++|.|.
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   87 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   87 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEE
Confidence            3467899999999 9999999999999999999999875     57999999999999999998886  45999999999


Q ss_pred             eccCch
Q psy12549        185 KFIPRK  190 (336)
Q Consensus       185 ~~~~~~  190 (336)
                      ++....
T Consensus        88 ~a~~~~   93 (102)
T 1x4d_A           88 LSQKYK   93 (102)
T ss_dssp             EECCCT
T ss_pred             ECCCCC
Confidence            988654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=4.6e-17  Score=115.21  Aligned_cols=78  Identities=28%  Similarity=0.527  Sum_probs=72.7

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      +.++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|++.|||..+.|+.+++.++.
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            347899999999999999999999999999999987  568889999999999999999999999999999999988765

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=5.8e-17  Score=112.39  Aligned_cols=75  Identities=25%  Similarity=0.454  Sum_probs=70.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ++|||+|||.++++++|+++|++||.|..+.++.++ +|.++|||||+|.+.++|.+|++.++ ..+.|+.|.|.++
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            469999999999999999999999999999999987 68899999999999999999999988 9999999999875

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.67  E-value=3.5e-16  Score=114.83  Aligned_cols=80  Identities=19%  Similarity=0.370  Sum_probs=73.8

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ..++|||+|||..+++++|+++|+.|| |..+.++.  .++.++|||||+|.+.++|.+|+ .|||..+.|+.|+|.++.
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~   91 (103)
T 2dng_A           14 PPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAE   91 (103)
T ss_dssp             SCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEECC
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEec
Confidence            448899999999999999999999997 99999987  56889999999999999999999 899999999999999998


Q ss_pred             cchh
Q psy12549        280 KKAE  283 (336)
Q Consensus       280 ~~~~  283 (336)
                      ++..
T Consensus        92 ~~~~   95 (103)
T 2dng_A           92 GRKQ   95 (103)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>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=99.67  E-value=8.6e-16  Score=112.75  Aligned_cols=83  Identities=22%  Similarity=0.385  Sum_probs=75.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ....++|||+|||..+++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|+.  ++..+.|+.|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            3456789999999999999999999999999999999997 68999999999999999999999  47899999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.++..
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            887643

>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=7.3e-16  Score=114.36  Aligned_cols=83  Identities=18%  Similarity=0.273  Sum_probs=75.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ....++|||+|||.++++++|+++|+.||.|..+.+..+  +.++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            345689999999999999999999999999999999654  457899999999999999999999999999999999998


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      .+...
T Consensus        97 ~~~~~  101 (109)
T 1x4a_A           97 RSGRG  101 (109)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            77543

>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=99.67  E-value=1.4e-16  Score=118.80  Aligned_cols=79  Identities=15%  Similarity=0.290  Sum_probs=71.7

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhC--CceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN--GKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~--g~~~~g~~l~v~~~  278 (336)
                      .+.++|||+|||+++++++|+++|++||.|.++.++..    +|+|||+|.+.++|.+|++.++  +..+.|++|+|.++
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a  104 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS  104 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEc
Confidence            44588999999999999999999999999999999864    8999999999999999999887  46899999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus       105 ~~k~~  109 (119)
T 2ad9_A          105 NHKEL  109 (119)
T ss_dssp             SSSSC
T ss_pred             cCCCC
Confidence            87643

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.67  E-value=1.3e-16  Score=120.98  Aligned_cols=83  Identities=20%  Similarity=0.300  Sum_probs=74.4

Q ss_pred             cccceEEEcCCCCCCcHHHHH----HhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEe
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLK----EMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG  276 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~----~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~  276 (336)
                      .+.++|||+|||+.+++++|+    ++|++||.|.+|.+.. ++.++|||||+|.+.++|..|+..|||..+.|+.|+|.
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~-~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~  105 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL-SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVIT  105 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC-CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc-CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEE
Confidence            345789999999999999876    6999999999988754 67889999999999999999999999999999999999


Q ss_pred             ecccchhh
Q psy12549        277 RAQKKAER  284 (336)
Q Consensus       277 ~~~~~~~~  284 (336)
                      |+..+...
T Consensus       106 ~a~~~~~~  113 (127)
T 2a3j_A          106 FSETPQSQ  113 (127)
T ss_dssp             ECCCCCHH
T ss_pred             EccCcchh
Confidence            99877543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.67  E-value=6.2e-17  Score=111.64  Aligned_cols=73  Identities=26%  Similarity=0.543  Sum_probs=68.7

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       205 ~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      +|||+|||.++++++|+++|+.||+|..+.++.  .++.++|+|||+|.+.++|++|++ ++|..+.|+.|.|.+|
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            489999999999999999999999999999887  478899999999999999999998 9999999999999875

>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=2.6e-16  Score=115.79  Aligned_cols=80  Identities=21%  Similarity=0.398  Sum_probs=73.7

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CC-CccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--ND-GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~-~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ..++|||+|||..+++++|+++|+.|| |..+.++.  .+ +.++|||||+|.+.++|.+|+ .|||..+.|+.|.|.++
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   91 (104)
T 1wi8_A           14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEEc
Confidence            448999999999999999999999999 99999987  33 888999999999999999999 89999999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus        92 ~~~~~   96 (104)
T 1wi8_A           92 DQAQD   96 (104)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87643

>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=99.66  E-value=2e-16  Score=118.42  Aligned_cols=79  Identities=18%  Similarity=0.384  Sum_probs=73.8

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|+ .|||..+.|+.|.|.++.+
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            47899999999999999999999999999999987  55788999999999999999999 8999999999999999876


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      +.
T Consensus       104 ~~  105 (114)
T 2cq4_A          104 EK  105 (114)
T ss_dssp             HH
T ss_pred             Cc
Confidence            53

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.66  E-value=2.5e-16  Score=119.71  Aligned_cols=84  Identities=21%  Similarity=0.344  Sum_probs=77.2

Q ss_pred             cccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEee
Q psy12549        199 KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR  277 (336)
Q Consensus       199 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~  277 (336)
                      .....++|||+|||..+++++|+++|+.||.|..+.+.. .+|.++|+|||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            334558999999999999999999999999999999987 6778899999999999999999999999999999999999


Q ss_pred             cccch
Q psy12549        278 AQKKA  282 (336)
Q Consensus       278 ~~~~~  282 (336)
                      +.+..
T Consensus       111 a~~~~  115 (124)
T 2kt5_A          111 VASQI  115 (124)
T ss_dssp             ECCTT
T ss_pred             eCCCC
Confidence            97653

>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=99.66  E-value=6.8e-16  Score=122.25  Aligned_cols=84  Identities=21%  Similarity=0.346  Sum_probs=78.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|+.||.|..|.++.++ ++.++|||||+|.+.++|.+|+..|++..+.|+.|.|.++
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            456899999999999999999999999999999999997 6889999999999999999999999999999999999999


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      .+...
T Consensus       117 ~~~~~  121 (156)
T 1h2v_Z          117 AGFKE  121 (156)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            87544

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.66  E-value=2.9e-16  Score=114.84  Aligned_cols=79  Identities=22%  Similarity=0.384  Sum_probs=72.5

Q ss_pred             cccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        199 KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       199 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      .....++|||+|||..+++++|+++|+.||.|.++.+..    ++|||||+|.+.++|.+|+..|||..+.|+.|+|.|+
T Consensus        23 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           23 APPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP----EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SCSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec----CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            334458999999999999999999999999999999974    5899999999999999999999999999999999998


Q ss_pred             ccc
Q psy12549        279 QKK  281 (336)
Q Consensus       279 ~~~  281 (336)
                      .++
T Consensus        99 ~~~  101 (101)
T 2la4_A           99 KER  101 (101)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>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=1.3e-16  Score=115.88  Aligned_cols=83  Identities=24%  Similarity=0.388  Sum_probs=75.5

Q ss_pred             cccceEEEcCCCCCCcHHHHH----HhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEe
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLK----EMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG  276 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~----~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~  276 (336)
                      .+.++|||+|||.++++++|+    ++|+.||.|..+.+.. +|.++|+|||+|.+.++|.+|+..|||..+.|+.|+|.
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   84 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH-HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc-CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            345899999999999999999    9999999999998874 56678999999999999999999999999999999999


Q ss_pred             ecccchhh
Q psy12549        277 RAQKKAER  284 (336)
Q Consensus       277 ~~~~~~~~  284 (336)
                      ++.++...
T Consensus        85 ~a~~~~~~   92 (97)
T 1nu4_A           85 YAKTDSDI   92 (97)
T ss_dssp             ECSSCCTH
T ss_pred             EccCCCcc
Confidence            99887554

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.66  E-value=1.9e-16  Score=117.05  Aligned_cols=78  Identities=22%  Similarity=0.248  Sum_probs=70.9

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCC-ceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYG-TITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g-~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ..++|||+|||+++++++|+++|+.|| .|..+.+..  ..++|||||+|.+.++|++|++.|||..+.|+.|+|.++..
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~--~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~  104 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT--RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN  104 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS--CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc--CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            347899999999999999999999999 899998853  34789999999999999999999999999999999999875


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      .
T Consensus       105 ~  105 (111)
T 2jvr_A          105 P  105 (111)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.66  E-value=1e-16  Score=121.93  Aligned_cols=78  Identities=18%  Similarity=0.374  Sum_probs=73.5

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||.++++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|+ .|||..+.|+.|+|.++.+
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            47899999999999999999999999999999887  57889999999999999999999 7999999999999999875


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      .
T Consensus       115 ~  115 (124)
T 2jwn_A          115 N  115 (124)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.66  E-value=1.9e-16  Score=115.87  Aligned_cols=81  Identities=16%  Similarity=0.193  Sum_probs=74.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||.++|+++|+++|+.||.+ .|.++.+++|.++|||||+|.+.++|++|++ +|+..+.++.|.|.++.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            445789999999999999999999999955 9999999999999999999999999999996 79999999999998876


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      +..
T Consensus        91 ~~~   93 (102)
T 1wez_A           91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            553

>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=99.66  E-value=2.1e-16  Score=120.52  Aligned_cols=84  Identities=24%  Similarity=0.364  Sum_probs=77.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.++ ++.++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
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            345799999999999999999999999999999999987 8889999999999999999999999999999999999998


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      .+...
T Consensus       100 ~~~~~  104 (126)
T 3ex7_B          100 FVRGP  104 (126)
T ss_dssp             EESSS
T ss_pred             cCCCC
Confidence            76543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=1.2e-16  Score=117.64  Aligned_cols=82  Identities=23%  Similarity=0.365  Sum_probs=76.1

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhcc-CCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCce-ecCEEEEEee
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEP-YGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKE-VDGKILYVGR  277 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~-~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~-~~g~~l~v~~  277 (336)
                      ...++|||+|||.++++++|+++|+. ||.|..+.++. .++.++|||||+|.+.++|.+|++.|+|.. +.|+.|.|.+
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            34488999999999999999999999 99999999987 578889999999999999999999999999 9999999999


Q ss_pred             cccch
Q psy12549        278 AQKKA  282 (336)
Q Consensus       278 ~~~~~  282 (336)
                      +.++.
T Consensus        87 a~~~~   91 (104)
T 2dhg_A           87 AIPKA   91 (104)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            97664

>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=99.66  E-value=2.2e-16  Score=117.19  Aligned_cols=84  Identities=19%  Similarity=0.297  Sum_probs=76.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCC-eeEEEEe-eCC-CCCcccEEEEEeCCHHHHHHHHHHhC--CceeCCeEEEE
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGS-ILSCKVA-QDE-QGNSKGYGFVHFETEEAANKSIEKVN--GMLLNSKIVFV  183 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~-v~~~~~~-~~~-~~~~~g~afV~F~~~~~a~~a~~~l~--~~~~~~~~i~v  183 (336)
                      ..++|||+|||.++++++|+++|+.||. |..+.++ .++ +|.++|||||+|.+.++|.+|+..|+  +..+.|+.|.|
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            4578999999999999999999999998 9999998 555 67899999999999999999999996  58999999999


Q ss_pred             eeccCchhh
Q psy12549        184 GKFIPRKER  192 (336)
Q Consensus       184 ~~~~~~~~~  192 (336)
                      .++.+....
T Consensus        87 ~~a~~~~~~   95 (109)
T 2dis_A           87 DWAEPEIDV   95 (109)
T ss_dssp             EESCSSCST
T ss_pred             EEcCCCCCc
Confidence            999876553

>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=99.66  E-value=2e-16  Score=115.79  Aligned_cols=78  Identities=19%  Similarity=0.259  Sum_probs=70.3

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCc--eecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGK--EVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~--~~~g~~l~v~~~  278 (336)
                      .+.++|||+|||.++++++|+++|++||.|..+.+++.    +|+|||+|.+.++|.+|++.|++.  .+.|++|+|.|+
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a   88 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEc
Confidence            34588999999999999999999999999999998863    899999999999999999988654  599999999999


Q ss_pred             ccch
Q psy12549        279 QKKA  282 (336)
Q Consensus       279 ~~~~  282 (336)
                      ..+.
T Consensus        89 ~~~~   92 (104)
T 1wex_A           89 TSKR   92 (104)
T ss_dssp             SSSS
T ss_pred             cCcc
Confidence            8764

>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=99.66  E-value=2.4e-16  Score=115.85  Aligned_cols=81  Identities=22%  Similarity=0.299  Sum_probs=74.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeE-EEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILS-CKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~-~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|+.||.|.. +.++.+.+|.++|||||+|.+.++|.+|+.. ++..++|+.|.|.++
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            45689999999999999999999999999987 8888888899999999999999999999997 999999999999887


Q ss_pred             cCc
Q psy12549        187 IPR  189 (336)
Q Consensus       187 ~~~  189 (336)
                      .+.
T Consensus        92 ~~~   94 (104)
T 1wg5_A           92 SRA   94 (104)
T ss_dssp             CTT
T ss_pred             CHH
Confidence            654

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

Probab=99.66  E-value=5.7e-16  Score=111.24  Aligned_cols=77  Identities=23%  Similarity=0.424  Sum_probs=71.3

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.+.      +++|||+|.+.++|.+|+..|||..+.|+.|+|.++.+
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   81 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTS   81 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccC
Confidence            345889999999999999999999999999999997      55999999999999999999999999999999999987


Q ss_pred             chh
Q psy12549        281 KAE  283 (336)
Q Consensus       281 ~~~  283 (336)
                      +..
T Consensus        82 ~~~   84 (92)
T 2dgt_A           82 RLR   84 (92)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            643

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=3e-16  Score=117.87  Aligned_cols=80  Identities=31%  Similarity=0.491  Sum_probs=74.2

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|++|++.+++ .+.|+.|+|.++
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a   93 (116)
T 2cqd_A           15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   93 (116)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEc
Confidence            3458999999999999999999999999999999987  5688899999999999999999999998 899999999999


Q ss_pred             ccc
Q psy12549        279 QKK  281 (336)
Q Consensus       279 ~~~  281 (336)
                      .+.
T Consensus        94 ~~~   96 (116)
T 2cqd_A           94 YLG   96 (116)
T ss_dssp             TTT
T ss_pred             ccC
Confidence            654

>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=99.66  E-value=8.9e-17  Score=117.34  Aligned_cols=80  Identities=20%  Similarity=0.373  Sum_probs=72.5

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCC---CCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEee
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN---DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR  277 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~---~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~  277 (336)
                      ...++|||+|||.++++++|+++|+.|| |.++.+...   +|.++|||||+|.+.++|.+|+ .|+|..+.|+.|+|.+
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            3448999999999999999999999999 999999872   6889999999999999999999 8999999999999999


Q ss_pred             cccch
Q psy12549        278 AQKKA  282 (336)
Q Consensus       278 ~~~~~  282 (336)
                      +.++.
T Consensus        95 a~~~~   99 (100)
T 2j76_E           95 ADQAQ   99 (100)
T ss_dssp             CCCSC
T ss_pred             ccCCC
Confidence            98763

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.66  E-value=7.7e-17  Score=112.89  Aligned_cols=72  Identities=22%  Similarity=0.405  Sum_probs=66.7

Q ss_pred             ceEEEcCCCCCC------CHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCe-EEEE
Q psy12549        111 GNVFIKNLDKSI------DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSK-IVFV  183 (336)
Q Consensus       111 ~~l~v~nlp~~~------t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~-~i~v  183 (336)
                      ++|||+|||..+      ++++|+++|++||.|..+.++ ..+|.++|||||+|.+.++|.+|+..|||..+.|+ +|.|
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 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            689999999999      779999999999999999987 45788999999999999999999999999999998 7765

>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=99.66  E-value=2e-17  Score=151.81  Aligned_cols=81  Identities=27%  Similarity=0.556  Sum_probs=75.7

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ..++|||+|||..+|+++|.++|+.||.|..|.|+.  .++.++|||||+|.+.++|.+||..|||..|.|+.|.|.++.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            347899999999999999999999999999999987  578889999999999999999999999999999999999998


Q ss_pred             cch
Q psy12549        280 KKA  282 (336)
Q Consensus       280 ~~~  282 (336)
                      ++.
T Consensus       181 ~~~  183 (437)
T 3pgw_S          181 GRT  183 (437)
T ss_pred             CCC
Confidence            653

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.66  E-value=3.5e-16  Score=116.00  Aligned_cols=82  Identities=24%  Similarity=0.361  Sum_probs=73.4

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.+..  .+|.++|||||+|.+.++|.+|+..+ |..++|+.|.|.++
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVA  101 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEc
Confidence            3448899999999999999999999999999999987  46889999999999999999999975 69999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus       102 ~~~~~  106 (109)
T 2rs2_A          102 FPRRA  106 (109)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87643

>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=99.65  E-value=6e-16  Score=112.16  Aligned_cols=77  Identities=22%  Similarity=0.459  Sum_probs=70.9

Q ss_pred             cccccceEEEcCCCC-CCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEee
Q psy12549        199 KAKLFTNVYIKNFGE-DFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR  277 (336)
Q Consensus       199 ~~~~~~~l~V~nlp~-~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~  277 (336)
                      .....++|||+|||. .+++++|+++|+.||.|..+.+.      +|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   91 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEV   91 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            334558999999998 99999999999999999999984      89999999999999999999999999999999999


Q ss_pred             cccc
Q psy12549        278 AQKK  281 (336)
Q Consensus       278 ~~~~  281 (336)
                      +.++
T Consensus        92 a~~~   95 (97)
T 2xnq_A           92 SSSN   95 (97)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8765

>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=1.8e-16  Score=116.89  Aligned_cols=82  Identities=20%  Similarity=0.456  Sum_probs=75.9

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|+.||+|..+.++.  .++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a   92 (105)
T 2dh8_A           14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPC   92 (105)
T ss_dssp             SSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEc
Confidence            3458899999999999999999999999999999987  5788999999999999999999998 999999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus        93 ~~~~~   97 (105)
T 2dh8_A           93 TPRGM   97 (105)
T ss_dssp             CCSSC
T ss_pred             cCCCC
Confidence            87754

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=6.7e-16  Score=112.93  Aligned_cols=81  Identities=25%  Similarity=0.406  Sum_probs=73.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||.++++++|+++|+.||.|   .++.+.++.++|||||+|.+.++|.+|+..||+..+.|+.|.|.++.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   89 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQG   89 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcC
Confidence            456899999999999999999999999977   56666778899999999999999999999999999999999999988


Q ss_pred             Cchh
Q psy12549        188 PRKE  191 (336)
Q Consensus       188 ~~~~  191 (336)
                      +...
T Consensus        90 ~~~~   93 (101)
T 2fc9_A           90 PRGS   93 (101)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7643

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.65  E-value=4.7e-16  Score=117.97  Aligned_cols=85  Identities=18%  Similarity=0.263  Sum_probs=75.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMY----DTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~----~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      ...++|||+|||+.+++++|+    ++|++||.|..|.+..  ++.++|||||+|.+.++|..|+..|||..+.|+.|.|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~--~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V  104 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL--SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI  104 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC--CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc--CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEE
Confidence            345789999999999999876    6999999999887753  5778999999999999999999999999999999999


Q ss_pred             eeccCchhhhH
Q psy12549        184 GKFIPRKEREK  194 (336)
Q Consensus       184 ~~~~~~~~~~~  194 (336)
                      .++.+......
T Consensus       105 ~~a~~~~~~~~  115 (127)
T 2a3j_A          105 TFSETPQSQVA  115 (127)
T ss_dssp             EECCCCCHHHH
T ss_pred             EEccCcchhcc
Confidence            99987765443

>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=99.65  E-value=4.8e-16  Score=114.77  Aligned_cols=89  Identities=9%  Similarity=0.021  Sum_probs=79.3

Q ss_pred             CCCccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCcccc
Q psy12549         11 EEGIIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDAL   89 (336)
Q Consensus        11 ~~~~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~   89 (336)
                      +.....+.++|||+|||.++++++|+++| .++.+..++++.++   .+|.++|||||+|.+.  ++|++|++.+++..+
T Consensus         6 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~---~~g~~~g~afV~f~~~--~~A~~A~~~l~g~~~   80 (106)
T 2dgp_A            6 SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDR---FTGMHKGCAFLTYCER--ESALKAQSALHEQKT   80 (106)
T ss_dssp             CSCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCS---SSCSCCSEEEEEESSH--HHHHHHHHHHTTTCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecC---CCCCcceEEEEEECCH--HHHHHHHHHhcCCcc
Confidence            34455678899999999999999999999 77789999999987   3789999999999999  999999999999887


Q ss_pred             ---CCeeeEEEeccCCCC
Q psy12549         90 ---KGRPIRIMWSQRDPS  104 (336)
Q Consensus        90 ---~g~~i~v~~~~~~~~  104 (336)
                         .|++|.|.++.....
T Consensus        81 ~~~~g~~l~v~~a~~~~~   98 (106)
T 2dgp_A           81 LPGMNRPIQVKPADSESR   98 (106)
T ss_dssp             CTTCSSCCEEEECCCCSC
T ss_pred             cCCCCceEEEEECCcccc
Confidence               899999999877554

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.65  E-value=5.5e-16  Score=114.61  Aligned_cols=78  Identities=28%  Similarity=0.534  Sum_probs=72.1

Q ss_pred             ccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        200 AKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       200 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ....++|||+|||..+++++|+++|+.||.|..+.+.      +|||||+|.+.++|.+|+..|||..+.|+.|.|.++.
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  101 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSK  101 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            3445899999999999999999999999999999997      8899999999999999999999999999999999998


Q ss_pred             cchh
Q psy12549        280 KKAE  283 (336)
Q Consensus       280 ~~~~  283 (336)
                      ++..
T Consensus       102 ~~~~  105 (108)
T 2jvo_A          102 LPAK  105 (108)
T ss_dssp             CCC-
T ss_pred             CCCC
Confidence            7643

>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=99.65  E-value=4.5e-16  Score=115.99  Aligned_cols=79  Identities=16%  Similarity=0.233  Sum_probs=71.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCC--ceeCCeEEEEee
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG--MLLNSKIVFVGK  185 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~--~~~~~~~i~v~~  185 (336)
                      ...++|||+|||+++++++|+++|++||.|..+.++++     +|||||+|.+.++|.+|++.+++  ..+.|++|.|.+
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~  103 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF  103 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEE
Confidence            44678999999999999999999999999999999875     78999999999999999998874  689999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.+...
T Consensus       104 a~~k~~  109 (119)
T 2ad9_A          104 SNHKEL  109 (119)
T ss_dssp             CSSSSC
T ss_pred             ccCCCC
Confidence            876644

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

Probab=99.65  E-value=3.6e-16  Score=111.77  Aligned_cols=77  Identities=21%  Similarity=0.486  Sum_probs=71.8

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.+.      ++||||+|.+.++|.+|++.|||..+.|+.|+|.++.+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   79 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKN   79 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCC
Confidence            345889999999999999999999999999999997      78999999999999999999999999999999999987


Q ss_pred             chh
Q psy12549        281 KAE  283 (336)
Q Consensus       281 ~~~  283 (336)
                      +..
T Consensus        80 ~~~   82 (90)
T 2dnq_A           80 KSK   82 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.65  E-value=3.3e-16  Score=117.16  Aligned_cols=81  Identities=16%  Similarity=0.218  Sum_probs=74.4

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCce-eEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTI-TSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i-~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||.++++++|+++|+.||.| ..+.++. .+|.++|||||+|.+.++|.+|++. |+..+.|+.|.|.++
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            345889999999999999999999999999 8888877 6788999999999999999999987 999999999999999


Q ss_pred             ccch
Q psy12549        279 QKKA  282 (336)
Q Consensus       279 ~~~~  282 (336)
                      .++.
T Consensus        92 ~~~~   95 (114)
T 2cpy_A           92 TLED   95 (114)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            8764

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.65  E-value=3.2e-16  Score=121.64  Aligned_cols=83  Identities=28%  Similarity=0.515  Sum_probs=76.7

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++
T Consensus        40 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  119 (139)
T 1u6f_A           40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3448899999999999999999999999999999987  56888999999999999999999999999999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus       120 ~~~~~  124 (139)
T 1u6f_A          120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87643

>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=99.65  E-value=4.9e-17  Score=116.36  Aligned_cols=80  Identities=26%  Similarity=0.502  Sum_probs=72.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      ++|||+|||.++++++|+++|+.||.|..+.+..++ +|.++|||||+|.+.+ |.+|+..|||..+.|+.|.|.++.+.
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            579999999999999999999999999999999987 6889999999999999 99999999999999999999998776


Q ss_pred             hh
Q psy12549        190 KE  191 (336)
Q Consensus       190 ~~  191 (336)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            44

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=1.1e-16  Score=110.88  Aligned_cols=74  Identities=27%  Similarity=0.443  Sum_probs=69.7

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ++|||+|||.++++++|+++|++||+|..+.+..  .+|.++|+|||+|.+.++|.+|++.++ ..+.|+.|.|.+|
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            4799999999999999999999999999999987  468889999999999999999999988 9999999999886

>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=99.65  E-value=2.5e-16  Score=120.15  Aligned_cols=84  Identities=20%  Similarity=0.354  Sum_probs=77.2

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|+|||+|.+.++|.+|++.|||..+.|+.|.|.++
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            3457899999999999999999999999999999987  48888999999999999999999999999999999999999


Q ss_pred             ccchhh
Q psy12549        279 QKKAER  284 (336)
Q Consensus       279 ~~~~~~  284 (336)
                      .++...
T Consensus       100 ~~~~~~  105 (126)
T 3ex7_B          100 FVRGPP  105 (126)
T ss_dssp             EESSSC
T ss_pred             cCCCCC
Confidence            876543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.65  E-value=9.3e-16  Score=119.18  Aligned_cols=79  Identities=24%  Similarity=0.434  Sum_probs=73.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
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            456799999999999999999999999999999999986 7889999999999999999999999999999999999864

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.65  E-value=3.6e-16  Score=117.64  Aligned_cols=80  Identities=13%  Similarity=0.180  Sum_probs=73.5

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCc---eeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEe
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGT---ITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG  276 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~---i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~  276 (336)
                      ...++|||+|||+++++++|+++|+.||.   |..+.++. ..|+++|||||+|.+.++|++|++ +||..+.|+.|.|.
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            34478999999999999999999999999   88998886 558899999999999999999999 99999999999999


Q ss_pred             ecccc
Q psy12549        277 RAQKK  281 (336)
Q Consensus       277 ~~~~~  281 (336)
                      ++..+
T Consensus        94 ~a~~~   98 (118)
T 2db1_A           94 KSHRT   98 (118)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            98754

>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=99.65  E-value=4.5e-16  Score=112.94  Aligned_cols=78  Identities=21%  Similarity=0.360  Sum_probs=72.2

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceec--CEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD--GKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~--g~~l~v~~~  278 (336)
                      .+.++|||+|||..+++++|+++|++||.|..+.+...    +++|||+|.+.++|.+|++.|||..+.  |+.|+|.++
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a   90 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA   90 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC----CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEEC
Confidence            34488999999999999999999999999999998754    789999999999999999999999999  999999999


Q ss_pred             ccch
Q psy12549        279 QKKA  282 (336)
Q Consensus       279 ~~~~  282 (336)
                      .++.
T Consensus        91 ~~~~   94 (97)
T 1why_A           91 KSGP   94 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=5.1e-16  Score=116.59  Aligned_cols=81  Identities=20%  Similarity=0.469  Sum_probs=76.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++.+
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCC
Confidence            4799999999999999999999999999999999986 688999999999999999999997 99999999999999887


Q ss_pred             chh
Q psy12549        189 RKE  191 (336)
Q Consensus       189 ~~~  191 (336)
                      +..
T Consensus       106 ~~~  108 (116)
T 1x4b_A          106 REE  108 (116)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.65  E-value=5.7e-16  Score=117.78  Aligned_cols=80  Identities=19%  Similarity=0.376  Sum_probs=75.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|.+|+ .|++..+.|+.|.|.++.+
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            5799999999999999999999999999999999986 7889999999999999999999 7999999999999999876


Q ss_pred             ch
Q psy12549        189 RK  190 (336)
Q Consensus       189 ~~  190 (336)
                      ..
T Consensus       115 ~~  116 (124)
T 2jwn_A          115 NM  116 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.65  E-value=5.6e-16  Score=114.58  Aligned_cols=78  Identities=17%  Similarity=0.190  Sum_probs=70.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccC-CeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFG-SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G-~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+|||.++++++|+++|++|| .|..+.+...   .++|||||+|.+.++|++|++.|||..+.|+.|.|.++.
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~  103 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDD  103 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECC
Confidence            347899999999999999999999999 8999988643   378999999999999999999999999999999999886


Q ss_pred             Cc
Q psy12549        188 PR  189 (336)
Q Consensus       188 ~~  189 (336)
                      ..
T Consensus       104 ~~  105 (111)
T 2jvr_A          104 NP  105 (111)
T ss_dssp             C-
T ss_pred             CC
Confidence            54

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.65  E-value=3.4e-16  Score=113.35  Aligned_cols=79  Identities=28%  Similarity=0.458  Sum_probs=72.4

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+   ..++.++|+|||+|.+.++|.+|+..|+|..+.|+.|.|.++.+
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~---~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   90 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV---SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE---EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe---CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCC
Confidence            345899999999999999999999999998777   55678899999999999999999999999999999999999987


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      +.
T Consensus        91 ~~   92 (96)
T 1fjc_A           91 KG   92 (96)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=7.6e-16  Score=112.62  Aligned_cols=79  Identities=25%  Similarity=0.450  Sum_probs=71.5

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ...++|||+|||..+++++|+++|+.||.|   .++. .++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   89 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQG   89 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcC
Confidence            345899999999999999999999999987   3444 678889999999999999999999999999999999999998


Q ss_pred             cch
Q psy12549        280 KKA  282 (336)
Q Consensus       280 ~~~  282 (336)
                      ++.
T Consensus        90 ~~~   92 (101)
T 2fc9_A           90 PRG   92 (101)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            763

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.64  E-value=1.2e-16  Score=122.60  Aligned_cols=82  Identities=15%  Similarity=0.330  Sum_probs=76.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeE--EEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCc----eeCCeE
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILS--CKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGM----LLNSKI  180 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~--~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~----~~~~~~  180 (336)
                      ...++|||+|||.++|+++|+++|+.||.|..  |+++.++ +|.++|||||+|.+. +|.+|+..||+.    .+.|+.
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~   99 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKT   99 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEE
Confidence            45679999999999999999999999999977  9999998 899999999999999 999999999999    999999


Q ss_pred             EEEeeccCch
Q psy12549        181 VFVGKFIPRK  190 (336)
Q Consensus       181 i~v~~~~~~~  190 (336)
                      |.|.++.+..
T Consensus       100 l~V~~a~~~~  109 (131)
T 2m2b_A          100 INVEFAKGSK  109 (131)
T ss_dssp             CCCEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999987754

>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=99.64  E-value=6.5e-16  Score=109.19  Aligned_cols=75  Identities=24%  Similarity=0.452  Sum_probs=69.7

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHh-CCceecCEEEEEeecc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW-NGKEVDGKILYVGRAQ  279 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l-~g~~~~g~~l~v~~~~  279 (336)
                      ...++|||+|||..+++++|+++|++||.|..+.+.+    ++|+|||+|.+.++|.+|+..| +|..+.|+.|+|.|++
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 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ----RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWGR   85 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG----GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEECC
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC----CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEecC
Confidence            3447899999999999999999999999999999986    4899999999999999999999 9999999999999874

>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=1.2e-15  Score=113.02  Aligned_cols=76  Identities=16%  Similarity=0.167  Sum_probs=71.2

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecC-----EEEEEe
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG-----KILYVG  276 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g-----~~l~v~  276 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+.++..     |||||+|.+.++|++|++.|||..+.|     +.|.|.
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-----g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~   88 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   88 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-----TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-----CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEE
Confidence            3488999999999999999999999999999999864     899999999999999999999999999     999999


Q ss_pred             ecccch
Q psy12549        277 RAQKKA  282 (336)
Q Consensus       277 ~~~~~~  282 (336)
                      ++.++.
T Consensus        89 ~a~~~~   94 (108)
T 1x4c_A           89 VDGPRS   94 (108)
T ss_dssp             ESSCCS
T ss_pred             eCCCCC
Confidence            998764

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.64  E-value=2.9e-16  Score=120.54  Aligned_cols=80  Identities=11%  Similarity=0.151  Sum_probs=73.6

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCc---eeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEe
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGT---ITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG  276 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~---i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~  276 (336)
                      ...++|||+|||+++|+++|+++|+.||.   |..+.++. ..|+++|||||+|.+.++|++|++ +||..++|+.|.|.
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            34588999999999999999999999999   88898886 558999999999999999999999 99999999999999


Q ss_pred             ecccc
Q psy12549        277 RAQKK  281 (336)
Q Consensus       277 ~~~~~  281 (336)
                      ++.++
T Consensus       121 ~a~~~  125 (136)
T 2hgl_A          121 KSHRT  125 (136)
T ss_dssp             ECCHH
T ss_pred             ECChH
Confidence            98755

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

Probab=99.64  E-value=5.6e-16  Score=110.77  Aligned_cols=76  Identities=26%  Similarity=0.425  Sum_probs=70.7

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.+.      +++|||+|.+.++|.+|+..|||..+.|+.|+|.++.+
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   80 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTK   80 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCC
Confidence            345889999999999999999999999999999997      55999999999999999999999999999999999987


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      +.
T Consensus        81 ~~   82 (90)
T 2dnp_A           81 GQ   82 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=6.9e-16  Score=115.86  Aligned_cols=80  Identities=30%  Similarity=0.579  Sum_probs=74.7

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|+.. ++..+.|+.|+|.++.+
T Consensus        27 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCC
Confidence            37899999999999999999999999999999987  5688899999999999999999998 99999999999999987


Q ss_pred             chh
Q psy12549        281 KAE  283 (336)
Q Consensus       281 ~~~  283 (336)
                      +..
T Consensus       106 ~~~  108 (116)
T 1x4b_A          106 REE  108 (116)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            743

>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=1.3e-16  Score=117.64  Aligned_cols=79  Identities=23%  Similarity=0.339  Sum_probs=70.7

Q ss_pred             ccccceEEEcCCCCC-CcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhC--CceecCEEEEEe
Q psy12549        200 AKLFTNVYIKNFGED-FNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN--GKEVDGKILYVG  276 (336)
Q Consensus       200 ~~~~~~l~V~nlp~~-~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~--g~~~~g~~l~v~  276 (336)
                      ..+.++|||+|||++ +++++|+++|++||.|.++.+.+    ++|||||+|.+.++|.+|++.|+  +..+.|++|+|.
T Consensus        22 ~~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           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR----MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   97 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET----TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec----CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            344589999999998 99999999999999999999975    48999999999999999999885  456999999999


Q ss_pred             ecccch
Q psy12549        277 RAQKKA  282 (336)
Q Consensus       277 ~~~~~~  282 (336)
                      ++..+.
T Consensus        98 ~a~~~~  103 (112)
T 1x4f_A           98 LSEKYK  103 (112)
T ss_dssp             EECSCS
T ss_pred             ECcccc
Confidence            998664

>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=99.64  E-value=5.8e-17  Score=115.97  Aligned_cols=79  Identities=24%  Similarity=0.513  Sum_probs=70.8

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ++|||+|||.++++++|+++|+.||.|.++.+..  .+|.++|+|||+|.+.+ |.+|+..|||..+.|+.|+|.++.+.
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            5799999999999999999999999999999987  46888999999999999 99999999999999999999999876


Q ss_pred             hh
Q psy12549        282 AE  283 (336)
Q Consensus       282 ~~  283 (336)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>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=99.64  E-value=1.3e-15  Score=107.64  Aligned_cols=75  Identities=24%  Similarity=0.399  Sum_probs=69.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV-NGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l-~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|++||.|..+.+.++     +|||||+|.+.++|.+|+..| ++..+.|+.|.|.++
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~a   84 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWG   84 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEEC
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEec
Confidence            45579999999999999999999999999999999863     789999999999999999998 999999999999886


Q ss_pred             c
Q psy12549        187 I  187 (336)
Q Consensus       187 ~  187 (336)
                      +
T Consensus        85 k   85 (85)
T 2ytc_A           85 R   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=1.1e-15  Score=112.65  Aligned_cols=76  Identities=16%  Similarity=0.272  Sum_probs=70.8

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      .+|||+|||+++++++|+++|+.| .|..+.++. ..|+++|+|||+|.+.++|.+|+ .+|+..++|+.|.|..+.++
T Consensus        17 ~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           17 LYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             HEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCcc
Confidence            689999999999999999999999 899999987 56889999999999999999999 58999999999999888654

>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=5.1e-16  Score=113.10  Aligned_cols=78  Identities=27%  Similarity=0.478  Sum_probs=72.4

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.+.+.    +|||||+|.+.++|.+|++.|||..+.|+.|+|.++.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~----kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   88 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   88 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCC
Confidence            34478999999999999999999999999999999854    89999999999999999999999999999999999987


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      +.
T Consensus        89 ~~   90 (99)
T 2cpj_A           89 SA   90 (99)
T ss_dssp             CS
T ss_pred             CC
Confidence            63

>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=1.1e-15  Score=109.29  Aligned_cols=77  Identities=29%  Similarity=0.541  Sum_probs=71.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.+.       ++||||+|.+.++|.+|+..|++..+.|+.|.|.++.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   78 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASK   78 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECC
Confidence            456899999999999999999999999999999987       5799999999999999999999999999999999988


Q ss_pred             Cchh
Q psy12549        188 PRKE  191 (336)
Q Consensus       188 ~~~~  191 (336)
                      +...
T Consensus        79 ~~~~   82 (90)
T 2dnq_A           79 NKSK   82 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.64  E-value=9.7e-16  Score=121.35  Aligned_cols=83  Identities=27%  Similarity=0.325  Sum_probs=76.8

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|+.||.|..|.++.  .++.+++||||+|.+.++|.+|++.|||..|.|+.|+|.++
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            3458999999999999999999999999999999987  46888999999999999999999999999999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .+...
T Consensus       117 ~~~~~  121 (156)
T 1h2v_Z          117 AGFKE  121 (156)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            87654

>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=99.64  E-value=4e-16  Score=113.22  Aligned_cols=83  Identities=22%  Similarity=0.362  Sum_probs=75.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHH----HHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMY----DTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~----~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      ...++|||+|||.++++++|+    ++|+.||.|..+.+..  +|.++|||||+|.+.++|.+|+..|+|..+.|+.|.|
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   83 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEE
Confidence            345789999999999999999    9999999999998874  4567899999999999999999999999999999999


Q ss_pred             eeccCchhh
Q psy12549        184 GKFIPRKER  192 (336)
Q Consensus       184 ~~~~~~~~~  192 (336)
                      .++.+....
T Consensus        84 ~~a~~~~~~   92 (97)
T 1nu4_A           84 QYAKTDSDI   92 (97)
T ss_dssp             EECSSCCTH
T ss_pred             EEccCCCcc
Confidence            999876543

>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=99.64  E-value=9.4e-16  Score=113.77  Aligned_cols=81  Identities=22%  Similarity=0.505  Sum_probs=74.3

Q ss_pred             cccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        199 KAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       199 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      .....++|||+|||..+++++|+++|+.||.|..+.+...    +|||||+|.+.++|.+|+..|+|..+.|+.|+|.++
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            3345589999999999999999999999999999999865    899999999999999999999999999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus        97 ~~~~~  101 (109)
T 1x4g_A           97 KESPD  101 (109)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            87643

>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=99.64  E-value=1.3e-15  Score=111.78  Aligned_cols=81  Identities=22%  Similarity=0.396  Sum_probs=73.8

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|+.  ++..+.|+.|.|.++
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            3447899999999999999999999999999999987  568899999999999999999998  478999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus        91 ~~~~~   95 (103)
T 2cqg_A           91 NSKQS   95 (103)
T ss_dssp             CTTCC
T ss_pred             CCCCc
Confidence            87643

>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=99.64  E-value=1.9e-16  Score=117.12  Aligned_cols=83  Identities=17%  Similarity=0.187  Sum_probs=76.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCC---eeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGS---ILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~---v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      ....++|||+|||.++|+++|+++|+.||.   |..+.++.++.|.++|||||+|.+.++|.+|+. +++..++|+.|.|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            345678999999999999999999999998   899999999889999999999999999999999 9999999999999


Q ss_pred             eeccCch
Q psy12549        184 GKFIPRK  190 (336)
Q Consensus       184 ~~~~~~~  190 (336)
                      .++.+..
T Consensus        87 ~~a~~~~   93 (107)
T 2lmi_A           87 YEINNED   93 (107)
T ss_dssp             EECCHHH
T ss_pred             EECCHHH
Confidence            8887654

>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=99.64  E-value=4.1e-16  Score=115.95  Aligned_cols=75  Identities=19%  Similarity=0.177  Sum_probs=70.3

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      .++|||+|||..+++++|+++|++||.|..+.+..    ++++|||+|.+.++|.+|+..|||..+.|+.|.|.|+...
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC----CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            47899999999999999999999999999998874    4789999999999999999999999999999999998754

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.63  E-value=8.1e-16  Score=119.52  Aligned_cols=79  Identities=32%  Similarity=0.502  Sum_probs=72.9

Q ss_pred             ccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEee
Q psy12549        200 AKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR  277 (336)
Q Consensus       200 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~  277 (336)
                      ....++|||+|||..+++++|+++|+.||.|..+.++.  .++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.+
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34458999999999999999999999999999999887  5688899999999999999999999999999999999988


Q ss_pred             c
Q psy12549        278 A  278 (336)
Q Consensus       278 ~  278 (336)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            5

>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=99.63  E-value=8.8e-16  Score=114.92  Aligned_cols=80  Identities=31%  Similarity=0.536  Sum_probs=74.0

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCcee--------cCEE
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEV--------DGKI  272 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~--------~g~~  272 (336)
                      ..++|||+|||..+++++|+++|+.||.|..+.++. .++.++|||||+|.+.++|.+|+..|||..+        .|++
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~  103 (114)
T 1x5o_A           24 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP  103 (114)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCc
Confidence            448899999999999999999999999999999987 5788899999999999999999999999999        5788


Q ss_pred             EEEeecccc
Q psy12549        273 LYVGRAQKK  281 (336)
Q Consensus       273 l~v~~~~~~  281 (336)
                      |.|.|+.++
T Consensus       104 l~v~~a~p~  112 (114)
T 1x5o_A          104 LLCKFSGPS  112 (114)
T ss_dssp             BEEEECCCS
T ss_pred             eeEEccCCC
Confidence            999998864

>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=99.63  E-value=2.1e-15  Score=109.26  Aligned_cols=77  Identities=18%  Similarity=0.403  Sum_probs=70.3

Q ss_pred             CCCCCceEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        106 RKSGVGNVFIKNLDK-SIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       106 ~~~~~~~l~v~nlp~-~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      .....++|||+|||. ++++++|+++|+.||.|..+.+.       +|||||+|.+.++|.+|+..|+|..+.|+.|.|.
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 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            344568999999998 99999999999999999999883       6899999999999999999999999999999999


Q ss_pred             eccCc
Q psy12549        185 KFIPR  189 (336)
Q Consensus       185 ~~~~~  189 (336)
                      ++.+.
T Consensus        91 ~a~~~   95 (97)
T 2xnq_A           91 VSSSN   95 (97)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            98754

>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=99.63  E-value=1.6e-16  Score=109.46  Aligned_cols=74  Identities=19%  Similarity=0.365  Sum_probs=69.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      +|||+|||.++++++|+++|++||.|..+.++.++ +|.++|||||+|.+.++|.+|++ +++..+.|+.+.|.++
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            58999999999999999999999999999999886 68899999999999999999999 4899999999988764

>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=99.63  E-value=1.1e-15  Score=110.84  Aligned_cols=77  Identities=18%  Similarity=0.324  Sum_probs=71.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeC--CeEEEEeec
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLN--SKIVFVGKF  186 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~--~~~i~v~~~  186 (336)
                      ..++|||+|||.++++++|+++|++||.|..+.+..+     +|||||+|.+.++|.+|++.||+..+.  |+.|.|.++
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a   90 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA   90 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEEC
Confidence            3478999999999999999999999999999998864     679999999999999999999999999  999999998


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .++.
T Consensus        91 ~~~~   94 (97)
T 1why_A           91 KSGP   94 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8754

>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=99.63  E-value=5.2e-16  Score=114.09  Aligned_cols=80  Identities=18%  Similarity=0.274  Sum_probs=72.9

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeE-EEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS-YRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~-~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||+++++++|+++|+.||.|.. +.++. .+|.++|||||+|.++++|.+|+.. ++..++|+.|.|.++
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            34488999999999999999999999999987 77766 6888999999999999999999997 999999999999988


Q ss_pred             ccc
Q psy12549        279 QKK  281 (336)
Q Consensus       279 ~~~  281 (336)
                      ..+
T Consensus        92 ~~~   94 (104)
T 1wg5_A           92 SRA   94 (104)
T ss_dssp             CTT
T ss_pred             CHH
Confidence            755

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.63  E-value=1.4e-15  Score=112.43  Aligned_cols=79  Identities=23%  Similarity=0.410  Sum_probs=71.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       106 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      .....++|||+|||.++++++|+++|+.||.|..+.+.       +|||||+|.+.++|.+|+..|+|..+.|+.|.|.+
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            33456899999999999999999999999999999988       57999999999999999999999999999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.+...
T Consensus       100 a~~~~~  105 (108)
T 2jvo_A          100 SKLPAK  105 (108)
T ss_dssp             CSCCC-
T ss_pred             ecCCCC
Confidence            877643

>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=99.63  E-value=9.4e-16  Score=113.95  Aligned_cols=94  Identities=27%  Similarity=0.417  Sum_probs=78.2

Q ss_pred             CCeeeEEEeccCCCC-cCCCCCceEEEcCCCCC-CCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHH
Q psy12549         90 KGRPIRIMWSQRDPS-LRKSGVGNVFIKNLDKS-IDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS  167 (336)
Q Consensus        90 ~g~~i~v~~~~~~~~-~~~~~~~~l~v~nlp~~-~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a  167 (336)
                      .|.++.+..+..... ......++|||+|||.. +++++|+++|+.||.|..+.+       ++|||||+|.+.++|.+|
T Consensus         6 ~g~~~~~~~s~~~~~~~~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A   78 (110)
T 1wf1_A            6 SGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAA   78 (110)
T ss_dssp             CSCCCCCCCCCSCCSCCCTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHH
T ss_pred             CCcccccccCCCCCCCCCCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHH
Confidence            455666655543322 22334579999999999 999999999999999999998       468999999999999999


Q ss_pred             HHHhCCceeCCeEEEEeeccCch
Q psy12549        168 IEKVNGMLLNSKIVFVGKFIPRK  190 (336)
Q Consensus       168 ~~~l~~~~~~~~~i~v~~~~~~~  190 (336)
                      +..|++..+.|+.|.|.++.+..
T Consensus        79 ~~~l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           79 VLGENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             HHHHTTCEETTEECCEEESCCCC
T ss_pred             HHHcCCCEECCeEEEEEECCCCC
Confidence            99999999999999999987543

>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=99.63  E-value=1.9e-15  Score=111.85  Aligned_cols=77  Identities=22%  Similarity=0.275  Sum_probs=71.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCC-----eEEE
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNS-----KIVF  182 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~-----~~i~  182 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.+      |||||+|.+.++|++|++.||+..+.|     +.|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~   86 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   86 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEE
Confidence            34579999999999999999999999999999999876      799999999999999999999999999     9999


Q ss_pred             EeeccCch
Q psy12549        183 VGKFIPRK  190 (336)
Q Consensus       183 v~~~~~~~  190 (336)
                      |.++.++.
T Consensus        87 V~~a~~~~   94 (108)
T 1x4c_A           87 VKVDGPRS   94 (108)
T ss_dssp             EEESSCCS
T ss_pred             EEeCCCCC
Confidence            99988754

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1.2e-15  Score=111.74  Aligned_cols=89  Identities=13%  Similarity=0.144  Sum_probs=77.6

Q ss_pred             cCCCCccccCceeeeecCchhhhhhhHHhhhcccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccc
Q psy12549          9 LSEEGIIIPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDA   88 (336)
Q Consensus         9 ~~~~~~~~p~~~v~v~~lp~~~~e~~l~~~f~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~   88 (336)
                      .++.....+.++|||+|||.++++++|+++|+..  ..++++.++   .++.++|||||+|.+.  ++|++|++.+++..
T Consensus         6 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~--~~~~~~~~~---~~~~~~g~afV~f~~~--~~A~~A~~~l~g~~   78 (102)
T 2fc8_A            6 SGPNARSQPSKTLFVKGLSEDTTEETLKESFDGS--VRARIVTDR---ETGSSKGFGFVDFNSE--EDAKAAKEAMEDGE   78 (102)
T ss_dssp             CTTSSSSCCCSSEEEECCCTTCCHHHHHHTSTTC--SEEEEEECS---SSCSEEEEEEEECSSH--HHHHHHHHHHTTCE
T ss_pred             CCCCCCCCCCCEEEEeCCCCccCHHHHHHHhcCC--eEEEEEecC---CCCCcCcEEEEEECCH--HHHHHHHHHhCCCe
Confidence            3455566788999999999999999999999743  478888776   3688999999999999  99999999999999


Q ss_pred             cCCeeeEEEeccCCCC
Q psy12549         89 LKGRPIRIMWSQRDPS  104 (336)
Q Consensus        89 ~~g~~i~v~~~~~~~~  104 (336)
                      +.|+.|.|.++.+...
T Consensus        79 ~~g~~l~V~~a~~~~~   94 (102)
T 2fc8_A           79 IDGNKVTLDWAKPKGE   94 (102)
T ss_dssp             ETTEECEEEECCCCCS
T ss_pred             ECCeEEEEEEecCCCC
Confidence            9999999999877654

>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=99.63  E-value=1.4e-15  Score=112.74  Aligned_cols=79  Identities=29%  Similarity=0.458  Sum_probs=73.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.+..+     +|||||+|.+.++|.+|+..|++..+.|+.|.|.++.
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   97 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   97 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecC
Confidence            34579999999999999999999999999999999876     6899999999999999999999999999999999988


Q ss_pred             Cchh
Q psy12549        188 PRKE  191 (336)
Q Consensus       188 ~~~~  191 (336)
                      +...
T Consensus        98 ~~~~  101 (109)
T 1x4g_A           98 ESPD  101 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7654

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.63  E-value=9.6e-16  Score=112.08  Aligned_cols=75  Identities=23%  Similarity=0.312  Sum_probs=70.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+.+..     ++|||||+|.+.++|.+|+..||+..+.|+.|.|.++.+
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP-----EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            357899999999999999999999999999999883     578999999999999999999999999999999998765

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.63  E-value=4.6e-16  Score=112.66  Aligned_cols=80  Identities=21%  Similarity=0.323  Sum_probs=71.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ....++|||+|||..+++++|+++|+.||.|..+    ..++.++|||||+|.+.++|.+|+..|++..+.|+.|.|.++
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   88 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            3456899999999999999999999999988765    346778999999999999999999999999999999999998


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .++.
T Consensus        89 ~~~~   92 (96)
T 1fjc_A           89 GEKG   92 (96)
T ss_dssp             SSSC
T ss_pred             CCCC
Confidence            7654

>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=99.63  E-value=7.8e-16  Score=112.59  Aligned_cols=79  Identities=16%  Similarity=0.246  Sum_probs=70.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCC--ceeCCeEEEEee
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG--MLLNSKIVFVGK  185 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~--~~~~~~~i~v~~  185 (336)
                      ...++|||+|||.++++++|+++|++||.|..+.++++     +|||||+|.+.++|.+|++.|++  ..+.|+.|.|.+
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~   87 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            34578999999999999999999999999999998864     78999999999999999998865  459999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.+...
T Consensus        88 a~~~~~   93 (104)
T 1wex_A           88 STSKRI   93 (104)
T ss_dssp             CSSSSC
T ss_pred             ccCccc
Confidence            876543

>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=99.63  E-value=1.2e-15  Score=111.02  Aligned_cols=78  Identities=24%  Similarity=0.375  Sum_probs=72.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.+.++     +|||||+|.+.++|.+|++.|++..+.|+.|.|.++.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   87 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   87 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcC
Confidence            45679999999999999999999999999999999854     6899999999999999999999999999999999987


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      +..
T Consensus        88 ~~~   90 (99)
T 2cpj_A           88 HSA   90 (99)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            754

>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=99.63  E-value=8.1e-16  Score=112.90  Aligned_cols=76  Identities=18%  Similarity=0.473  Sum_probs=71.0

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+.+.      ++||||+|.+.++|.+|++.|||..+.|+.|.|.++.++
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   83 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPP   83 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCC
Confidence            34789999999999999999999999999999986      679999999999999999999999999999999999876


Q ss_pred             hh
Q psy12549        282 AE  283 (336)
Q Consensus       282 ~~  283 (336)
                      ..
T Consensus        84 ~~   85 (103)
T 2dgu_A           84 DQ   85 (103)
T ss_dssp             CC
T ss_pred             cc
Confidence            44

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=5.3e-16  Score=116.91  Aligned_cols=81  Identities=19%  Similarity=0.194  Sum_probs=73.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCe----eEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSI----LSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v----~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      ...+|||+|||.++|+++|+++|+.||.|    ..|.++.+++|+++|||||+|.+.++|.+|+.. |+..+.|+.|.|.
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V~  100 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIELF  100 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEEE
Confidence            45789999999999999999999999975    689999998999999999999999999999995 9999999999998


Q ss_pred             eccCch
Q psy12549        185 KFIPRK  190 (336)
Q Consensus       185 ~~~~~~  190 (336)
                      .+.+..
T Consensus       101 ~a~~~e  106 (123)
T 2dha_A          101 RSTAAE  106 (123)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            876543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=2.1e-15  Score=110.44  Aligned_cols=84  Identities=25%  Similarity=0.454  Sum_probs=74.8

Q ss_pred             cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        105 LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       105 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      ......++|||+|||.++++++|+++|+.|+   .+.++.++ ++.++|||||+|.+.++|.+|+..|++..+.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   86 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL   86 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            3445668999999999999999999999874   56777775 7889999999999999999999999999999999999


Q ss_pred             eeccCchh
Q psy12549        184 GKFIPRKE  191 (336)
Q Consensus       184 ~~~~~~~~  191 (336)
                      .++.++..
T Consensus        87 ~~a~~~~~   94 (102)
T 2fc8_A           87 DWAKPKGE   94 (102)
T ss_dssp             EECCCCCS
T ss_pred             EEecCCCC
Confidence            99987654

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

Probab=99.63  E-value=3.2e-15  Score=107.26  Aligned_cols=78  Identities=21%  Similarity=0.440  Sum_probs=71.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ....++|||+|||.++++++|+++|+.||.|..+.+.+       +||||+|.+.++|.+|+..||+..+.|+.|.|.++
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS-------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            34568999999999999999999999999999999884       39999999999999999999999999999999999


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      .+...
T Consensus        80 ~~~~~   84 (92)
T 2dgt_A           80 TSRLR   84 (92)
T ss_dssp             SCCCS
T ss_pred             cCCCC
Confidence            87644

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

Probab=99.63  E-value=2.2e-15  Score=109.69  Aligned_cols=76  Identities=25%  Similarity=0.411  Sum_probs=70.5

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccC--CceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPY--GTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~--g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...++|||+|||..+++++|+++|+.|  |.|..+.+.      +|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   86 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            345889999999999999999999999  899999875      789999999999999999999999999999999999


Q ss_pred             ccch
Q psy12549        279 QKKA  282 (336)
Q Consensus       279 ~~~~  282 (336)
                      .++.
T Consensus        87 ~~~~   90 (99)
T 2cpd_A           87 KPVD   90 (99)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>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=99.63  E-value=4.4e-16  Score=115.61  Aligned_cols=82  Identities=22%  Similarity=0.236  Sum_probs=74.6

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCc-eeEEEEe-C--CCCccceEEEEEeCCHHHHHHHHHHhC--CceecCEEEEE
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGT-ITSYRVM-N--NDGKSRGFGFVAYESPEFAEKAVQAWN--GKEVDGKILYV  275 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~-i~~~~i~-~--~~~~~~g~afV~F~~~~~a~~a~~~l~--g~~~~g~~l~v  275 (336)
                      ..++|||+|||..+++++|+++|+.||. |..+.++ .  .+|.++|||||+|.+.++|.+|+..|+  +..+.|+.|+|
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            3478999999999999999999999998 9999988 3  556889999999999999999999996  58999999999


Q ss_pred             eecccchh
Q psy12549        276 GRAQKKAE  283 (336)
Q Consensus       276 ~~~~~~~~  283 (336)
                      .++.++..
T Consensus        87 ~~a~~~~~   94 (109)
T 2dis_A           87 DWAEPEID   94 (109)
T ss_dssp             EESCSSCS
T ss_pred             EEcCCCCC
Confidence            99987754

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.62  E-value=3.2e-15  Score=122.29  Aligned_cols=116  Identities=17%  Similarity=0.142  Sum_probs=93.2

Q ss_pred             hhHHHHHhhc--CccccCCeeeEEEeccCCCCcC-------CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeC
Q psy12549         75 LDTERALDTM--NFDALKGRPIRIMWSQRDPSLR-------KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD  145 (336)
Q Consensus        75 ~~A~~A~~~~--~~~~~~g~~i~v~~~~~~~~~~-------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~  145 (336)
                      +.+..|+...  ....+.+....+......+.+.       ....++|||+|||.++++++|+++|+.||.|..|.++++
T Consensus        65 ~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~  144 (193)
T 2voo_A           65 NVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT  144 (193)
T ss_dssp             HHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC
T ss_pred             HHHHHHHhhcccceEEEecccceEEecccCCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEEC
Confidence            6777788866  4556666666676653333221       123479999999999999999999999999999999999


Q ss_pred             CCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchh
Q psy12549        146 EQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKE  191 (336)
Q Consensus       146 ~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~  191 (336)
                      .+|.++|||||+|.+.++|.+|+..+ +..+.|+.|.|.+......
T Consensus       145 ~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~y~~  189 (193)
T 2voo_A          145 LHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDYFA  189 (193)
T ss_dssp             TTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC--
T ss_pred             CCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHHHH
Confidence            88999999999999999999999855 5699999999998776543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.62  E-value=1e-16  Score=117.35  Aligned_cols=83  Identities=22%  Similarity=0.295  Sum_probs=73.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ....++|||+|||.++++++|+++|+.||.|.. .++.+. +|.++|||||+|.+.++|.+|++ |++..+.|+.|.|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            345689999999999999999999999999887 444443 67899999999999999999999 999999999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.++..
T Consensus        92 a~~~~~   97 (101)
T 1fj7_A           92 PKGRDG   97 (101)
T ss_dssp             CSCCCC
T ss_pred             cCCCCC
Confidence            877543

>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=99.62  E-value=1.7e-15  Score=110.69  Aligned_cols=83  Identities=14%  Similarity=0.119  Sum_probs=73.1

Q ss_pred             ccccCceeeeecCchhhhhhhHHhhhcccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCee
Q psy12549         14 IIIPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRP   93 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~~~e~~l~~~f~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~   93 (336)
                      ...+.++|||+|||+++||++|+++|+..+++.++++.++    +|+++|||||+|.+.  ++|++|++ +|+..+.|+.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~v~i~~d~----~g~~~G~afV~F~~~--~~a~~Al~-~~~~~~~gr~   83 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGP----DGRVTGEADVEFATH--EDAVAAMA-KDKANMQHRY   83 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCSEEEEEESS----SSCEEEEEEEECSSS--HHHHHHHT-TSSCCSSSSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCceEEEEEECC----CCCEeeEEEEEECCH--HHHHHHHH-hCCCeECCcE
Confidence            3456788999999999999999999965557799999876    589999999999999  99999996 7999999999


Q ss_pred             eEEEeccCCC
Q psy12549         94 IRIMWSQRDP  103 (336)
Q Consensus        94 i~v~~~~~~~  103 (336)
                      |.|.++....
T Consensus        84 i~V~~~~~~~   93 (102)
T 1wez_A           84 VELFLNSTAG   93 (102)
T ss_dssp             CEEEEECCCC
T ss_pred             EEEEECCCCC
Confidence            9999876544

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=1.5e-15  Score=110.12  Aligned_cols=80  Identities=15%  Similarity=0.320  Sum_probs=71.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ....++|||+|||.++++++|+++|+.||.|. +.++.+   .++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            34467999999999999999999999999987 666654   57899999999999999999999999999999999998


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .++.
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7753

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

Probab=99.62  E-value=2.7e-15  Score=107.21  Aligned_cols=76  Identities=24%  Similarity=0.451  Sum_probs=70.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.+.+       +||||+|.+.++|.+|+..||+..+.|+.|.|.++.
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   79 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK-------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELST   79 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS-------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECC
Confidence            4568899999999999999999999999999999884       399999999999999999999999999999999988


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      +..
T Consensus        80 ~~~   82 (90)
T 2dnp_A           80 KGQ   82 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.62  E-value=3.2e-15  Score=112.77  Aligned_cols=75  Identities=16%  Similarity=0.312  Sum_probs=69.0

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceE-EEEEeCCHHHHHHHHHHhCCceecC--EEEEEeeccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGF-GFVAYESPEFAEKAVQAWNGKEVDG--KILYVGRAQK  280 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~-afV~F~~~~~a~~a~~~l~g~~~~g--~~l~v~~~~~  280 (336)
                      ..|||+||++.+|+++|+++|++||.|.++.+...   .+|+ |||+|.+.++|.+|++.|||..+.|  +.|+|.|+++
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~---~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~  105 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL  105 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE---TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC---CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCC
Confidence            56889999999999999999999999999988752   3677 9999999999999999999999998  9999999987


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      +
T Consensus       106 ~  106 (130)
T 3zzy_A          106 T  106 (130)
T ss_dssp             S
T ss_pred             C
Confidence            6

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

Probab=99.62  E-value=7.1e-16  Score=111.65  Aligned_cols=77  Identities=23%  Similarity=0.448  Sum_probs=71.0

Q ss_pred             cccceEEEcCCCC-CCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        201 KLFTNVYIKNFGE-DFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       201 ~~~~~l~V~nlp~-~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      .+.++|||+|||. .+++++|+++|+.||.|..+.+.      +|||||+|.+.++|.+|+..|+|..+.|+.|+|.++.
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~   81 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSS   81 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcC
Confidence            3458899999998 99999999999999999999995      8899999999999999999999999999999999997


Q ss_pred             cchh
Q psy12549        280 KKAE  283 (336)
Q Consensus       280 ~~~~  283 (336)
                      ++..
T Consensus        82 ~~~~   85 (96)
T 2kvi_A           82 SNAR   85 (96)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            6644

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.62  E-value=6.9e-16  Score=113.05  Aligned_cols=81  Identities=28%  Similarity=0.519  Sum_probs=74.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+.++.+++|.++|||||+|.+.++|.+|+.  ++..+.|+.|.|.++.+
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            3478999999999999999999999999999999999988999999999999999999999  99999999999988875


Q ss_pred             chh
Q psy12549        189 RKE  191 (336)
Q Consensus       189 ~~~  191 (336)
                      ...
T Consensus        86 ~~~   88 (102)
T 2xs2_A           86 KQN   88 (102)
T ss_dssp             CC-
T ss_pred             Ccc
Confidence            543

>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=99.62  E-value=2.2e-15  Score=107.13  Aligned_cols=74  Identities=22%  Similarity=0.330  Sum_probs=69.4

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      .++|||+|||.++++++|+++|++| .|..+.+.    .++|+|||+|.+.++|.+|++.|||..+.|+.|+|.++...
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A            5 SSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            4789999999999999999999999 99999885    57999999999999999999999999999999999998755

>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=99.62  E-value=5.2e-16  Score=117.94  Aligned_cols=82  Identities=20%  Similarity=0.308  Sum_probs=73.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEE-EEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~-~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+ .+..+.+|.++|||||+|.+.++|.+|+. +|+..+.|+.|.|.++
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            455899999999999999999999999999884 44455588999999999999999999999 9999999999999998


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .+..
T Consensus       102 ~~~~  105 (124)
T 1wel_A          102 TKKG  105 (124)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            7654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=5.8e-16  Score=112.34  Aligned_cols=79  Identities=24%  Similarity=0.363  Sum_probs=70.9

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ...++|||+|||..+++++|+++|+.||.|. +.++.  +.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.+
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~--~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~   93 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW--QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ   93 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE--ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc--CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCC
Confidence            3458999999999999999999999999996 55543  46789999999999999999999999999999999999987


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      +.
T Consensus        94 ~~   95 (97)
T 2e5j_A           94 QR   95 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>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=99.61  E-value=2e-16  Score=121.80  Aligned_cols=123  Identities=12%  Similarity=0.121  Sum_probs=72.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCcee
Q psy12549        152 GYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTIT  231 (336)
Q Consensus       152 g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~  231 (336)
                      ++|+.+|..++.+..+...+... ..+...--...      ...........++|||+|||+++++++|+++|+.|| +.
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g------~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~   73 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSG------DSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PV   73 (139)
T ss_dssp             --------------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CS
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCCC------CcccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-Ce
Confidence            46778888888777777654333 22222111000      001112223447899999999999999999999999 66


Q ss_pred             EEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchh
Q psy12549        232 SYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAE  283 (336)
Q Consensus       232 ~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~  283 (336)
                      .+.++. .+++++|||||+|.+.++|++|+ .+|+..+.|+.|.|..+.+...
T Consensus        74 ~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           74 RVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             EEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEECCCSCC
T ss_pred             EEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEECCCCCC
Confidence            888877 56889999999999999999999 6899999999999999887644

>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=99.60  E-value=5.9e-16  Score=117.65  Aligned_cols=80  Identities=18%  Similarity=0.269  Sum_probs=72.1

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEe-C-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-N-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~-~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ..++|||+|||+++++++|+++|+.||.|..+.++ . .+|.++|||||+|.+.++|.+|+. +||..+.|+.|.|.++.
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a~  102 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT  102 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEECC
Confidence            44789999999999999999999999999874333 3 788899999999999999999999 99999999999999998


Q ss_pred             cch
Q psy12549        280 KKA  282 (336)
Q Consensus       280 ~~~  282 (336)
                      ++.
T Consensus       103 ~~~  105 (124)
T 1wel_A          103 KKG  105 (124)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            764

>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=99.60  E-value=1.6e-15  Score=111.81  Aligned_cols=80  Identities=20%  Similarity=0.349  Sum_probs=70.7

Q ss_pred             cccccceEEE--cCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCcee-----cCE
Q psy12549        199 KAKLFTNVYI--KNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEV-----DGK  271 (336)
Q Consensus       199 ~~~~~~~l~V--~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~-----~g~  271 (336)
                      ...+.++|||  +||+..+++++|+++|++||.|.++.+..    .+|||||+|.+.++|++|++.|||..+     .|+
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~----~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT----TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC----CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            3445578999  66999999999999999999999988764    378999999999999999999999998     789


Q ss_pred             EEEEeecccch
Q psy12549        272 ILYVGRAQKKA  282 (336)
Q Consensus       272 ~l~v~~~~~~~  282 (336)
                      .|.|.|+....
T Consensus        97 ~l~v~~a~~~p  107 (114)
T 2cq2_A           97 TLYLNFVEKVQ  107 (114)
T ss_dssp             ECEEEEESCCC
T ss_pred             EEEEEecccCc
Confidence            99999987543

>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=99.60  E-value=3.9e-16  Score=115.40  Aligned_cols=80  Identities=15%  Similarity=0.136  Sum_probs=73.5

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCc---eeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEe
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGT---ITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG  276 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~---i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~  276 (336)
                      ...++|||+|||+++++++|+++|+.||.   |..+.++. ..|.++|+|||+|.+.++|.+|+. ++|..++|+.|.|.
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            34578999999999999999999999998   89999887 458899999999999999999999 99999999999999


Q ss_pred             ecccc
Q psy12549        277 RAQKK  281 (336)
Q Consensus       277 ~~~~~  281 (336)
                      ++.++
T Consensus        88 ~a~~~   92 (107)
T 2lmi_A           88 EINNE   92 (107)
T ss_dssp             ECCHH
T ss_pred             ECCHH
Confidence            98765

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.60  E-value=3.1e-16  Score=120.36  Aligned_cols=80  Identities=21%  Similarity=0.377  Sum_probs=74.0

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeE--EEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCc----eecCEE
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS--YRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGK----EVDGKI  272 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~--~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~----~~~g~~  272 (336)
                      ...++|||+|||+++++++|+++|+.||.|..  ++++.  .+|.++|||||+|.+. +|.+|+..|||.    .+.|+.
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~   99 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKT   99 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEE
Confidence            34478999999999999999999999999976  88887  4789999999999999 999999999999    999999


Q ss_pred             EEEeecccc
Q psy12549        273 LYVGRAQKK  281 (336)
Q Consensus       273 l~v~~~~~~  281 (336)
                      |.|.++.++
T Consensus       100 l~V~~a~~~  108 (131)
T 2m2b_A          100 INVEFAKGS  108 (131)
T ss_dssp             CCCEECCCS
T ss_pred             EEEEECCCC
Confidence            999999875

>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=99.60  E-value=1.7e-15  Score=112.57  Aligned_cols=75  Identities=17%  Similarity=0.141  Sum_probs=69.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      .++|||+|||..+++++|+++|++||.|..|.++.     ++|||||+|.+.++|.+|+..|||..+.|+.|.|.|+...
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            47899999999999999999999999999998874     4789999999999999999999999999999999998653

>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=99.60  E-value=9.2e-16  Score=115.01  Aligned_cols=80  Identities=26%  Similarity=0.486  Sum_probs=72.5

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCce----eEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEee
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTI----TSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR  277 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i----~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~  277 (336)
                      +.++|||+|||..+++++|+++|+.||.|    ..+++.  ++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.+
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~--~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM--TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE--CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC--CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            44899999999999999999999999998    455554  788899999999999999999999999999999999999


Q ss_pred             cccchh
Q psy12549        278 AQKKAE  283 (336)
Q Consensus       278 ~~~~~~  283 (336)
                      +.++..
T Consensus       102 a~~~~~  107 (115)
T 2cpx_A          102 GKNKKQ  107 (115)
T ss_dssp             CCCCSC
T ss_pred             ccCCCC
Confidence            987643

>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=99.60  E-value=3.1e-16  Score=108.09  Aligned_cols=73  Identities=22%  Similarity=0.407  Sum_probs=67.9

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       205 ~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      +|||+|||.++++++|+++|++||+|..+.++.  .++.++|+|||+|.+.++|.+|++. ++..+.|+.|.|.+|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            589999999999999999999999999999877  5688899999999999999999985 999999999999875

>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=99.60  E-value=1.8e-15  Score=127.12  Aligned_cols=83  Identities=19%  Similarity=0.263  Sum_probs=76.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccC--CeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFG--SILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G--~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ..++|||+|||.++|+++|+++|+.||  .|..|.|+.++ +|.++|||||+|.+.++|.+|++.||+..|.|+.|.|.+
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            457899999999999999999999999  99999999997 899999999999999999999999999999999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.+...
T Consensus       147 a~~~~~  152 (229)
T 3q2s_C          147 VNKQFL  152 (229)
T ss_dssp             CCHHHH
T ss_pred             CCCCcc
Confidence            876543

>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=99.60  E-value=1.4e-15  Score=109.48  Aligned_cols=77  Identities=23%  Similarity=0.468  Sum_probs=69.5

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCc-eeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCC-ceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGT-ITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG-KEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~-i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g-~~~~g~~l~v~~~~  279 (336)
                      ..++|||+|||.++++++|+++|++||. |..+.+.     ++|||||+|.+.++|.+|++.||| ..+.|+.|+|.++.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~   81 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSV   81 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-----ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-----CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEcc
Confidence            4478999999999999999999999999 6666663     489999999999999999999999 99999999999998


Q ss_pred             cchh
Q psy12549        280 KKAE  283 (336)
Q Consensus       280 ~~~~  283 (336)
                      ++..
T Consensus        82 ~~~~   85 (93)
T 2cqh_A           82 SKKL   85 (93)
T ss_dssp             CCCC
T ss_pred             Cccc
Confidence            7643

>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=99.59  E-value=8.4e-15  Score=107.42  Aligned_cols=77  Identities=26%  Similarity=0.503  Sum_probs=71.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+.+++       +||||+|.+.++|.+|++.|++..+.|+.|.|.++.+
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   82 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK-------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKP   82 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS-------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC-------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCC
Confidence            457899999999999999999999999999999873       5999999999999999999999999999999999987


Q ss_pred             chhh
Q psy12549        189 RKER  192 (336)
Q Consensus       189 ~~~~  192 (336)
                      ....
T Consensus        83 ~~~~   86 (103)
T 2dgu_A           83 PDQK   86 (103)
T ss_dssp             CCCC
T ss_pred             Cccc
Confidence            6543

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.59  E-value=3.3e-15  Score=120.41  Aligned_cols=83  Identities=23%  Similarity=0.390  Sum_probs=78.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||..+++++|+++|+.||.|..|.+..+++|.++|||||+|.+.++|.+|++.|++..+.|+.|.|.++.
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            34579999999999999999999999999999999999888899999999999999999999999999999999999987


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      ...
T Consensus       166 ~~~  168 (177)
T 2f3j_A          166 SQI  168 (177)
T ss_dssp             SGG
T ss_pred             CCC
Confidence            654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=1.5e-15  Score=114.46  Aligned_cols=80  Identities=16%  Similarity=0.241  Sum_probs=72.0

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCce----eEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEE
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTI----TSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV  275 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i----~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v  275 (336)
                      ....+|||+|||+++++++|+++|+.||.|    ..+.++. .+|+++|+|||+|.+.++|.+|++. |+..+.|+.|.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            344789999999999999999999999975    5788776 6888999999999999999999996 999999999999


Q ss_pred             eecccc
Q psy12549        276 GRAQKK  281 (336)
Q Consensus       276 ~~~~~~  281 (336)
                      ..+.++
T Consensus       100 ~~a~~~  105 (123)
T 2dha_A          100 FRSTAA  105 (123)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            988654

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

Probab=99.59  E-value=2.1e-15  Score=109.09  Aligned_cols=78  Identities=18%  Similarity=0.399  Sum_probs=70.5

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDK-SIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~-~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||. .+++++|+++|+.||.|..+.+.       +|||||+|.+.++|.+|+..|++..+.|+.|.|.++
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   80 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVS   80 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEc
Confidence            3468999999998 99999999999999999999984       679999999999999999999999999999999998


Q ss_pred             cCchhh
Q psy12549        187 IPRKER  192 (336)
Q Consensus       187 ~~~~~~  192 (336)
                      .+....
T Consensus        81 ~~~~~~   86 (96)
T 2kvi_A           81 SSNARP   86 (96)
T ss_dssp             ECCCC-
T ss_pred             CcCCCC
Confidence            765543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.59  E-value=7.2e-16  Score=112.75  Aligned_cols=83  Identities=14%  Similarity=0.031  Sum_probs=71.6

Q ss_pred             ccccCceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCe
Q psy12549         14 IIIPKHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGR   92 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~   92 (336)
                      ...+.++|||+|||.++++++|+++| .++.+.. .++.+.   .+|.++|||||+|.+.  ++|++|++ +++..+.|+
T Consensus        13 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~---~~g~~~g~afV~f~~~--~~a~~A~~-l~g~~~~g~   85 (101)
T 1fj7_A           13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDV---RTGTNRKFGYVDFESA--EDLEKALE-LTGLKVFGN   85 (101)
T ss_dssp             TCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEE---EEETTTTEEEEEESSH--HHHHHHHH-GGGCCBTTB
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecC---CCCCcCcEEEEEECCH--HHHHHHHh-cCCcEECCc
Confidence            44578899999999999999999999 6666656 555544   4689999999999999  99999999 999999999


Q ss_pred             eeEEEeccCCC
Q psy12549         93 PIRIMWSQRDP  103 (336)
Q Consensus        93 ~i~v~~~~~~~  103 (336)
                      .|.|.++....
T Consensus        86 ~l~V~~a~~~~   96 (101)
T 1fj7_A           86 EIKLEKPKGRD   96 (101)
T ss_dssp             CCEEECCSCCC
T ss_pred             EEEEEEcCCCC
Confidence            99999987654

>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=99.59  E-value=3e-15  Score=112.19  Aligned_cols=81  Identities=22%  Similarity=0.401  Sum_probs=72.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCe----eEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSI----LSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v----~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      ...++|||+|||.++++++|+++|+.||.|    ..+.+.   +|.++|||||+|.+.++|.+|+..|++..+.|+.|.|
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~---~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v   99 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVI   99 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE---CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC---CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            345899999999999999999999999998    444444   6778999999999999999999999999999999999


Q ss_pred             eeccCchh
Q psy12549        184 GKFIPRKE  191 (336)
Q Consensus       184 ~~~~~~~~  191 (336)
                      .++.+...
T Consensus       100 ~~a~~~~~  107 (115)
T 2cpx_A          100 EFGKNKKQ  107 (115)
T ss_dssp             EECCCCSC
T ss_pred             EEccCCCC
Confidence            99887654

>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=99.59  E-value=3.2e-15  Score=107.51  Aligned_cols=78  Identities=24%  Similarity=0.417  Sum_probs=69.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCC-eeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCC-ceeCCeEEEEee
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGS-ILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG-MLLNSKIVFVGK  185 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~-v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~-~~~~~~~i~v~~  185 (336)
                      ...++|||+|||.++++++|+++|+.||. +..+.+.      ++|||||+|.+.++|.+|+..||+ ..+.|+.|.|.+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~   79 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDY   79 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEE
Confidence            34578999999999999999999999999 6666653      478999999999999999999999 999999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.+...
T Consensus        80 a~~~~~   85 (93)
T 2cqh_A           80 SVSKKL   85 (93)
T ss_dssp             CCCCCC
T ss_pred             ccCccc
Confidence            887643

>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=99.59  E-value=1.3e-15  Score=118.86  Aligned_cols=82  Identities=27%  Similarity=0.430  Sum_probs=72.5

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEE--------EEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEE
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSY--------RVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKI  272 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~--------~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~  272 (336)
                      .+.++|||+|||..+++++|+++|+.||.|..+        .+. .+|.++|||||+|.+.++|.+|+..|||..+.|+.
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~-~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM-KEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE-EETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec-cCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            345789999999999999999999999998764        222 46888999999999999999999999999999999


Q ss_pred             EEEeecccchh
Q psy12549        273 LYVGRAQKKAE  283 (336)
Q Consensus       273 l~v~~~~~~~~  283 (336)
                      |.|.++.+...
T Consensus       122 l~V~~a~~~~~  132 (143)
T 3egn_A          122 MVVQFARSARP  132 (143)
T ss_dssp             CEEEECCCSCC
T ss_pred             EEEEECCCCCC
Confidence            99999976543

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=2.3e-15  Score=105.22  Aligned_cols=72  Identities=21%  Similarity=0.332  Sum_probs=64.1

Q ss_pred             ceEEEcCCCCCCcHHH----HHHhhccCC-ceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        204 TNVYIKNFGEDFNDEK----LKEMFEPYG-TITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~----l~~~f~~~g-~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      +.|||+|||+.+++++    |+++|++|| .|.+|     ++   |+|||+|.+.++|.+|++.|+|..+.||+|+|.||
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-----tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A   81 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-----TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFT   81 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-----CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESS
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-----ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEec
Confidence            3499999999999988    558999994 99877     22   99999999999999999999999999999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      +.+.+
T Consensus        82 ~~~sd   86 (96)
T 2diu_A           82 PKNRE   86 (96)
T ss_dssp             CCSCC
T ss_pred             CCCcc
Confidence            87643

>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=99.59  E-value=1.3e-15  Score=114.97  Aligned_cols=79  Identities=22%  Similarity=0.306  Sum_probs=71.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCee--EEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSIL--SCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~--~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ...++|||+|||+++|+++|+++|+.| .|.  .|.++.++.|.++|||||+|.++++|++|++ +++..+.|+.|.|..
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            345789999999999999999999999 566  8999999889999999999999999999999 478999999999987


Q ss_pred             ccC
Q psy12549        186 FIP  188 (336)
Q Consensus       186 ~~~  188 (336)
                      +.+
T Consensus       118 a~~  120 (126)
T 2hgm_A          118 SSQ  120 (126)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            653

>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=3.4e-15  Score=110.90  Aligned_cols=74  Identities=26%  Similarity=0.521  Sum_probs=69.5

Q ss_pred             ccceEEEcCCCCC-CcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        202 LFTNVYIKNFGED-FNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       202 ~~~~l~V~nlp~~-~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ..++|||+|||.. +++++|+++|+.||.|..+.+      +++||||+|.+.++|.+|++.|+|..+.|+.|+|.++.+
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   99 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE   99 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            3478999999999 999999999999999999998      489999999999999999999999999999999999975


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      .
T Consensus       100 ~  100 (110)
T 1wf1_A          100 P  100 (110)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.58  E-value=6.3e-15  Score=104.76  Aligned_cols=75  Identities=20%  Similarity=0.313  Sum_probs=69.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..++|||+|||.++++++|+++|++| .|..+.+.     .++|||||+|.+.++|.+|++.||+..+.|+.|.|.++..
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            34789999999999999999999999 99999884     4789999999999999999999999999999999998755


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      .
T Consensus        78 ~   78 (88)
T 1wg1_A           78 D   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.58  E-value=4.3e-15  Score=109.44  Aligned_cols=83  Identities=8%  Similarity=-0.019  Sum_probs=72.5

Q ss_pred             CCCccccCceeeeecCchh-hhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCc--
Q psy12549         11 EEGIIIPKHNVATRELSAK-VVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNF--   86 (336)
Q Consensus        11 ~~~~~~p~~~v~v~~lp~~-~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~--   86 (336)
                      .+....|.++|||+|||++ ++|++|+++| .+|.+.++.+.+         ++|||||+|.+.  ++|++|++.+++  
T Consensus        18 ~~~~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~---------~kg~aFVef~~~--~~A~~Ai~~l~~~~   86 (112)
T 1x4f_A           18 FDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR---------MKSQAFIEMETR--EDAMAMVDHCLKKA   86 (112)
T ss_dssp             CCCSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET---------TTTEEEEECSSH--HHHHHHHHHHHHSC
T ss_pred             ccccCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec---------CCCEEEEEECCH--HHHHHHHHHhccCC
Confidence            3556789999999999998 9999999999 778899999875         458999999999  999999998865  


Q ss_pred             cccCCeeeEEEeccCCCC
Q psy12549         87 DALKGRPIRIMWSQRDPS  104 (336)
Q Consensus        87 ~~~~g~~i~v~~~~~~~~  104 (336)
                      ..+.|++|+|.++.....
T Consensus        87 ~~l~Gr~l~V~~a~~~~~  104 (112)
T 1x4f_A           87 LWFQGRCVKVDLSEKYKK  104 (112)
T ss_dssp             CCSSSSCCEEEEECSCSS
T ss_pred             ceECCEEEEEEECccccc
Confidence            569999999999876544

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

Probab=99.58  E-value=1.8e-14  Score=104.82  Aligned_cols=77  Identities=26%  Similarity=0.443  Sum_probs=70.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhcc--CCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAF--GSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~--G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ...++|||+|||..+++++|+++|+.|  |.|..+.+.       +|||||+|.+.++|.+|+..||+..+.|+.|.|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL   85 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            446799999999999999999999999  899988765       56999999999999999999999999999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.+...
T Consensus        86 a~~~~~   91 (99)
T 2cpd_A           86 AKPVDK   91 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            887643

>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=99.58  E-value=3.3e-15  Score=116.95  Aligned_cols=77  Identities=14%  Similarity=0.257  Sum_probs=70.2

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecC--EEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG--KILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g--~~l~v~~~~~~  281 (336)
                      .+|||+||++.+++++|+++|++||.|.++.+...  .++++|||+|.+.++|.+|++.|||..|.|  +.|+|.|++++
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k--~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~  124 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK--NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  124 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES--SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSS
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC--CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCC
Confidence            56899999999999999999999999999998642  357899999999999999999999999966  99999999876


Q ss_pred             h
Q psy12549        282 A  282 (336)
Q Consensus       282 ~  282 (336)
                      .
T Consensus       125 ~  125 (164)
T 1sjr_A          125 S  125 (164)
T ss_dssp             S
T ss_pred             c
Confidence            3

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.58  E-value=1.6e-15  Score=111.03  Aligned_cols=80  Identities=23%  Similarity=0.528  Sum_probs=73.4

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ..++|||+|||..+++++|+++|+.||.|..+.++. .+|.++|||||+|.+.++|.+|+.  +|..+.|+.|.|.++.+
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            347899999999999999999999999999999987 678889999999999999999998  99999999999999987


Q ss_pred             chh
Q psy12549        281 KAE  283 (336)
Q Consensus       281 ~~~  283 (336)
                      +..
T Consensus        86 ~~~   88 (102)
T 2xs2_A           86 KQN   88 (102)
T ss_dssp             CC-
T ss_pred             Ccc
Confidence            654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.36  E-value=1.4e-16  Score=119.71  Aligned_cols=84  Identities=20%  Similarity=0.330  Sum_probs=77.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeE--------EEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCe
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILS--------CKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSK  179 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~--------~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~  179 (336)
                      ..++|||+|||.++++++|+++|+.||.|..        +.++.++ ++.++|||||+|.+.++|.+|+..||+..+.|+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   85 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGN   85 (116)
Confidence            4578999999999999999999999999998        8899885 688999999999999999999999999999999


Q ss_pred             EEEEeeccCchhh
Q psy12549        180 IVFVGKFIPRKER  192 (336)
Q Consensus       180 ~i~v~~~~~~~~~  192 (336)
                      .|.|.++.+....
T Consensus        86 ~l~V~~a~~~~~~   98 (116)
T 2lcw_A           86 PIKVSFATRRADF   98 (116)
Confidence            9999998876554

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.58  E-value=8.8e-15  Score=109.93  Aligned_cols=75  Identities=23%  Similarity=0.265  Sum_probs=67.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceE-EEEEeCCHHHHHHHHHHhCCceecC--EEEEEeeccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGF-GFVAYESPEFAEKAVQAWNGKEVDG--KILYVGRAQK  280 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~-afV~F~~~~~a~~a~~~l~g~~~~g--~~l~v~~~~~  280 (336)
                      ..|||+||++.+++++|+++|++||.|.++.+...    .|+ |||+|.+.++|..|++.|||..|.|  +.|+|.++.+
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~  101 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP  101 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecC
Confidence            34789999999999999999999999999998753    375 9999999999999999999999987  6999999987


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      +.
T Consensus       102 ~~  103 (124)
T 2e5i_A          102 TR  103 (124)
T ss_dssp             SC
T ss_pred             Cc
Confidence            63

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=6.7e-15  Score=106.03  Aligned_cols=77  Identities=19%  Similarity=0.346  Sum_probs=67.7

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ..++|||+|||..+++++|+++|+.||.|.++.+.+.++.   ||||+|.+.++|.+|+. |+|..+.|+.|.|.++.++
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~~~   82 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPREQK   82 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSCCS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECCcC
Confidence            3478999999999999999999999999999833224443   99999999999999999 9999999999999998765


Q ss_pred             h
Q psy12549        282 A  282 (336)
Q Consensus       282 ~  282 (336)
                      .
T Consensus        83 ~   83 (94)
T 2e5g_A           83 E   83 (94)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=1.6e-14  Score=104.64  Aligned_cols=76  Identities=30%  Similarity=0.467  Sum_probs=69.6

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ...++|||+|+  ++++++|+++|++||.|..+.+.    .++|+|||+|.+.++|.+|+..|||..+.|+.|+|.++.+
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~   86 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   86 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSS
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCC
Confidence            34578999996  89999999999999999999985    4589999999999999999999999999999999999987


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      +.
T Consensus        87 ~~   88 (97)
T 1x5p_A           87 QP   88 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.57  E-value=3.2e-15  Score=125.66  Aligned_cols=81  Identities=25%  Similarity=0.332  Sum_probs=75.0

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCC--ceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEee
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYG--TITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR  277 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g--~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~  277 (336)
                      ..++|||+|||..+++++|+++|+.||  .|..|.|+.  .++.++|||||+|.+.++|.+||+.|||..|.|+.|+|.+
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            347899999999999999999999999  999999987  5889999999999999999999999999999999999999


Q ss_pred             cccch
Q psy12549        278 AQKKA  282 (336)
Q Consensus       278 ~~~~~  282 (336)
                      +.+..
T Consensus       147 a~~~~  151 (229)
T 3q2s_C          147 VNKQF  151 (229)
T ss_dssp             CCHHH
T ss_pred             CCCCc
Confidence            98654

>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=99.57  E-value=1.2e-14  Score=103.40  Aligned_cols=76  Identities=22%  Similarity=0.444  Sum_probs=62.7

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCcee--cCEEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEV--DGKILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~--~g~~l~v~~~  278 (336)
                      ...++|||+|||+++++++|+++|++||.|.++.++..   ++|||||+|.+.++|.+    ++|..+  .|+.|.|.++
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~---srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a   81 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP---FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNA   81 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS---CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC---CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEc
Confidence            34488999999999999999999999999999999863   79999999999999883    566655  5999999999


Q ss_pred             ccchh
Q psy12549        279 QKKAE  283 (336)
Q Consensus       279 ~~~~~  283 (336)
                      .++..
T Consensus        82 ~~k~~   86 (89)
T 3d2w_A           82 EPKHN   86 (89)
T ss_dssp             C----
T ss_pred             CCCCc
Confidence            87643

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.57  E-value=5.5e-15  Score=109.34  Aligned_cols=79  Identities=10%  Similarity=0.115  Sum_probs=70.3

Q ss_pred             ceEEEcCC----CCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCC----HHH----HHHHHH--HhCCce
Q psy12549        111 GNVFIKNL----DKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFET----EEA----ANKSIE--KVNGML  175 (336)
Q Consensus       111 ~~l~v~nl----p~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~----~~~----a~~a~~--~l~~~~  175 (336)
                      .+|||+||    |+.+++.+|+++|++||+|.++.++.|+ +|.++|||||+|.+    +++    |.+|+.  .++|..
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            57999999    9999999999999999999999999999 89999999999996    333    788888  789999


Q ss_pred             eCCeEEEEeeccCc
Q psy12549        176 LNSKIVFVGKFIPR  189 (336)
Q Consensus       176 ~~~~~i~v~~~~~~  189 (336)
                      ++|+.|.|..-...
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            99999999875543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.35  E-value=1.7e-16  Score=119.17  Aligned_cols=83  Identities=24%  Similarity=0.473  Sum_probs=75.5

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeE--------EEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCE
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITS--------YRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK  271 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~--------~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~  271 (336)
                      ..++|||+|||..+++++|+++|+.||.|..        +.++.  .++.++|||||+|.+.++|.+|+..|||..+.|+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   85 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGN   85 (116)
Confidence            3478999999999999999999999999988        77776  5678899999999999999999999999999999


Q ss_pred             EEEEeecccchhh
Q psy12549        272 ILYVGRAQKKAER  284 (336)
Q Consensus       272 ~l~v~~~~~~~~~  284 (336)
                      .|+|.++.++...
T Consensus        86 ~l~V~~a~~~~~~   98 (116)
T 2lcw_A           86 PIKVSFATRRADF   98 (116)
Confidence            9999999877543

>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=99.57  E-value=4.3e-15  Score=109.49  Aligned_cols=76  Identities=12%  Similarity=0.274  Sum_probs=67.6

Q ss_pred             CCceEEE--cCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcee-----CCeEE
Q psy12549        109 GVGNVFI--KNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLL-----NSKIV  181 (336)
Q Consensus       109 ~~~~l~v--~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~-----~~~~i  181 (336)
                      ..++|||  +||+.++++++|+++|++||.|..+.++.     .+|||||+|.+.++|++|++.|||..+     .|++|
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~-----~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l   98 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITL   98 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-----TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEEC
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEE
Confidence            3578999  77999999999999999999999988764     378999999999999999999999988     68999


Q ss_pred             EEeeccCc
Q psy12549        182 FVGKFIPR  189 (336)
Q Consensus       182 ~v~~~~~~  189 (336)
                      .|.++...
T Consensus        99 ~v~~a~~~  106 (114)
T 2cq2_A           99 YLNFVEKV  106 (114)
T ss_dssp             EEEEESCC
T ss_pred             EEEecccC
Confidence            99876543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.57  E-value=1.7e-14  Score=108.79  Aligned_cols=76  Identities=12%  Similarity=0.201  Sum_probs=69.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccE-EEEEeCCHHHHHHHHHHhCCceeCC--eEEEEeecc
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGY-GFVHFETEEAANKSIEKVNGMLLNS--KIVFVGKFI  187 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~-afV~F~~~~~a~~a~~~l~~~~~~~--~~i~v~~~~  187 (336)
                      -.|||+||++.+|+++|+++|++||.|.+|.+...    .+|+ |||+|.+.++|.+|++.|||..+.|  +.|+|.+++
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak  104 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  104 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECS
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecC
Confidence            46889999999999999999999999999998864    3567 9999999999999999999999988  999999988


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      +..
T Consensus       105 ~~~  107 (130)
T 3zzy_A          105 LTS  107 (130)
T ss_dssp             CSS
T ss_pred             CCc
Confidence            753

>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=99.57  E-value=4e-15  Score=115.99  Aligned_cols=84  Identities=24%  Similarity=0.355  Sum_probs=72.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEE------EEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC------KVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIV  181 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~------~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i  181 (336)
                      ...++|||+|||.++|+++|+++|+.||.|..+      .+....+|.++|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            345789999999999999999999999998764      12222467889999999999999999999999999999999


Q ss_pred             EEeeccCchh
Q psy12549        182 FVGKFIPRKE  191 (336)
Q Consensus       182 ~v~~~~~~~~  191 (336)
                      .|.++.+...
T Consensus       123 ~V~~a~~~~~  132 (143)
T 3egn_A          123 VVQFARSARP  132 (143)
T ss_dssp             EEEECCCSCC
T ss_pred             EEEECCCCCC
Confidence            9999976544

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=5.3e-15  Score=107.01  Aligned_cols=78  Identities=22%  Similarity=0.299  Sum_probs=69.5

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEE-EeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYR-VMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~-i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ..++|||+|||..+++++|+++|+.||.|..++ ++....  .+.|||+|.+.++|.+|+..|||..+.|+.|+|.++.+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~--~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   91 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE--TAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPD   91 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS--SEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC--CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCc
Confidence            347899999999999999999999999999995 655322  33499999999999999999999999999999999988


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      +
T Consensus        92 ~   92 (96)
T 2e44_A           92 E   92 (96)
T ss_dssp             C
T ss_pred             c
Confidence            7

>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=3.2e-14  Score=103.03  Aligned_cols=77  Identities=18%  Similarity=0.333  Sum_probs=69.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+||  ++++++|+++|++||.|..+.+.     .++|||||+|.+.++|.+|+..|++..+.|+.|.|.++.
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~   85 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   85 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCS
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECC
Confidence            35679999996  89999999999999999999985     367899999999999999999999999999999999987


Q ss_pred             Cchh
Q psy12549        188 PRKE  191 (336)
Q Consensus       188 ~~~~  191 (336)
                      +...
T Consensus        86 ~~~~   89 (97)
T 1x5p_A           86 KQPM   89 (97)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7643

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.56  E-value=6.2e-15  Score=118.79  Aligned_cols=82  Identities=22%  Similarity=0.357  Sum_probs=76.2

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ...++|||+|||..+++++|+++|+.||.|..+.+.. .++.++|+|||+|.+.++|.+|++.|||..+.|+.|.|.++.
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            3458999999999999999999999999999999987 568889999999999999999999999999999999999997


Q ss_pred             cch
Q psy12549        280 KKA  282 (336)
Q Consensus       280 ~~~  282 (336)
                      ...
T Consensus       166 ~~~  168 (177)
T 2f3j_A          166 SQI  168 (177)
T ss_dssp             SGG
T ss_pred             CCC
Confidence            654

>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=99.56  E-value=4.3e-15  Score=112.14  Aligned_cols=81  Identities=17%  Similarity=0.072  Sum_probs=71.2

Q ss_pred             ccccCceeeeecCchhhhhhhHHhhhcccCCc--eEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCC
Q psy12549         14 IIIPKHNVATRELSAKVVEGVSRSLSSLIDGN--TVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKG   91 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~~~e~~l~~~f~~~~~~--~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g   91 (336)
                      ...+.++|||+|||+++||++|+++|+..++.  +++++.++    .|+++|||||+|.++  ++|++|++ +++..+.|
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~~i~~~~v~i~~d~----~GrsrGfaFV~F~~~--e~A~~Al~-~~~~~l~g  110 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDP----EGKITGEAFVQFASQ--ELAEKALG-KHKERIGH  110 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTSCEEEEEEECCCCS----SSSSCSEEEEEESST--THHHHHHT-TTTCCBTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcCCceeeEEEEEECC----CCCCceEEEEEECCH--HHHHHHHH-HCCCEECC
Confidence            34567889999999999999999999666777  88988877    289999999999999  99999999 57899999


Q ss_pred             eeeEEEeccC
Q psy12549         92 RPIRIMWSQR  101 (336)
Q Consensus        92 ~~i~v~~~~~  101 (336)
                      +.|.|.++..
T Consensus       111 R~I~V~~a~~  120 (126)
T 2hgm_A          111 RYIEVFKSSQ  120 (126)
T ss_dssp             BCCCCEEECH
T ss_pred             EEEEEEECCH
Confidence            9999988754

>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=99.56  E-value=1.2e-14  Score=118.81  Aligned_cols=121  Identities=20%  Similarity=0.169  Sum_probs=89.9

Q ss_pred             CHHHHHHHHHHh--CCceeCCeEEEEeecc--CchhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEE
Q psy12549        160 TEEAANKSIEKV--NGMLLNSKIVFVGKFI--PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV  235 (336)
Q Consensus       160 ~~~~a~~a~~~l--~~~~~~~~~i~v~~~~--~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i  235 (336)
                      +.+.+..|+...  ....+.+....+....  +...... ........++|||+|||.++++++|+++|+.||.|..+.+
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~-~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i  141 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTD-EYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQM  141 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCH-HHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccch-hhhhccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEE
Confidence            567788888866  4555555444444432  1111000 0001123478999999999999999999999999999999


Q ss_pred             eC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        236 MN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       236 ~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      +. .++.++|+|||+|.+.++|.+|+..+ +..+.|+.|.|.++....
T Consensus       142 ~~~~~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~y~  188 (193)
T 2voo_A          142 RRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDDYF  188 (193)
T ss_dssp             EECTTCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTTC-
T ss_pred             EECCCCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHHHH
Confidence            87 66888999999999999999999865 569999999999987653

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=1.7e-14  Score=103.89  Aligned_cols=76  Identities=20%  Similarity=0.360  Sum_probs=67.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+|||.++++++|+++|+.||.|..|  +.++ +|.   ||||+|.+.++|.+|+. |++..+.|+.|.|.++.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECC
Confidence            45789999999999999999999999999987  4443 443   99999999999999999 99999999999998876


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      +..
T Consensus        81 ~~~   83 (94)
T 2e5g_A           81 QKE   83 (94)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            554

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.56  E-value=2.4e-14  Score=104.86  Aligned_cols=81  Identities=21%  Similarity=0.192  Sum_probs=70.5

Q ss_pred             cccceEEEcCCCC-----CCcHHHHHHhhccCCceeEEEEeCC---CCccceEEEEEeCCHHHHHHHHHHhCCceecCEE
Q psy12549        201 KLFTNVYIKNFGE-----DFNDEKLKEMFEPYGTITSYRVMNN---DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKI  272 (336)
Q Consensus       201 ~~~~~l~V~nlp~-----~~t~~~l~~~f~~~g~i~~~~i~~~---~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~  272 (336)
                      .+.++|+|.|+..     +-++++|++.|++||.|.++.++..   ++.++|+|||+|.+.++|.+|+..|||+.+.||.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            3457899999963     2378999999999999999999873   3678999999999999999999999999999999


Q ss_pred             EEEeecccc
Q psy12549        273 LYVGRAQKK  281 (336)
Q Consensus       273 l~v~~~~~~  281 (336)
                      |+|.++.+.
T Consensus        86 i~v~~a~~~   94 (105)
T 2pe8_A           86 VKACFYNLD   94 (105)
T ss_dssp             CEEEECCHH
T ss_pred             EEEEEcCHH
Confidence            999998753

>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=99.56  E-value=1.8e-14  Score=112.74  Aligned_cols=79  Identities=13%  Similarity=0.161  Sum_probs=71.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEeec
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNS--KIVFVGKF  186 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~--~~i~v~~~  186 (336)
                      ...+|||+||++.+|+++|+++|++||.|.++.+....   ++|||||+|.+.++|..|++.|||..+.|  +.|.|.++
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~---~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS---SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC---CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            34579999999999999999999999999999987643   46899999999999999999999999965  99999998


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .+..
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            8763

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=1.4e-14  Score=104.69  Aligned_cols=79  Identities=18%  Similarity=0.354  Sum_probs=70.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEE-EEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~-~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+ .++.++.   .+.|||+|.+.++|.+|+..|||..+.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~---~~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   89 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSS---SEEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            345789999999999999999999999999999 4777652   234999999999999999999999999999999998


Q ss_pred             cCc
Q psy12549        187 IPR  189 (336)
Q Consensus       187 ~~~  189 (336)
                      .+.
T Consensus        90 ~~~   92 (96)
T 2e44_A           90 PDE   92 (96)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            876

>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=99.55  E-value=2.1e-14  Score=102.09  Aligned_cols=74  Identities=15%  Similarity=0.372  Sum_probs=62.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCce--eCCeEEEEeec
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGML--LNSKIVFVGKF  186 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~--~~~~~i~v~~~  186 (336)
                      ...+|||+|||.++|+++|+++|++||.|.++.++.+    ++|||||+|.+.++|.+    +++..  +.|+.|.|.++
T Consensus        10 ~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~~a   81 (89)
T 3d2w_A           10 HGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHISNA   81 (89)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEEEc
Confidence            4578999999999999999999999999999999875    68999999999999983    45544  56999999998


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .++.
T Consensus        82 ~~k~   85 (89)
T 3d2w_A           82 EPKH   85 (89)
T ss_dssp             C---
T ss_pred             CCCC
Confidence            7764

>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=1.6e-14  Score=102.36  Aligned_cols=71  Identities=20%  Similarity=0.453  Sum_probs=66.0

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccC----C-------ceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecC
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPY----G-------TITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG  270 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~----g-------~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g  270 (336)
                      ..++|||+|||.++++++|+++|+.|    |       .|.++.+...    +|||||+|.+.++|.+|+ .|||..+.|
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~----kg~afV~f~~~~~a~~A~-~l~g~~~~g   79 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD----KNFAFLEFRSVDETTQAM-AFDGIIFQG   79 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS----SSEEEEEESSHHHHHHHG-GGTTCEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC----CcEEEEEcCCHHHHHHHH-hcCCCEECC
Confidence            34889999999999999999999999    8       8999988754    899999999999999999 999999999


Q ss_pred             EEEEEee
Q psy12549        271 KILYVGR  277 (336)
Q Consensus       271 ~~l~v~~  277 (336)
                      +.|+|++
T Consensus        80 ~~l~V~r   86 (87)
T 2hzc_A           80 QSLKIRR   86 (87)
T ss_dssp             EECEEEC
T ss_pred             eEEEEeC
Confidence            9999975

>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=2.1e-14  Score=101.81  Aligned_cols=71  Identities=21%  Similarity=0.543  Sum_probs=65.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhcc----C-------CeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAF----G-------SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLN  177 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~----G-------~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~  177 (336)
                      ..++|||+|||.++++++|+++|+.|    |       .|.++.+..+     +|||||+|.+.++|.+|+ .||+..+.
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~g~~~~   78 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGIIFQ   78 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcCCCEEC
Confidence            35789999999999999999999999    8       8999998864     789999999999999999 89999999


Q ss_pred             CeEEEEee
Q psy12549        178 SKIVFVGK  185 (336)
Q Consensus       178 ~~~i~v~~  185 (336)
                      |+.|.|.+
T Consensus        79 g~~l~V~r   86 (87)
T 2hzc_A           79 GQSLKIRR   86 (87)
T ss_dssp             TEECEEEC
T ss_pred             CeEEEEeC
Confidence            99999865

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.54  E-value=4.4e-14  Score=103.43  Aligned_cols=81  Identities=16%  Similarity=0.215  Sum_probs=71.6

Q ss_pred             CCceEEEcCCCC-----CCCHHHHHHHhhccCCeeEEEEeeCC--CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q psy12549        109 GVGNVFIKNLDK-----SIDNKAMYDTFSAFGSILSCKVAQDE--QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIV  181 (336)
Q Consensus       109 ~~~~l~v~nlp~-----~~t~~~l~~~f~~~G~v~~~~~~~~~--~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i  181 (336)
                      .+++|+|+||..     +-++++|++.|++||.|.++.++.++  ++.++|+|||+|.+.++|.+|+..|||..+.|+.|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i   86 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV   86 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEE
Confidence            457899999963     23789999999999999999999986  36789999999999999999999999999999999


Q ss_pred             EEeeccCc
Q psy12549        182 FVGKFIPR  189 (336)
Q Consensus       182 ~v~~~~~~  189 (336)
                      .+.++.+.
T Consensus        87 ~v~~a~~~   94 (105)
T 2pe8_A           87 KACFYNLD   94 (105)
T ss_dssp             EEEECCHH
T ss_pred             EEEEcCHH
Confidence            99998653

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=2e-14  Score=107.43  Aligned_cols=76  Identities=24%  Similarity=0.408  Sum_probs=65.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-C---CCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-Q---GNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~---~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      ...++|||+|||.++++++|+++|++||.|. +.++.+. +   |.++|||||+|.+.++|++|++.|+  .+.|+.+.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            3458899999999999999999999999999 7777765 3   6899999999999999999999883  367777766


Q ss_pred             eec
Q psy12549        184 GKF  186 (336)
Q Consensus       184 ~~~  186 (336)
                      ...
T Consensus        83 ~~~   85 (114)
T 2dnl_A           83 VSS   85 (114)
T ss_dssp             ECC
T ss_pred             ccC
Confidence            543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.54  E-value=1.4e-14  Score=107.28  Aligned_cols=79  Identities=20%  Similarity=0.237  Sum_probs=69.8

Q ss_pred             ceEEEcCC----CCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCC----HHH----HHHHHH--HhCCce
Q psy12549        204 TNVYIKNF----GEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYES----PEF----AEKAVQ--AWNGKE  267 (336)
Q Consensus       204 ~~l~V~nl----p~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~----~~~----a~~a~~--~l~g~~  267 (336)
                      ..|+|+||    |+.+++++|+++|+.||+|.++.++.  .+|.++|||||+|.+    +++    |.+|+.  .++|..
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            57999999    99999999999999999999999887  889999999999996    433    888988  789999


Q ss_pred             ecCEEEEEeecccch
Q psy12549        268 VDGKILYVGRAQKKA  282 (336)
Q Consensus       268 ~~g~~l~v~~~~~~~  282 (336)
                      ++|+.|+|.+-....
T Consensus        83 I~Gr~irV~ln~~g~   97 (136)
T 2j8a_A           83 IMGFKFEVILNKHSI   97 (136)
T ss_dssp             ETTEEEEEEECCTTH
T ss_pred             ecCcEEEEEECcccH
Confidence            999999999865543

>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=99.53  E-value=1.1e-14  Score=108.86  Aligned_cols=73  Identities=16%  Similarity=0.162  Sum_probs=65.7

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEE-----EEEee
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKI-----LYVGR  277 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~-----l~v~~  277 (336)
                      .++|||.|||.++++++|+++|+.||+|..+.++..     |||||+|.+.++|.+|++.|||..+.|+.     ++|..
T Consensus        16 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-----g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~   90 (115)
T 3beg_B           16 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   90 (115)
T ss_dssp             -CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-----SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-----CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEecc
Confidence            478999999999999999999999999999999754     89999999999999999999999999988     66666


Q ss_pred             ccc
Q psy12549        278 AQK  280 (336)
Q Consensus       278 ~~~  280 (336)
                      +.+
T Consensus        91 ~~~   93 (115)
T 3beg_B           91 DGP   93 (115)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            554

>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=99.52  E-value=1.5e-14  Score=108.25  Aligned_cols=75  Identities=23%  Similarity=0.278  Sum_probs=65.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeE-----EEE
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKI-----VFV  183 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~-----i~v  183 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+.++.+      |||||+|.+.++|.+|++.||+..+.|+.     +.+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v   88 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   88 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEe
Confidence            3578999999999999999999999999999999865      79999999999999999999999999988     666


Q ss_pred             eeccCc
Q psy12549        184 GKFIPR  189 (336)
Q Consensus       184 ~~~~~~  189 (336)
                      ....+.
T Consensus        89 ~~~~~~   94 (115)
T 3beg_B           89 KVDGPR   94 (115)
T ss_dssp             EECC--
T ss_pred             ccCCCC
Confidence            665543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.52  E-value=7.3e-14  Score=104.90  Aligned_cols=75  Identities=19%  Similarity=0.223  Sum_probs=67.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccE-EEEEeCCHHHHHHHHHHhCCceeCC--eEEEEeecc
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGY-GFVHFETEEAANKSIEKVNGMLLNS--KIVFVGKFI  187 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~-afV~F~~~~~a~~a~~~l~~~~~~~--~~i~v~~~~  187 (336)
                      ..|||+|||..+++++|+++|++||.|.+|.+...     .|+ |||+|.+.++|..|++.|||..+.|  +.|.|.++.
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            35789999999999999999999999999999763     275 9999999999999999999999977  699999988


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      +..
T Consensus       101 ~~~  103 (124)
T 2e5i_A          101 PTR  103 (124)
T ss_dssp             CSC
T ss_pred             CCc
Confidence            764

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=3.9e-14  Score=99.04  Aligned_cols=72  Identities=17%  Similarity=0.260  Sum_probs=64.4

Q ss_pred             ceEEEcCCCCCCCHHH----HHHHhhccC-CeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        111 GNVFIKNLDKSIDNKA----MYDTFSAFG-SILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~----l~~~f~~~G-~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      +.|||+|||.++++++    |+++|++|| .|..|      +|   |+|||.|.+.++|.+|++.|+|..+.|++|.|.+
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~   80 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSF   80 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEES
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEe
Confidence            3499999999999988    558999994 99988      22   8999999999999999999999999999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +....+
T Consensus        81 A~~~sd   86 (96)
T 2diu_A           81 TPKNRE   86 (96)
T ss_dssp             SCCSCC
T ss_pred             cCCCcc
Confidence            887654

>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=99.49  E-value=2.9e-14  Score=101.28  Aligned_cols=76  Identities=20%  Similarity=0.420  Sum_probs=65.0

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      .++|||+|||.++++++|+++|+.||+|..+.++..   ++|||||+|.+.++|++|...  +..+.|+.|.|.++.++.
T Consensus         5 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~---~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~~~~   79 (88)
T 1wf0_A            5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP---FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS---CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCCCCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC---CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecCCCC
Confidence            488999999999999999999999999999998753   689999999999999764321  344589999999998764


Q ss_pred             h
Q psy12549        283 E  283 (336)
Q Consensus       283 ~  283 (336)
                      .
T Consensus        80 ~   80 (88)
T 1wf0_A           80 N   80 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.49  E-value=2.7e-14  Score=101.50  Aligned_cols=77  Identities=16%  Similarity=0.425  Sum_probs=66.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..++|||+|||.++++++|+++|+.||.|..+.++.+    ++|||||+|.+.++|++|..  ....+.|+.|.|.++.+
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecCC
Confidence            4588999999999999999999999999999999865    68899999999999986533  23456999999999877


Q ss_pred             chh
Q psy12549        189 RKE  191 (336)
Q Consensus       189 ~~~  191 (336)
                      +..
T Consensus        78 ~~~   80 (88)
T 1wf0_A           78 KHN   80 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.49  E-value=4.3e-14  Score=118.14  Aligned_cols=81  Identities=22%  Similarity=0.371  Sum_probs=71.0

Q ss_pred             ccccceEEEcCCCCCC---------cHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCcee--
Q psy12549        200 AKLFTNVYIKNFGEDF---------NDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEV--  268 (336)
Q Consensus       200 ~~~~~~l~V~nlp~~~---------t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~--  268 (336)
                      ....++|||+||+..+         ++++|+++|++||+|.+|.++.    ++|+|||+|.+.++|+.|++.|+|..+  
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~----~kG~AFV~F~~~~~Ae~A~~am~g~~l~~  206 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE----SKNCGFVKFKYQANAEFAKEAMSNQTLLL  206 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG----GGTEEEEEESSHHHHHHHHHHHTTCCCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC----CCCEEEEEeCCHHHHHHHHHHhCCCEEec
Confidence            3455899999999998         7999999999999999999985    489999999999999999999999999  


Q ss_pred             ----------cCEEEEEeecccchhh
Q psy12549        269 ----------DGKILYVGRAQKKAER  284 (336)
Q Consensus       269 ----------~g~~l~v~~~~~~~~~  284 (336)
                                .|+.|.|.||......
T Consensus       207 ~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          207 PSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             TTSTTGGGGGGSCCCEEEECC-----
T ss_pred             cccccccccCCCCEEEEEEccCCCCH
Confidence                      8999999999876543

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=8.2e-14  Score=104.03  Aligned_cols=75  Identities=15%  Similarity=0.346  Sum_probs=63.3

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CC---CccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEe
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--ND---GKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG  276 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~---~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~  276 (336)
                      ..++|||+|||.++++++|+++|++||.|. +.++.  .+   |.++|||||+|.+.++|.+|++.++  .++|+.+.+.
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~   83 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCV   83 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEec
Confidence            348899999999999999999999999999 66665  33   6889999999999999999999983  3677777665


Q ss_pred             ecc
Q psy12549        277 RAQ  279 (336)
Q Consensus       277 ~~~  279 (336)
                      .+.
T Consensus        84 ~~~   86 (114)
T 2dnl_A           84 SSP   86 (114)
T ss_dssp             CCS
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=2.3e-13  Score=101.16  Aligned_cols=80  Identities=20%  Similarity=0.297  Sum_probs=68.8

Q ss_pred             cccceEEEcCCCCCC-----------cHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceec
Q psy12549        201 KLFTNVYIKNFGEDF-----------NDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD  269 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~-----------t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~  269 (336)
                      .+.++|+|.||....           ++++|+++|++||.|..+.+...  .++|+|||+|.+.++|.+|+..|||..+.
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~--~~~G~afV~f~~~~~A~~Ai~~lng~~~~   90 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR--HPDGVASVSFRDPEEADYCIQTLDGRWFG   90 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT--CTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecC--CCCEEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            445889999995433           25899999999999999977432  37999999999999999999999999999


Q ss_pred             CEEEEEeecccch
Q psy12549        270 GKILYVGRAQKKA  282 (336)
Q Consensus       270 g~~l~v~~~~~~~  282 (336)
                      |+.|.|.++.++.
T Consensus        91 gr~l~v~~a~~~~  103 (112)
T 2dit_A           91 GRQITAQAWDGTT  103 (112)
T ss_dssp             TEECEEEECCSCC
T ss_pred             CcEEEEEEeCCCC
Confidence            9999999998753

>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=99.46  E-value=2.1e-13  Score=99.86  Aligned_cols=80  Identities=18%  Similarity=0.228  Sum_probs=68.2

Q ss_pred             ccceEEEcCC--CCCC--------cHHHHHHhhccCCceeEEEEeCCC----CccceEEEEEeCCHHHHHHHHHHhCCce
Q psy12549        202 LFTNVYIKNF--GEDF--------NDEKLKEMFEPYGTITSYRVMNND----GKSRGFGFVAYESPEFAEKAVQAWNGKE  267 (336)
Q Consensus       202 ~~~~l~V~nl--p~~~--------t~~~l~~~f~~~g~i~~~~i~~~~----~~~~g~afV~F~~~~~a~~a~~~l~g~~  267 (336)
                      +++.|.+.|+  |.++        .+++|++.|++||.|.++.++.+.    +.++|+|||+|.+.++|.+|+..|||+.
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            3477889997  4444        337999999999999999998732    3578999999999999999999999999


Q ss_pred             ecCEEEEEeecccc
Q psy12549        268 VDGKILYVGRAQKK  281 (336)
Q Consensus       268 ~~g~~l~v~~~~~~  281 (336)
                      +.||.|+|.++...
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

>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=99.44  E-value=6.9e-14  Score=102.30  Aligned_cols=72  Identities=22%  Similarity=0.326  Sum_probs=61.5

Q ss_pred             EcCCCCCCcHHHHHHhh------------ccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEE
Q psy12549        208 IKNFGEDFNDEKLKEMF------------EPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILY  274 (336)
Q Consensus       208 V~nlp~~~t~~~l~~~f------------~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~  274 (336)
                      +.|||..+++++|++.|            ++||.|.++.++. ..+.++|+|||+|.+.++|.+|+..|||..+.|+.|+
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            45666666776666555            9999999999987 5577899999999999999999999999999999999


Q ss_pred             Eeecc
Q psy12549        275 VGRAQ  279 (336)
Q Consensus       275 v~~~~  279 (336)
                      |.|+.
T Consensus       100 v~~sp  104 (104)
T 1jmt_A          100 AELSP  104 (104)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            99863

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.42  E-value=2.6e-13  Score=113.43  Aligned_cols=79  Identities=19%  Similarity=0.261  Sum_probs=70.1

Q ss_pred             CCCceEEEcCCCCCC---------CHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcee--
Q psy12549        108 SGVGNVFIKNLDKSI---------DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLL--  176 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~---------t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~--  176 (336)
                      ...++|||+|||..+         ++++|+++|++||.|.+|.++.     ++|||||+|.+.++|..|++.|+|..+  
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~-----~kG~AFV~F~~~~~Ae~A~~am~g~~l~~  206 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQANAEFAKEAMSNQTLLL  206 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG-----GGTEEEEEESSHHHHHHHHHHHTTCCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC-----CCCEEEEEeCCHHHHHHHHHHhCCCEEec
Confidence            346899999999998         7999999999999999999985     479999999999999999999999999  


Q ss_pred             ----------CCeEEEEeeccCchh
Q psy12549        177 ----------NSKIVFVGKFIPRKE  191 (336)
Q Consensus       177 ----------~~~~i~v~~~~~~~~  191 (336)
                                .|+.|.|.|+.+...
T Consensus       207 ~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          207 PSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             TTSTTGGGGGGSCCCEEEECC----
T ss_pred             cccccccccCCCCEEEEEEccCCCC
Confidence                      899999999986543

>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=99.42  E-value=9e-14  Score=101.69  Aligned_cols=72  Identities=18%  Similarity=0.333  Sum_probs=64.0

Q ss_pred             EcCCCCCCCHHHHHHHh------------hccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q psy12549        115 IKNLDKSIDNKAMYDTF------------SAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF  182 (336)
Q Consensus       115 v~nlp~~~t~~~l~~~f------------~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~  182 (336)
                      +.|||..+++++|++.|            ++||.|.++.++++..+.++|||||+|.++++|.+|+..|||..+.|+.|.
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            55677777777776666            999999999999988888999999999999999999999999999999999


Q ss_pred             Eeec
Q psy12549        183 VGKF  186 (336)
Q Consensus       183 v~~~  186 (336)
                      |.++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9875

>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=99.42  E-value=1.3e-12  Score=97.07  Aligned_cols=80  Identities=21%  Similarity=0.288  Sum_probs=68.6

Q ss_pred             CCCceEEEcCCCCCCC-----------HHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcee
Q psy12549        108 SGVGNVFIKNLDKSID-----------NKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLL  176 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t-----------~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~  176 (336)
                      ...++|+|+||....+           +++|+++|++||.|..+.+ .++  .++|||||+|.+.++|.+|+..|||..+
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng~~~   89 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDGRWF   89 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCCCEE
Confidence            4468899999954332           5899999999999999966 443  3789999999999999999999999999


Q ss_pred             CCeEEEEeeccCch
Q psy12549        177 NSKIVFVGKFIPRK  190 (336)
Q Consensus       177 ~~~~i~v~~~~~~~  190 (336)
                      .|+.|.|.++.+..
T Consensus        90 ~gr~l~v~~a~~~~  103 (112)
T 2dit_A           90 GGRQITAQAWDGTT  103 (112)
T ss_dssp             TTEECEEEECCSCC
T ss_pred             CCcEEEEEEeCCCC
Confidence            99999999987653

>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=99.41  E-value=8.3e-13  Score=96.64  Aligned_cols=81  Identities=16%  Similarity=0.231  Sum_probs=69.7

Q ss_pred             CCceEEEcCC--CCCCC--------HHHHHHHhhccCCeeEEEEeeCCC---CCcccEEEEEeCCHHHHHHHHHHhCCce
Q psy12549        109 GVGNVFIKNL--DKSID--------NKAMYDTFSAFGSILSCKVAQDEQ---GNSKGYGFVHFETEEAANKSIEKVNGML  175 (336)
Q Consensus       109 ~~~~l~v~nl--p~~~t--------~~~l~~~f~~~G~v~~~~~~~~~~---~~~~g~afV~F~~~~~a~~a~~~l~~~~  175 (336)
                      .++.|.+.|+  |....        +++|++.|++||.|.++.+++++.   +.++|+|||+|.++++|.+|+..|||..
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            3467899998  33332        368999999999999999998864   3578999999999999999999999999


Q ss_pred             eCCeEEEEeeccCc
Q psy12549        176 LNSKIVFVGKFIPR  189 (336)
Q Consensus       176 ~~~~~i~v~~~~~~  189 (336)
                      +.|+.|.+.++...
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            99999999987654

>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=99.40  E-value=1.2e-12  Score=97.63  Aligned_cols=80  Identities=19%  Similarity=0.246  Sum_probs=68.8

Q ss_pred             ccceEEEcCCC--CCC---cHHHHHHhhccCCceeEEEEeCC------CCccceEEEEEeCCHHHHHHHHHHhCCceecC
Q psy12549        202 LFTNVYIKNFG--EDF---NDEKLKEMFEPYGTITSYRVMNN------DGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG  270 (336)
Q Consensus       202 ~~~~l~V~nlp--~~~---t~~~l~~~f~~~g~i~~~~i~~~------~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g  270 (336)
                      ++++|++.|+-  .++   .+++|++.|++||.|.++.|+.+      ++.++|++||+|.+.++|.+|+..|||+.|.|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            45789999984  222   46899999999999999999872      34578999999999999999999999999999


Q ss_pred             EEEEEeecccc
Q psy12549        271 KILYVGRAQKK  281 (336)
Q Consensus       271 ~~l~v~~~~~~  281 (336)
                      |.|+|.++...
T Consensus        99 R~i~v~~~~~~  109 (118)
T 3ue2_A           99 RKVVAEVYDQE  109 (118)
T ss_dssp             EECEEEEECHH
T ss_pred             cEEEEEEcChH
Confidence            99999998653

>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=99.34  E-value=3.4e-12  Score=95.20  Aligned_cols=80  Identities=18%  Similarity=0.265  Sum_probs=69.3

Q ss_pred             CceEEEcCCCC--CC---CHHHHHHHhhccCCeeEEEEeeCCC-----CCcccEEEEEeCCHHHHHHHHHHhCCceeCCe
Q psy12549        110 VGNVFIKNLDK--SI---DNKAMYDTFSAFGSILSCKVAQDEQ-----GNSKGYGFVHFETEEAANKSIEKVNGMLLNSK  179 (336)
Q Consensus       110 ~~~l~v~nlp~--~~---t~~~l~~~f~~~G~v~~~~~~~~~~-----~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~  179 (336)
                      +++|+++|+-.  .+   .+++|++.|++||.|.++.++.++.     +.++|++||+|.+.++|.+|+..|||..+.|+
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            47899999832  22   3689999999999999999998853     45789999999999999999999999999999


Q ss_pred             EEEEeeccCc
Q psy12549        180 IVFVGKFIPR  189 (336)
Q Consensus       180 ~i~v~~~~~~  189 (336)
                      .|.+.++...
T Consensus       100 ~i~v~~~~~~  109 (118)
T 3ue2_A          100 KVVAEVYDQE  109 (118)
T ss_dssp             ECEEEEECHH
T ss_pred             EEEEEEcChH
Confidence            9999987643

>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=99.33  E-value=6e-12  Score=93.15  Aligned_cols=78  Identities=19%  Similarity=0.148  Sum_probs=65.6

Q ss_pred             ccceEEEcCCCCCC----------cHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCE
Q psy12549        202 LFTNVYIKNFGEDF----------NDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK  271 (336)
Q Consensus       202 ~~~~l~V~nlp~~~----------t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~  271 (336)
                      +.+.|.+.|+=..-          .+++|++.|++||.|.++.+.+.+  ++|+|||+|.+.++|.+|+..|||+.|+||
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~--~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR   83 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS--AQGNVYVKCPSIAAAIAAVNALHGRWFAGK   83 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC--TTCCEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC--CcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            34678888873221          236899999999999999997643  489999999999999999999999999999


Q ss_pred             EEEEeecccc
Q psy12549        272 ILYVGRAQKK  281 (336)
Q Consensus       272 ~l~v~~~~~~  281 (336)
                      .|+|.|+...
T Consensus        84 ~i~v~~~~~~   93 (114)
T 3s6e_A           84 MITAAYVPLP   93 (114)
T ss_dssp             ECEEEEECHH
T ss_pred             EEEEEEEcHH
Confidence            9999998644

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.27  E-value=8.4e-12  Score=90.08  Aligned_cols=65  Identities=20%  Similarity=0.308  Sum_probs=58.2

Q ss_pred             CCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        213 EDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       213 ~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      ..+++++|+++|++||.|..+.++   +.++|||||+|.+.++|..|++.+++  +.|+.|+|.|+.++.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~---~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS---SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE---SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc---cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCC
Confidence            568999999999999999999998   46799999999999999999998554  689999999998764

>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=99.24  E-value=1.6e-11  Score=108.15  Aligned_cols=76  Identities=22%  Similarity=0.420  Sum_probs=66.2

Q ss_pred             ccccceEEEcC--CCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceec---CE--E
Q psy12549        200 AKLFTNVYIKN--FGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD---GK--I  272 (336)
Q Consensus       200 ~~~~~~l~V~n--lp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~---g~--~  272 (336)
                      ..+..+|||+|  |+..+++++|+++|++||.|.++.+..    ++|||||+|.+.++|++|++.|||..+.   |+  .
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~   90 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   90 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceE
Confidence            44558899999  578999999999999999999987754    4899999999999999999999999983   44  6


Q ss_pred             EEEeecc
Q psy12549        273 LYVGRAQ  279 (336)
Q Consensus       273 l~v~~~~  279 (336)
                      |.+.|+.
T Consensus        91 ly~~~~~   97 (345)
T 3tht_A           91 LYLNFVE   97 (345)
T ss_dssp             CEEEECS
T ss_pred             EEEEEee
Confidence            8888874

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.23  E-value=4.6e-11  Score=86.17  Aligned_cols=66  Identities=15%  Similarity=0.266  Sum_probs=57.8

Q ss_pred             CCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCch
Q psy12549        119 DKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRK  190 (336)
Q Consensus       119 p~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~  190 (336)
                      +..+++++|+++|++||.|..|.++.    .++|||||+|.+.++|..|++.+++  +.|++|.|.|+.+..
T Consensus        26 ~~~~te~~L~~~F~~~G~V~~v~i~~----~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           26 KGGYSKDVLLRLLQKYGEVLNLVLSS----KKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQP   91 (100)
T ss_dssp             CCSCCHHHHHHHHHTTSCEEEEEEES----SSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCC
T ss_pred             CCCCCHHHHHHHHHhcCCEEEEEEcc----CCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCC
Confidence            36799999999999999999999883    5789999999999999999997444  679999999987664

>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=99.21  E-value=7.7e-11  Score=87.19  Aligned_cols=79  Identities=11%  Similarity=0.181  Sum_probs=66.0

Q ss_pred             CCceEEEcCCCCCC----------CHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCC
Q psy12549        109 GVGNVFIKNLDKSI----------DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNS  178 (336)
Q Consensus       109 ~~~~l~v~nlp~~~----------t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~  178 (336)
                      .++.|.+.|+=..-          .+++|++.|++||.|.++.+.++.   .+|+|||+|.+.++|.+|+..|||..++|
T Consensus         6 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            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            35678898883221          235889999999999999987653   48999999999999999999999999999


Q ss_pred             eEEEEeeccCch
Q psy12549        179 KIVFVGKFIPRK  190 (336)
Q Consensus       179 ~~i~v~~~~~~~  190 (336)
                      +.|.+.++....
T Consensus        83 R~i~v~~~~~~~   94 (114)
T 3s6e_A           83 KMITAAYVPLPT   94 (114)
T ss_dssp             EECEEEEECHHH
T ss_pred             EEEEEEEEcHHH
Confidence            999999986543

>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=99.19  E-value=4.2e-11  Score=105.52  Aligned_cols=75  Identities=13%  Similarity=0.303  Sum_probs=63.9

Q ss_pred             CCCceEEEcC--CCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeC---Ce--E
Q psy12549        108 SGVGNVFIKN--LDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLN---SK--I  180 (336)
Q Consensus       108 ~~~~~l~v~n--lp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~---~~--~  180 (336)
                      ..+.+|||+|  |+..+|+++|+++|++||.|.++.+..     ++|||||+|.+.++|++|++.|||..+.   |+  .
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~   90 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   90 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceE
Confidence            4457899999  578999999999999999999987754     4789999999999999999999999872   44  5


Q ss_pred             EEEeecc
Q psy12549        181 VFVGKFI  187 (336)
Q Consensus       181 i~v~~~~  187 (336)
                      +.+.+..
T Consensus        91 ly~~~~~   97 (345)
T 3tht_A           91 LYLNFVE   97 (345)
T ss_dssp             CEEEECS
T ss_pred             EEEEEee
Confidence            6777664

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.05  E-value=5.7e-10  Score=77.29  Aligned_cols=72  Identities=18%  Similarity=0.277  Sum_probs=60.0

Q ss_pred             cceEEEcCCC----CCCcH----HHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEE
Q psy12549        203 FTNVYIKNFG----EDFND----EKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILY  274 (336)
Q Consensus       203 ~~~l~V~nlp----~~~t~----~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~  274 (336)
                      ..+|+|.-.+    ..+..    .+|.+.|+.||.|..+++..      +.+||+|.+.++|.+|++ |||..+.||.|+
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~------d~~fVtF~d~~sAlaAi~-mnG~~v~Gr~Lk   79 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVE------DKMWVTFLEGSSALNVLS-LNGKELLNRTIT   79 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECS------SSEEEEESSHHHHHHGGG-GTTCEETTEEEE
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEec------CCEEEEECChHHHHHHHh-cCCeEeCCeEEE
Confidence            3677777665    22333    57899999999999999985      338999999999999998 999999999999


Q ss_pred             Eeecccc
Q psy12549        275 VGRAQKK  281 (336)
Q Consensus       275 v~~~~~~  281 (336)
                      |.++++.
T Consensus        80 V~lkt~d   86 (91)
T 2dnr_A           80 IALKSPS   86 (91)
T ss_dssp             EEECCCS
T ss_pred             EEeCCCC
Confidence            9998764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.04  E-value=7.8e-10  Score=81.85  Aligned_cols=79  Identities=14%  Similarity=0.098  Sum_probs=68.1

Q ss_pred             ccceEEEcCCCCC-CcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCC-HHHHHHHHHHhC--CceecCEEEEEee
Q psy12549        202 LFTNVYIKNFGED-FNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYES-PEFAEKAVQAWN--GKEVDGKILYVGR  277 (336)
Q Consensus       202 ~~~~l~V~nlp~~-~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~-~~~a~~a~~~l~--g~~~~g~~l~v~~  277 (336)
                      ..+.|+|+||+.. ++.++|+++|+.||+|.+|.+...    ...|||+|.+ +++|..|+..++  +..+.|..++++.
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g----~~tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~ev   92 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   92 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecC----CCEEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEE
Confidence            3477999999999 999999999999999999999864    2359999999 899999999994  7889999999988


Q ss_pred             cccchhh
Q psy12549        278 AQKKAER  284 (336)
Q Consensus       278 ~~~~~~~  284 (336)
                      .....+.
T Consensus        93 L~GeeE~   99 (121)
T 1owx_A           93 LEGEVEK   99 (121)
T ss_dssp             CCHHHHH
T ss_pred             CCCHHHH
Confidence            7765443

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.92  E-value=5.3e-09  Score=72.43  Aligned_cols=73  Identities=19%  Similarity=0.387  Sum_probs=61.6

Q ss_pred             CCceEEEcCCCC----CC-CH---HHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeE
Q psy12549        109 GVGNVFIKNLDK----SI-DN---KAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKI  180 (336)
Q Consensus       109 ~~~~l~v~nlp~----~~-t~---~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~  180 (336)
                      ...||+|.-.|.    +. ++   .+|.+.|..||.|..+++..++       +||+|.+.++|.+|++ |||..+.|+.
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~-------~fVtF~d~~sAlaAi~-mnG~~v~Gr~   77 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK-------MWVTFLEGSSALNVLS-LNGKELLNRT   77 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS-------EEEEESSHHHHHHGGG-GTTCEETTEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC-------EEEEECChHHHHHHHh-cCCeEeCCeE
Confidence            347788877762    23 32   5789999999999999999873       8999999999999999 9999999999


Q ss_pred             EEEeeccCc
Q psy12549        181 VFVGKFIPR  189 (336)
Q Consensus       181 i~v~~~~~~  189 (336)
                      |+|+.+.+.
T Consensus        78 LkV~lkt~d   86 (91)
T 2dnr_A           78 ITIALKSPS   86 (91)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999887653

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.87  E-value=7.1e-09  Score=76.69  Aligned_cols=76  Identities=14%  Similarity=0.058  Sum_probs=65.7

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCC-HHHHHHHHHHhC--CceeCCeEEE
Q psy12549        107 KSGVGNVFIKNLDKS-IDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFET-EEAANKSIEKVN--GMLLNSKIVF  182 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~-~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~-~~~a~~a~~~l~--~~~~~~~~i~  182 (336)
                      -...+-|+|+||+.. ++.++|+++|+.||.|..|.+..++.     .|||.|.+ +++|..|+..++  +..+.|..+.
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~-----tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~   89 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK-----EGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   89 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS-----EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC-----EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEE
Confidence            345678999999999 99999999999999999999988743     59999999 899999999994  6788888887


Q ss_pred             Eeecc
Q psy12549        183 VGKFI  187 (336)
Q Consensus       183 v~~~~  187 (336)
                      +....
T Consensus        90 ~evL~   94 (121)
T 1owx_A           90 WEVLE   94 (121)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            76544

>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=6.3e-09  Score=72.36  Aligned_cols=73  Identities=18%  Similarity=0.234  Sum_probs=60.5

Q ss_pred             cccceEEEcCCCCC-----CcH----HHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCE
Q psy12549        201 KLFTNVYIKNFGED-----FND----EKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK  271 (336)
Q Consensus       201 ~~~~~l~V~nlp~~-----~t~----~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~  271 (336)
                      ++..+|+|.-++..     +..    .+|.+.|+.||.|..+++...      -+||+|.+.++|.+|++ |+|..+.||
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d------~~fVtF~d~~sAl~AI~-ldG~~v~Gr   85 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG------QMLVTFADSHSALSVLD-VDGMKVKGR   85 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT------EEEEECSCSHHHHHHHH-GGGSEETTE
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecC------cEEEEEcChHHHHHHHh-cCCeeeCCe
Confidence            44478888877632     222    568999999999999999853      39999999999999998 999999999


Q ss_pred             EEEEeeccc
Q psy12549        272 ILYVGRAQK  280 (336)
Q Consensus       272 ~l~v~~~~~  280 (336)
                      .|+|.+..+
T Consensus        86 ~L~V~~k~~   94 (95)
T 1ufw_A           86 AVKISGPSS   94 (95)
T ss_dssp             EEEEECCCC
T ss_pred             EEEEeccCC
Confidence            999988653

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.80  E-value=8.6e-09  Score=86.08  Aligned_cols=66  Identities=18%  Similarity=0.221  Sum_probs=59.8

Q ss_pred             CcHHHHHHhhccCCceeEEEEeC------CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        215 FNDEKLKEMFEPYGTITSYRVMN------NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       215 ~t~~~l~~~f~~~g~i~~~~i~~------~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      -.+++|++.|++||.|.++.+..      .++.++|++||+|.+.++|.+|+..|||+.+.||.|.+.+...
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            45689999999999999999975      3447899999999999999999999999999999999999764

>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=98.71  E-value=2.4e-08  Score=83.30  Aligned_cols=67  Identities=16%  Similarity=0.229  Sum_probs=60.5

Q ss_pred             CCHHHHHHHhhccCCeeEEEEeeCC-----CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        122 IDNKAMYDTFSAFGSILSCKVAQDE-----QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       122 ~t~~~l~~~f~~~G~v~~~~~~~~~-----~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      -.+++|++.|++||.|.++.++++.     +++++|++||+|.+.++|.+|+..|||..+.||.|.+.++..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            4567999999999999999998664     348999999999999999999999999999999999988754

>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=98.67  E-value=6.3e-08  Score=67.36  Aligned_cols=73  Identities=16%  Similarity=0.043  Sum_probs=61.0

Q ss_pred             ccccCceeeeecCchh-----hhh----hhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhh
Q psy12549         14 IIIPKHNVATRELSAK-----VVE----GVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDT   83 (336)
Q Consensus        14 ~~~p~~~v~v~~lp~~-----~~e----~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~   83 (336)
                      ...|..||+|.-++++     +-.    .+|.+.| .+|.+..++++.++           +||+|.+.  ++|.+|++ 
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-----------~fVtF~d~--~sAl~AI~-   76 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-----------MLVTFADS--HSALSVLD-   76 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-----------EEEECSCS--HHHHHHHH-
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-----------EEEEEcCh--HHHHHHHh-
Confidence            4568889999988743     222    4577788 67779999999987           89999999  99999999 


Q ss_pred             cCccccCCeeeEEEecc
Q psy12549         84 MNFDALKGRPIRIMWSQ  100 (336)
Q Consensus        84 ~~~~~~~g~~i~v~~~~  100 (336)
                      +||..+.||.|+|....
T Consensus        77 ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           77 VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             GGGSEETTEEEEEECCC
T ss_pred             cCCeeeCCeEEEEeccC
Confidence            99999999999998743

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.63  E-value=2.9e-07  Score=65.22  Aligned_cols=75  Identities=13%  Similarity=0.127  Sum_probs=67.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhcc-----CCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAF-----GSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF  182 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~-----G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~  182 (336)
                      ...++|-+-|||..++...|+.+.+++     |.+..+.+.+|-.     -|+|+|.+...|.+|.-.|+|..+.|++|.
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~-----GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN-----GAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT-----EEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC-----ceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            346889999999999999999999999     9999999988743     499999999999999999999999999999


Q ss_pred             Eeecc
Q psy12549        183 VGKFI  187 (336)
Q Consensus       183 v~~~~  187 (336)
                      +....
T Consensus        94 ~gTv~   98 (117)
T 2l9w_A           94 SGTIN   98 (117)
T ss_dssp             EECHH
T ss_pred             ecCHH
Confidence            96543

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.48  E-value=7.4e-07  Score=63.18  Aligned_cols=73  Identities=14%  Similarity=0.266  Sum_probs=65.8

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccC-----CceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEee
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPY-----GTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR  277 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~-----g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~  277 (336)
                      .++|-+-|||..+++..|+.+.+++     |.+..+.+.++    -+-|+|+|.+...|-+|.-.|+|..|.|+.|++.-
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD----H~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD----FNGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT----TTEEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC----CCceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            4789999999999999999999999     99999998875    33499999999999999999999999999999965


Q ss_pred             cc
Q psy12549        278 AQ  279 (336)
Q Consensus       278 ~~  279 (336)
                      ..
T Consensus        97 v~   98 (117)
T 2l9w_A           97 IN   98 (117)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.35  E-value=1.7e-06  Score=60.83  Aligned_cols=87  Identities=14%  Similarity=0.079  Sum_probs=68.7

Q ss_pred             cCceeeeecCchhhhhhhHHhhhcc----cC--CceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccC
Q psy12549         17 PKHNVATRELSAKVVEGVSRSLSSL----ID--GNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALK   90 (336)
Q Consensus        17 p~~~v~v~~lp~~~~e~~l~~~f~~----~~--~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~   90 (336)
                      -..+|.|.|||+.+.++.|.-+|..    ++  +.++....           +-|+|+|.+.  +.|+..++ .....++
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-----------~~AvItF~d~--~va~rVL~-k~~H~L~   72 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-----------CGGVLTFREP--ADAERVLA-QADHELH   72 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-----------TEEEEEESSH--HHHHHHHT-CSCCBSS
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-----------CcEEEEEcCh--HHHHHHhc-CCcceec
Confidence            4578999999999999999999922    43  34555554           1299999999  99999998 5567888


Q ss_pred             CeeeEEEeccCCCCcCCCCCceEEEcCCCCCCC
Q psy12549         91 GRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSID  123 (336)
Q Consensus        91 g~~i~v~~~~~~~~~~~~~~~~l~v~nlp~~~t  123 (336)
                      +.++.|.+.....      .++|+++|||+.++
T Consensus        73 ~~~LsV~P~~~~~------~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           73 GAQLSLRPAPPRA------PARLLLQGLPPGTS   99 (104)
T ss_dssp             SSBCEEEECCCCC------CCCCCCCSCCCCCC
T ss_pred             CeEEEEEcCCCCC------cceEeeecCCCCCC
Confidence            9999998865533      37799999998875

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.09  E-value=2.2e-05  Score=55.29  Aligned_cols=87  Identities=14%  Similarity=0.185  Sum_probs=71.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhc---c--CCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEe
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSA---F--GSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVG  184 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~---~--G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~  184 (336)
                      ..+|.|.|||+.++++.|.-+|+.   -  |.|..+....       +-|+|+|.+.+.|++.++. ..+.+.+..+.|.
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV~   79 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAERVLAQ-ADHELHGAQLSLR   79 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHHHHhcC-CcceecCeEEEEE
Confidence            468999999999999999999987   2  4788777654       3699999999999999983 4788999999997


Q ss_pred             eccCchhhhHhhhccccccceEEEcCCCCCCc
Q psy12549        185 KFIPRKEREKELGEKAKLFTNVYIKNFGEDFN  216 (336)
Q Consensus       185 ~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t  216 (336)
                      ...+...            .++++.+|++.++
T Consensus        80 P~~~~~~------------~r~ll~gl~~~t~   99 (104)
T 2dhx_A           80 PAPPRAP------------ARLLLQGLPPGTS   99 (104)
T ss_dssp             ECCCCCC------------CCCCCCSCCCCCC
T ss_pred             cCCCCCc------------ceEeeecCCCCCC
Confidence            7555433            6689999998775

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.01  E-value=2e-05  Score=55.79  Aligned_cols=75  Identities=17%  Similarity=0.162  Sum_probs=63.7

Q ss_pred             cceEEEcCCCCCC-c----HHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEee
Q psy12549        203 FTNVYIKNFGEDF-N----DEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR  277 (336)
Q Consensus       203 ~~~l~V~nlp~~~-t----~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~  277 (336)
                      .++|+|.||+.++ .    .+.++++|..|+++......+.-    .-..|.|.++++|.+|...||+..+.|+.++|.|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF----RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~YF   80 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF----KRVRINFSNPLSAADARLRLHKTEFLGKEMKLYF   80 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT----TEEEEECSSTTHHHHHHHTSTTSEETTEECEEEC
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc----eEEEEEeCChHHHHHHHHHhccceecCceeEEEe
Confidence            3789999998765 2    25778999999999988888632    2378999999999999999999999999999999


Q ss_pred             cccc
Q psy12549        278 AQKK  281 (336)
Q Consensus       278 ~~~~  281 (336)
                      +.+.
T Consensus        81 gq~~   84 (104)
T 1wey_A           81 AQTL   84 (104)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            8844

>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=97.76  E-value=0.00026  Score=49.21  Aligned_cols=76  Identities=16%  Similarity=0.197  Sum_probs=60.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCC---C-ccceEEEEEeCCHHHHHHHHHHhCCceecC-----EEEE
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND---G-KSRGFGFVAYESPEFAEKAVQAWNGKEVDG-----KILY  274 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~---~-~~~g~afV~F~~~~~a~~a~~~l~g~~~~g-----~~l~  274 (336)
                      ++|.|++||..+|++++.+.++....+.........   + ..-+.|||.|.+.+++..-.+.++|..|.+     .+..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            468999999999999999999999888777776511   1 224679999999999999999999999853     3345


Q ss_pred             Eeecc
Q psy12549        275 VGRAQ  279 (336)
Q Consensus       275 v~~~~  279 (336)
                      |++|.
T Consensus        82 VE~AP   86 (91)
T 1uw4_A           82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66654

>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=97.70  E-value=0.00022  Score=49.56  Aligned_cols=67  Identities=9%  Similarity=0.211  Sum_probs=55.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-C-C-CcccEEEEEeCCHHHHHHHHHHhCCceeC
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-Q-G-NSKGYGFVHFETEEAANKSIEKVNGMLLN  177 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~-~-~~~g~afV~F~~~~~a~~a~~~l~~~~~~  177 (336)
                      ++|.|++||+++|++++.+.+..+..+........+ + + ..-.-|||.|.+.+++....+.++|..+.
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            469999999999999999999999887776666654 1 1 23356999999999999999999998763

>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=97.46  E-value=0.00085  Score=47.43  Aligned_cols=74  Identities=15%  Similarity=0.177  Sum_probs=59.2

Q ss_pred             ccCceeeeecCchhh-hh----hhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCcccc
Q psy12549         16 IPKHNVATRELSAKV-VE----GVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDAL   89 (336)
Q Consensus        16 ~p~~~v~v~~lp~~~-~e----~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~   89 (336)
                      .|+ +|+|.||+..+ ..    +.++++| ...+.....+.+.-         +-..|.|.++  ++|.+|...+++..+
T Consensus         4 ~pn-tLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF---------RRirv~F~~~--~~A~~AR~~Lh~~~f   71 (104)
T 1wey_A            4 GSS-GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF---------KRVRINFSNP--LSAADARLRLHKTEF   71 (104)
T ss_dssp             CCC-EEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT---------TEEEEECSST--THHHHHHHTSTTSEE
T ss_pred             CCc-eEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc---------eEEEEEeCCh--HHHHHHHHHhcccee
Confidence            444 49999999877 33    4567788 55567777777754         2389999999  999999999999999


Q ss_pred             CCeeeEEEeccC
Q psy12549         90 KGRPIRIMWSQR  101 (336)
Q Consensus        90 ~g~~i~v~~~~~  101 (336)
                      +|+.+++-++++
T Consensus        72 ~g~~~r~YFgq~   83 (104)
T 1wey_A           72 LGKEMKLYFAQT   83 (104)
T ss_dssp             TTEECEEECCCC
T ss_pred             cCceeEEEecCC
Confidence            999999988764

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.46  E-value=0.00076  Score=49.07  Aligned_cols=72  Identities=21%  Similarity=0.237  Sum_probs=59.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecC-EEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG-KILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g-~~l~v~~~~~~  281 (336)
                      +.|.|-++|... ...+...|++||.|.+....    ...++..|+|.++.+|++|+.. ||..+.| ..|-|.....+
T Consensus        25 ~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~----~~~NWihI~Y~s~~~A~rAL~k-NG~ii~g~~mIGV~p~~d~   97 (119)
T 1wwh_A           25 TWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS----NTGNWMHIRYQSKLQARKALSK-DGRIFGESIMIGVKPCIDK   97 (119)
T ss_dssp             GEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC----SSSSEEEEEESSHHHHHHHHTT-TTCEETTTEECEEEECCCH
T ss_pred             CEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC----CCCCeEEEEeCCHHHHHHHHHh-CCeEecCCEEEEEEECCCH
Confidence            779999999886 46788999999999888762    2367899999999999999985 9999985 77777776544

>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=97.45  E-value=0.00077  Score=46.83  Aligned_cols=54  Identities=22%  Similarity=0.389  Sum_probs=45.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhC
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN  172 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~  172 (336)
                      ..+++ ++|+.+...||.++|+.||.+. |..+.|.      .|||.|.+++.|..|+..+.
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~WidDT------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEETT------EEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            34555 9999999999999999999544 6777663      69999999999999999763

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.19  E-value=0.0014  Score=45.73  Aligned_cols=76  Identities=13%  Similarity=0.131  Sum_probs=56.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC---CCCc-cceEEEEEeCCHHHHHHHHHHhCCceecC-----EEEE
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN---NDGK-SRGFGFVAYESPEFAEKAVQAWNGKEVDG-----KILY  274 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~---~~~~-~~g~afV~F~~~~~a~~a~~~l~g~~~~g-----~~l~  274 (336)
                      -+|.|+.||+.+|++++.+.++..-++.......   ..+. .-..|||.|.+.++...-.+.++|..|.+     -+..
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a~   89 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPAV   89 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeeeE
Confidence            4699999999999999998888776655444433   1111 13469999999999999999999999854     3455


Q ss_pred             Eeecc
Q psy12549        275 VGRAQ  279 (336)
Q Consensus       275 v~~~~  279 (336)
                      |++|.
T Consensus        90 VE~AP   94 (97)
T 2l08_A           90 VEFAP   94 (97)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            66664

>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=96.98  E-value=0.0014  Score=45.64  Aligned_cols=53  Identities=21%  Similarity=0.386  Sum_probs=45.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhC
Q psy12549        112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN  172 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~  172 (336)
                      .+++ ++|+.+...||.++|+.|| -..|.++.|.      .|||.|.+++.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            3455 9999999999999999999 4457777663      69999999999999999774

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.91  E-value=0.002  Score=47.49  Aligned_cols=74  Identities=20%  Similarity=0.366  Sum_probs=56.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeE-EEEeC--------------CCC-ccceEEEEEeCCHHHHHHHHHHhCCce
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITS-YRVMN--------------NDG-KSRGFGFVAYESPEFAEKAVQAWNGKE  267 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~-~~i~~--------------~~~-~~~g~afV~F~~~~~a~~a~~~l~g~~  267 (336)
                      ..|.|-+.|+..+. .+.+.|++||.|.+ +...+              -.. ...+|..|+|+++.+|.+|+.. ||..
T Consensus         8 ~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NGAV   85 (132)
T ss_dssp             CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TTCE
T ss_pred             eEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CCeE
Confidence            56888899877664 57788999999865 22211              011 2467899999999999999985 9999


Q ss_pred             ecCEEEEEeecc
Q psy12549        268 VDGKILYVGRAQ  279 (336)
Q Consensus       268 ~~g~~l~v~~~~  279 (336)
                      |.|..|-|....
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=96.84  E-value=0.0014  Score=45.82  Aligned_cols=66  Identities=8%  Similarity=0.158  Sum_probs=48.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC--CC-CcccEEEEEeCCHHHHHHHHHHhCCcee
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE--QG-NSKGYGFVHFETEEAANKSIEKVNGMLL  176 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~--~~-~~~g~afV~F~~~~~a~~a~~~l~~~~~  176 (336)
                      -+|.|+.||+.+|++++.+.+..+-.+........+  .+ ..-.-|||.|.+.++.....+..+|..+
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F   78 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIF   78 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            469999999999999988888776554332222222  11 1224599999999999999999999876

>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=96.75  E-value=0.01  Score=43.17  Aligned_cols=74  Identities=14%  Similarity=0.276  Sum_probs=58.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCC-eEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNS-KIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~-~~i~v~~~~  187 (336)
                      ..+-|.|-|.|+. ....|...|++||.|.+.....     ....-.|.|.+..+|++|+. .||..+.| .-|-|.+..
T Consensus        23 ~~~wVtVFGFp~~-~~~~VL~~F~~~G~Iv~~~~~~-----~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           23 DDTWVTVFGFPQA-SASYILLQFAQYGNILKHVMSN-----TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGGEEEEECCCGG-GHHHHHHHHHTTSCEEEEEECS-----SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             CCCEEEEECCCHH-HHHHHHHHHHhhCcEEEeccCC-----CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEECC
Confidence            3567999999997 4778889999999999877621     24589999999999999999 59999975 666676654


Q ss_pred             Cc
Q psy12549        188 PR  189 (336)
Q Consensus       188 ~~  189 (336)
                      ..
T Consensus        96 d~   97 (119)
T 1wwh_A           96 DK   97 (119)
T ss_dssp             CH
T ss_pred             CH
Confidence            33

>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=96.37  E-value=0.0067  Score=42.14  Aligned_cols=53  Identities=19%  Similarity=0.149  Sum_probs=43.9

Q ss_pred             eeeecCchhhhhhhHHhhhcccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcC
Q psy12549         21 VATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMN   85 (336)
Q Consensus        21 v~v~~lp~~~~e~~l~~~f~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~   85 (336)
                      |+.-+.|+.+.-.||.++|+.++...|+.+.|-.          |||.|.++  +.|..|+..+.
T Consensus        18 Vf~l~FP~ewKt~DI~~lFs~fggv~I~WidDTs----------Alvvf~~~--~~a~~al~~i~   70 (100)
T 1whv_A           18 VLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTS----------AFVSLSQP--EQVQIAVNTSK   70 (100)
T ss_dssp             EEEEECCTTCCHHHHHHHHTTTCSCCCEEEETTE----------EEEECSCH--HHHHHHHHHHH
T ss_pred             EEEEeCChhhhhHHHHHHhhccCCEEEEEEcCCe----------EEEEecCH--HHHHHHHHhcc
Confidence            5545999999999999999666677777776542          99999999  99999999653

>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=96.29  E-value=0.0058  Score=42.57  Aligned_cols=54  Identities=20%  Similarity=0.391  Sum_probs=43.1

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhC
Q psy12549        205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN  264 (336)
Q Consensus       205 ~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~  264 (336)
                      .|++-++|..+...||.++|+.||. ..|..+.     -..|||.|.+++.|..|+..+.
T Consensus         7 HV~~l~FP~ewKt~Di~~lFs~fgg-v~I~Wid-----DTsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHVTFPKEWKTSDLYQLFSAFGN-IQISWID-----DTSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEECCTTCCHHHHHHHTTTSEE-EEEEEEE-----TTEEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEEeCChhhhhHHHHHHHhccCC-EEEEEEc-----CCeEEEEecCHHHHHHHHHhcc
Confidence            3544599999999999999999993 3344443     3459999999999999999764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.67  E-value=0.025  Score=41.71  Aligned_cols=76  Identities=14%  Similarity=0.244  Sum_probs=54.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeE-EEEeeC------------C-CC-CcccEEEEEeCCHHHHHHHHHHhCCc
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILS-CKVAQD------------E-QG-NSKGYGFVHFETEEAANKSIEKVNGM  174 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~-~~~~~~------------~-~~-~~~g~afV~F~~~~~a~~a~~~l~~~  174 (336)
                      ...|.|-|.|++ ....+-..|++||.|.+ +...++            + .. .......|+|+++.+|.+|+. .||.
T Consensus         7 e~~VtVFGFp~~-~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPET-MANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGG-GHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHH-HHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            456888899775 45567788999999876 211110            0 00 124577899999999999999 6999


Q ss_pred             eeCCeEEEEeecc
Q psy12549        175 LLNSKIVFVGKFI  187 (336)
Q Consensus       175 ~~~~~~i~v~~~~  187 (336)
                      .+.|.-|-|.+..
T Consensus        85 ii~G~mIGV~Py~   97 (132)
T 3p3d_A           85 VFNGVLLGVIPYT   97 (132)
T ss_dssp             EETTEECEEEECC
T ss_pred             EeCcEEEEEEECC
Confidence            9999877777664

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.52  E-value=0.0076  Score=54.93  Aligned_cols=55  Identities=16%  Similarity=0.253  Sum_probs=42.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHH
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA  262 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~  262 (336)
                      ++|+|. .|...++.+|.++|++||+|.++......|   .||.|+|.+.+++..++..
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g---~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFG---LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSS---EEEEEECC---CCHHHHSS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCC---eEEEEEeCCHHHHHHHHhc
Confidence            789998 799999999999999999999999886433   6999999999998877654

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.14  E-value=0.011  Score=53.83  Aligned_cols=56  Identities=20%  Similarity=0.220  Sum_probs=42.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHH
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK  170 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~  170 (336)
                      .++|+|. .|...++.+|.+.|++||+|..+.+..+.    .-||.|+|.+.++++.++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~----g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF----GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS----SEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC----CeEEEEEeCCHHHHHHHHhc
Confidence            4689998 79999999999999999999999888653    36999999999999977663

>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=86.07  E-value=2.8  Score=38.83  Aligned_cols=55  Identities=22%  Similarity=0.360  Sum_probs=44.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCC
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNG  173 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~  173 (336)
                      ..++++ +|..+...+|.++|+.||.+ .|.++.+      ..|||.|.+.+.|..++..++.
T Consensus       441 ~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd------t~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          441 HVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD------TSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS------SEEEEECSCHHHHHHHHHHHTT
T ss_pred             cEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC------CeEEEEECCHHHHHHHHHHHHh
Confidence            455565 99999999999999999954 4555543      3699999999999999998753

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=81.94  E-value=9.4  Score=25.67  Aligned_cols=75  Identities=13%  Similarity=0.084  Sum_probs=55.7

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCC-------ceecCEEEE
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG-------KEVDGKILY  274 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g-------~~~~g~~l~  274 (336)
                      ..+-+.|-|+|..+-..++.-...-.|---.|..+      .|.|+++|.+.++...|+..|-+       ..+.|....
T Consensus        11 qnclikiinipqgtlkaevvlavrhlgyefycdyi------dgqamirfqnsdeqrlaiqkllnhnnnklqieirgqicd   84 (129)
T 4eyt_A           11 QNCLIKIINIPQGTLKAEVVLAVRHLGYEFYCDYI------DGQAMIRFQNSDEQRLAIQKLLNHNNNKLQIEIRGQICD   84 (129)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHTTCCCEEEEEC------SSCEEEEESSHHHHHHHHHHHEETTTTEEEEEETTEEEE
T ss_pred             hCcEEEEEecCCCceeeeeEEeehhcCeeEeeeee------cCeeEEEecCChHHHHHHHHHHhcCCCEEEEEEcceeee
Confidence            34678899999999888887777777777778776      56699999999999999887622       235677766


Q ss_pred             Eeecccch
Q psy12549        275 VGRAQKKA  282 (336)
Q Consensus       275 v~~~~~~~  282 (336)
                      |--..+..
T Consensus        85 vistiped   92 (129)
T 4eyt_A           85 VISTIPED   92 (129)
T ss_dssp             EECCCCHH
T ss_pred             eeecCCch
Confidence            65444443

---

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	336
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-22
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-09
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	0.003
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	6e-20
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	7e-18
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-19
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-15
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-15
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-11
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-15
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-10
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-15
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-11
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-04
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	0.001
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-15
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	7e-12
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-15
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-11
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-04
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 5e-15
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:) 6e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	5e-15
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	0.002
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-15
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-14
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	6e-10
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-11
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	6e-04
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-14
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	4e-14
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-09
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	8e-14
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-09
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	0.003
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-13
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-09
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-13
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-04
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-13
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-10
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	0.001
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-13
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-10
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	5e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	5e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-13
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-09
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	5e-13
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	9e-12
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-13
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.003
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-09
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-12
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	9e-10
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-12
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-07
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-12
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	5e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-12
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-09
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-12
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-12
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-09
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	6e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-12
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	8e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	5e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	6e-12
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	4e-09
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	6e-12
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	6e-07
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	7e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-07
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	7e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	7e-12
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-11
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-08
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-11
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-11
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-11
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	1e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	7e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-10
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	8e-09
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-10
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-10
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	3e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	6e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	5e-10
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	5e-05
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	0.002
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	5e-10
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	7e-10
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	7e-10
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	5e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	7e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	5e-09
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	8e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-05
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	9e-09
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	0.001
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-08
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	4e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-04
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	4e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	1e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-07
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.002
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-07
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	5e-04
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-07
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	1e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	6e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	4e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	7e-07
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	3e-06
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.004
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	3e-06
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	7e-04
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.003
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	4e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	7e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	2e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	0.001
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	2e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	0.002
d1x4fa1	99	d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus)	3e-05
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	5e-05
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-04

>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 = 91.2 bits (225), Expect = 1e-22
 Identities = 43/188 (22%), Positives = 77/188 (40%), Gaps = 13/188 (6%)

Query: 101 RDPS-LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHF 158
           ++P  LRK     +FI  L     ++++   F  +G++  C V +D     S+G+GFV +
Sbjct: 1   KEPEQLRK-----LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 55

Query: 159 ETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDE 218
            T E  + ++      +    +            + +          +++    ED  + 
Sbjct: 56  ATVEEVDAAMNARPHKVDGRVVEP---KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 112

Query: 219 KLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG 276
            L++ FE YG I    +M     GK RGF FV ++  +  +K V       V+G    V 
Sbjct: 113 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVR 171

Query: 277 RAQKKAER 284
           +A  K E 
Sbjct: 172 KALSKQEM 179

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (128), Expect = 2e-09
 Identities = 20/123 (16%), Positives = 46/123 (37%), Gaps = 5/123 (4%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSGV---GNVFIKNLDKSIDNKAMYDTFS 132
           + + A++                  R+ S R         +F+  + +  +   + D F 
Sbjct: 60  EVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 119

Query: 133 AFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKE 191
            +G I   ++  D   G  +G+ FV F+  ++ +K + +     +N     V K + ++E
Sbjct: 120 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQE 178

Query: 192 REK 194
              
Sbjct: 179 MAS 181

>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 = 51.9 bits (123), Expect = 1e-08
 Identities = 27/131 (20%), Positives = 47/131 (35%), Gaps = 15/131 (11%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITS--YRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           ++I     +  DE L+  FE +GT+T        N  +SRGFGFV Y + E  + A+ A 
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 264 NGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQGVNLYVKNLDDSIDDERLR 323
                          +      +  +                  ++V  + +  ++  LR
Sbjct: 69  PH-------------KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLR 115

Query: 324 KEFTPFGTITS 334
             F  +G I  
Sbjct: 116 DYFEQYGKIEV 126

>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 = 36.1 bits (82), Expect = 0.003
 Identities = 10/29 (34%), Positives = 14/29 (48%)

Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITSAK 336
           L++  L     DE LR  F  +GT+T   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCV 37

>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 = 80.9 bits (199), Expect = 6e-20
 Identities = 72/90 (80%), Positives = 81/90 (90%), Gaps = 1/90 (1%)

Query: 103 PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEE 162
           PSLRKSGVGN+FIKNLDKSIDNKA+YDTFSAFG+ILSCKV  DE G SKGYGFVHFET+E
Sbjct: 1   PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQE 59

Query: 163 AANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
           AA ++IEK+NGMLLN + VFVG+F  RKER
Sbjct: 60  AAERAIEKMNGMLLNDRKVFVGRFKSRKER 89

>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 = 75.1 bits (184), Expect = 7e-18
 Identities = 27/81 (33%), Positives = 53/81 (65%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
            N++IKN  +  +++ L + F  +G I S +V+ ++  S+G+GFV +E+ E AE+A++  
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 68

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           NG  ++ + ++VGR + + ER
Sbjct: 69  NGMLLNDRKVFVGRFKSRKER 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 = 79.7 bits (196), Expect = 4e-19
 Identities = 28/105 (26%), Positives = 49/105 (46%), Gaps = 4/105 (3%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             +YI+N       E++ ++F  YG I   RV N   ++RG  +V YE    A+ A    
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT-PETRGTAYVVYEDIFDAKNACDHL 66

Query: 264 NGKEVDGKILYVGRAQ-KKAERTQELKRRFEMLKIERLNRYQGVN 307
           +G  V  + L V      +A +  + K++ E  +++ L    G+N
Sbjct: 67  SGFNVCNRYLVVLYYNANRAFQKMDTKKKEE--QLKLLKEKYGIN 109

>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 = 68.1 bits (166), Expect = 5e-15
 Identities = 24/116 (20%), Positives = 49/116 (42%), Gaps = 18/116 (15%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           ++I+NL   I  + MYD F  +G I   +        ++G  +V +E    A  + + ++
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQIR--VGNTPETRGTAYVVYEDIFDAKNACDHLS 67

Query: 173 GMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYG 228
           G  + ++ + V  +   +  +K   +K +                E+LK + E YG
Sbjct: 68  GFNVCNRYLVVLYYNANRAFQKMDTKKKE----------------EQLKLLKEKYG 107

>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 = 69.6 bits (170), Expect = 1e-15
 Identities = 20/85 (23%), Positives = 41/85 (48%), Gaps = 4/85 (4%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM---NNDGKSRGFGFVAYESPEFAEKAV 260
           + + ++N     N  +++E+F  +G + + R+       G  RGFGFV + + + A+KA 
Sbjct: 9   SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 68

Query: 261 QA-WNGKEVDGKILYVGRAQKKAER 284
            A  +   + G+ L +  A  +   
Sbjct: 69  NALCHSTHLYGRRLVLEWADSEVTV 93

>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 = 56.5 bits (136), Expect = 5e-11
 Identities = 16/90 (17%), Positives = 43/90 (47%), Gaps = 4/90 (4%)

Query: 106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD--EQGNSKGYGFVHFETEEA 163
           +K     + ++N+    + + + + FS FG + + ++ +     G  +G+GFV F T++ 
Sbjct: 4   KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 63

Query: 164 ANKSIEKV-NGMLLNSKIVFVGKFIPRKER 192
           A K+   + +   L  + + + ++   +  
Sbjct: 64  AKKAFNALCHSTHLYGRRLVL-EWADSEVT 92

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.3 bits (169), Expect = 1e-15
 Identities = 23/79 (29%), Positives = 43/79 (54%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             +++ N    F D  L++MF  +G I    ++ N+  S+GFGFV +E+   A++A +  
Sbjct: 12  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 71

Query: 264 NGKEVDGKILYVGRAQKKA 282
           +G  V+G+ + V  A  + 
Sbjct: 72  HGTVVEGRKIEVNNATARV 90

>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 = 55.1 bits (132), Expect = 2e-10
 Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 1/83 (1%)

Query: 107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANK 166
           KS    + + N+     +  +   F  FG IL  ++  +E+  SKG+GFV FE    A++
Sbjct: 8   KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADR 66

Query: 167 SIEKVNGMLLNSKIVFVGKFIPR 189
           + EK++G ++  + + V     R
Sbjct: 67  AREKLHGTVVEGRKIEVNNATAR 89

>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 = 68.8 bits (168), Expect = 1e-15
 Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGK--SRGFGFVAYESPEFAEKAVQA 262
           ++Y+ +   D  +  L E F P G I S RV  +     S G+ +V ++ P  AE+A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 263 WNGKEVDGKILYVGRAQK 280
            N   + GK + +  +Q+
Sbjct: 62  MNFDVIKGKPVRIMWSQR 79

>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 = 57.6 bits (139), Expect = 1e-11
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVA-QDEQGNSKGYGFVHFETEEAANKSIEK 170
           ++++ +L   +    +Y+ FS  G ILS +V        S GY +V+F+    A ++++ 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 171 VNGMLLNSKIVFVGK 185
           +N  ++  K V +  
Sbjct: 62  MNFDVIKGKPVRIMW 76

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 22/27 (81%), Positives = 25/27 (92%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRD 102
           D ERALDTMNFD +KG+P+RIMWSQRD
Sbjct: 54  DAERALDTMNFDVIKGKPVRIMWSQRD 80

>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 = 35.3 bits (81), Expect = 0.001
 Identities = 10/29 (34%), Positives = 17/29 (58%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSA 335
           +LYV +L   + +  L ++F+P G I S 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSI 30

>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 = 67.8 bits (165), Expect = 3e-15
 Identities = 19/82 (23%), Positives = 42/82 (51%), Gaps = 3/82 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG---KSRGFGFVAYESPEFAEKAVQA 262
           ++I N   + +++ L + F  +G I     +  D     S+G+ F+ + S + ++ A++A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 263 WNGKEVDGKILYVGRAQKKAER 284
            NG+ +  + + V  A KK  +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 58.6 bits (141), Expect = 7e-12
 Identities = 31/82 (37%), Positives = 47/82 (57%), Gaps = 2/82 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN--SKGYGFVHFETEEAANKSIEK 170
           +FI NLD  ID K +YDTFSAFG IL       +     SKGY F++F + +A++ +IE 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 171 VNGMLLNSKIVFVGKFIPRKER 192
           +NG  L ++ + V     +  +
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 67.7 bits (165), Expect = 3e-15
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    +D  D +L  +F   G I + R+M     G S G+ FV + S   +++A++
Sbjct: 3   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 262 AWNGKEVDGKILYVGRAQ 279
             NG  V  K L V  A+
Sbjct: 63  VLNGITVRNKRLKVSYAR 80

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 56.9 bits (137), Expect = 2e-11
 Identities = 21/73 (28%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L + + ++ +Y  F A G I +C  +   + G S GY FV F +E  + ++I+ 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 171 VNGMLLNSKIVFV 183
           +NG+ + +K + V
Sbjct: 64  LNGITVRNKRLKV 76

>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 = 36.9 bits (85), Expect = 3e-04
 Identities = 9/29 (31%), Positives = 11/29 (37%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITSA 335
           NL V  L   + D  L   F   G I + 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTC 32

>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 = 68.1 bits (166), Expect = 5e-15
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQ 261
            ++V ++   ++F +E   EM E YG +    V  N      G  +V +   E AEKAV 
Sbjct: 27  VSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVI 86

Query: 262 AWNGKEVDGKILYV 275
             N +  +G+ ++ 
Sbjct: 87  DLNNRWFNGQPIHA 100

>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 = 53.5 bits (128), Expect = 6e-10
 Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 1/82 (1%)

Query: 107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANK 166
           +S V +V ++        +   +    +G +    V  +   +  G  +V F  EE A K
Sbjct: 24  RSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEK 83

Query: 167 SIEKVNGMLLNSKIVFVGKFIP 188
           ++  +N    N + +   +  P
Sbjct: 84  AVIDLNNRWFNGQPIHA-ELSP 104

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 67.4 bits (164), Expect = 5e-15
 Identities = 28/80 (35%), Positives = 39/80 (48%), Gaps = 5/80 (6%)

Query: 207 YIKNFGEDFNDEKLKEMFEPYGTITS-----YRVMNNDGKSRGFGFVAYESPEFAEKAVQ 261
           +IKN      +E LK +F   G I S      +       S GFGFV Y+ PE A+KA++
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 262 AWNGKEVDGKILYVGRAQKK 281
              G  VDG  L V  +++ 
Sbjct: 62  QLQGHTVDGHKLEVRISERA 81

>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 = 53.1 bits (127), Expect = 6e-10
 Identities = 23/83 (27%), Positives = 44/83 (53%), Gaps = 5/83 (6%)

Query: 114 FIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ----GNSKGYGFVHFETEEAANKSIE 169
           FIKNL+ S   + +   FS  G+I SC +++ +       S G+GFV ++  E A K+++
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 170 KVNGMLLNSKIVFVGKFIPRKER 192
           ++ G  ++   + V +   R  +
Sbjct: 62  QLQGHTVDGHKLEV-RISERATK 83

>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 = 34.6 bits (79), Expect = 0.002
 Identities = 11/27 (40%), Positives = 17/27 (62%)

Query: 308 LYVKNLDDSIDDERLRKEFTPFGTITS 334
           L++KNL+ S  +E L+  F+  G I S
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKS 27

>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 = 67.6 bits (165), Expect = 6e-15
 Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 7/82 (8%)

Query: 204 TNVYIKNFG-EDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
           + V+I N          ++ +F  YG I    V        GF FV Y +   A  AV  
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK------GFAFVQYVNERNARAAVAG 69

Query: 263 WNGKEVDGKILYVGRAQKKAER 284
            +G+ + G++L +  A +    
Sbjct: 70  EDGRMIAGQVLDINLAAEPKVN 91

>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 = 58.0 bits (140), Expect = 1e-11
 Identities = 21/97 (21%), Positives = 39/97 (40%), Gaps = 11/97 (11%)

Query: 99  SQRDPSLRKSGVGNVFIKNLD-KSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVH 157
            + DP    S    VFI NL+   +    +   FS +G I+ C V +       G+ FV 
Sbjct: 7   GKTDPRSMNS---RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK-------GFAFVQ 56

Query: 158 FETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
           +  E  A  ++   +G ++  +++ +      K    
Sbjct: 57  YVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRS 93

>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 = 66.2 bits (161), Expect = 2e-14
 Identities = 26/100 (26%), Positives = 50/100 (50%), Gaps = 7/100 (7%)

Query: 187 IPRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRG 244
           +P + +++E     + F  ++I     +  +E L+  +E +G +T   VM +    +SRG
Sbjct: 8   VPLERKKRE----KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRG 63

Query: 245 FGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
           FGFV + S    + A+ A     +DG+++   RA  + E 
Sbjct: 64  FGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREES 102

>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 = 53.5 bits (128), Expect = 6e-10
 Identities = 16/82 (19%), Positives = 38/82 (46%), Gaps = 2/82 (2%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
            +FI  L      +++ + +  +G +  C V +D     S+G+GFV F +    + ++  
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 81

Query: 171 VNGMLLNSKIVFVGKFIPRKER 192
                ++ ++V   + + R+E 
Sbjct: 82  -RPHSIDGRVVEPKRAVAREES 102

>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 = 65.4 bits (159), Expect = 2e-14
 Identities = 28/86 (32%), Positives = 41/86 (47%), Gaps = 5/86 (5%)

Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTIT--SYRVMNNDGKSRGFGFVAYESPE 254
           GE  K  TN+Y+ N      D++L  +F  YG+I   +       G+ RG  FV Y   E
Sbjct: 1   GESIK-DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE 59

Query: 255 FAEKAVQAWNGKEVDG--KILYVGRA 278
            A++A+ A N    +G  + L V  A
Sbjct: 60  EAQEAISALNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 56.1 bits (135), Expect = 5e-11
 Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           N+++ NL ++I +  +   F  +GSI+   + +D   G  +G  FV +   E A ++I  
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 171 VNGMLLN 177
           +N ++  
Sbjct: 68  LNNVIPE 74

>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 = 36.1 bits (83), Expect = 6e-04
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTIT 333
           NLYV NL  +I D++L   F  +G+I 
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIV 34

>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 = 3e-14
 Identities = 23/98 (23%), Positives = 45/98 (45%), Gaps = 10/98 (10%)

Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGF 245
           P  ER ++          VY+    E  ++  L E+F   G + +  +      G+ +G+
Sbjct: 2   PISERNQD--------ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGY 53

Query: 246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAE 283
           GFV + S E A+ A++  +  ++ GK + V +A    +
Sbjct: 54  GFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 54.3 bits (130), Expect = 3e-10
 Identities = 21/81 (25%), Positives = 43/81 (53%), Gaps = 1/81 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
            V++  LD+ +    +++ F   G +++  + +D   G  +GYGFV F +EE A+ +I+ 
Sbjct: 11  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 70

Query: 171 VNGMLLNSKIVFVGKFIPRKE 191
           ++ + L  K + V K     +
Sbjct: 71  MDMIKLYGKPIRVNKASAHNK 91

>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 = 65.5 bits (159), Expect = 4e-14
 Identities = 27/83 (32%), Positives = 49/83 (59%), Gaps = 2/83 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQ 261
            N++I +  ++F D+ L +MF P+G + S +V  +     S+ FGFV+Y++P  A+ A+Q
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 78

Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
           + NG ++  K L V   + K + 
Sbjct: 79  SMNGFQIGMKRLKVQLKRSKNDS 101

>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 = 51.6 bits (123), Expect = 3e-09
 Identities = 23/82 (28%), Positives = 44/82 (53%), Gaps = 1/82 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEK 170
           N+FI +L +   ++ +   F  FG+++S KV  D+Q   SK +GFV ++   +A  +I+ 
Sbjct: 20  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 79

Query: 171 VNGMLLNSKIVFVGKFIPRKER 192
           +NG  +  K + V     + + 
Sbjct: 80  MNGFQIGMKRLKVQLKRSKNDS 101

>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 = 64.3 bits (156), Expect = 8e-14
 Identities = 17/81 (20%), Positives = 36/81 (44%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             +Y+ N   D  +  + ++F   G   S +++     +  + FV +     A  A+ A 
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAM 68

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           NG+++ GK + V  A   + +
Sbjct: 69  NGRKILGKEVKVNWATTPSSQ 89

>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 = 51.2 bits (122), Expect = 4e-09
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +++ NL + +    +   FS  G   SCK+  +   ++  Y FV F     A  ++  +N
Sbjct: 11  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE-HTSNDPYCFVEFYEHRDAAAALAAMN 69

Query: 173 GMLLNSKIVFVGKFIPRKERE 193
           G  +  K V V        ++
Sbjct: 70  GRKILGKEVKVNWATTPSSQK 90

>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 = 34.2 bits (78), Expect = 0.003
 Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 1/32 (3%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRK 107
           D   AL  MN   + G+ +++ W+   PS +K
Sbjct: 60  DAAAALAAMNGRKILGKEVKVNWATT-PSSQK 90

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.5 bits (154), Expect = 1e-13
 Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 5/87 (5%)

Query: 206 VYIKNFGEDFNDEKLKEM----FEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQ 261
           +YI N  E    ++LK+     F  +G I    V  +  K RG  FV ++    A  A++
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL-KMRGQAFVIFKEVSSATNALR 64

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQEL 288
           +  G     K + +  A+  ++   ++
Sbjct: 65  SMQGFPFYDKPMRIQYAKTDSDIIAKM 91

>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 = 50.8 bits (121), Expect = 4e-09
 Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 6/88 (6%)

Query: 113 VFIKNLDKSIDN----KAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSI 168
           ++I NL++ I      K+++  FS FG IL   V        +G  FV F+   +A  ++
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV--SRSLKMRGQAFVIFKEVSSATNAL 63

Query: 169 EKVNGMLLNSKIVFVGKFIPRKEREKEL 196
             + G     K + +       +   ++
Sbjct: 64  RSMQGFPFYDKPMRIQYAKTDSDIIAKM 91

>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 = 63.2 bits (153), Expect = 2e-13
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQ 261
           TN+ +    ++   E+ + +F   G I S +++     G+S G+GFV Y  P+ AEKA+ 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 262 AWNGKEVDGKILYVGRAQ 279
             NG  +  K + V  A+
Sbjct: 63  TLNGLRLQTKTIKVSYAR 80

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 3e-09
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           N+ +  L +++  +     F + G I SCK+ +D   G S GYGFV++   + A K+I  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 171 VNGMLLNSKIVFVGKFIP 188
           +NG+ L +K + V    P
Sbjct: 64  LNGLRLQTKTIKVSYARP 81

>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 = 63.5 bits (154), Expect = 2e-13
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 4/82 (4%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             VY         D+ +++ F P+G I   RV       +G+ FV + + E A  A+ + 
Sbjct: 19  CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF----PEKGYSFVRFSTHESAAHAIVSV 74

Query: 264 NGKEVDGKILYVGRAQKKAERT 285
           NG  ++G ++     ++  + T
Sbjct: 75  NGTTIEGHVVKCYWGKESPDMT 96

>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 = 49.6 bits (118), Expect = 1e-08
 Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 10/88 (11%)

Query: 97  MWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFV 156
           + +Q  P         V+   +   + ++ M  TFS FG I+  +V  ++      Y FV
Sbjct: 10  VVNQSSPKNCT-----VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-----YSFV 59

Query: 157 HFETEEAANKSIEKVNGMLLNSKIVFVG 184
            F T E+A  +I  VNG  +   +V   
Sbjct: 60  RFSTHESAAHAIVSVNGTTIEGHVVKCY 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 = 37.6 bits (87), Expect = 2e-04
 Identities = 5/30 (16%), Positives = 14/30 (46%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSL 105
               A+ ++N   ++G  ++  W +  P +
Sbjct: 66  SAAHAIVSVNGTTIEGHVVKCYWGKESPDM 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 = 62.8 bits (152), Expect = 2e-13
 Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
            N+Y+    +    ++L+++F  YG I + R++     G SRG GF+ ++    AE+A++
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 262 AWNGKEVDGK 271
             NG++  G 
Sbjct: 67  GLNGQKPSGA 76

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 7e-10
 Identities = 19/67 (28%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           N+++  L K++  K +   FS +G I++ ++  D   G S+G GF+ F+    A ++I+ 
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 171 VNGMLLN 177
           +NG   +
Sbjct: 68  LNGQKPS 74

>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 = 35.0 bits (80), Expect = 0.001
 Identities = 9/28 (32%), Positives = 16/28 (57%)

Query: 307 NLYVKNLDDSIDDERLRKEFTPFGTITS 334
           NLYV  L  ++  + L + F+ +G I +
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIIT 35

>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 = 62.7 bits (152), Expect = 3e-13
 Identities = 18/99 (18%), Positives = 38/99 (38%), Gaps = 3/99 (3%)

Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGF 245
           P +E    L  + +    V+            L++ F   G +   R++   N  +S+G 
Sbjct: 3   PVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI 62

Query: 246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
            +V +   +    A+    G+ + G  + V  +Q +  R
Sbjct: 63  AYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNR 100

>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 = 54.7 bits (131), Expect = 2e-10
 Identities = 25/101 (24%), Positives = 37/101 (36%), Gaps = 4/101 (3%)

Query: 93  PIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SK 151
           P+R       P  R +    VF   L   I  + + D FSA G +   ++  D     SK
Sbjct: 3   PVREPVDNLSPEERDAR--TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 60

Query: 152 GYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
           G  +V F   ++   +I    G  L    + V      K R
Sbjct: 61  GIAYVEFCEIQSVPLAIGL-TGQRLLGVPIIVQASQAEKNR 100

>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 = 62.0 bits (150), Expect = 5e-13
 Identities = 17/94 (18%), Positives = 34/94 (36%), Gaps = 6/94 (6%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSY----RVMNNDGKSRGFGFVAYESPEFAEKA 259
             ++I    +    E++ E                   +  K+RGF FV YES   A  A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 260 VQAWNGK--EVDGKILYVGRAQKKAERTQELKRR 291
            +       ++ G  + V  A+ + +  +++   
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>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 = 50.8 bits (121), Expect = 5e-09
 Identities = 14/92 (15%), Positives = 38/92 (41%), Gaps = 5/92 (5%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVA---QDEQGNSKGYGFVHFETEEAANKSIE 169
           +FI  + K    + + +  +     +   +      ++  ++G+ FV +E+  AA  +  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 170 KVNG--MLLNSKIVFVGKFIPRKEREKELGEK 199
           K+    + L    + V    P  + ++++ E 
Sbjct: 64  KLMPGRIQLWGHQIAVDWAEPEIDVDEDVMET 95

>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 = 62.0 bits (150), Expect = 5e-13
 Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 2/80 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQAW 263
           ++I       ND+++KE+   +G + ++ ++  +  G S+G+ F  Y      ++A+   
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 264 NGKEVDGKILYVGRAQKKAE 283
           NG ++  K L V RA   A+
Sbjct: 64  NGMQLGDKKLLVQRASVGAK 83

>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 = 50.4 bits (120), Expect = 5e-09
 Identities = 18/80 (22%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKV 171
           +FI  L   +++  + +  ++FG + +  + +D     SKGY F  +      +++I  +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 172 NGMLLNSKIVFVGKFIPRKE 191
           NGM L  K + V +     +
Sbjct: 64  NGMQLGDKKLLVQRASVGAK 83

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 5e-13
 Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 2/81 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGK--SRGFGFVAYESPEFAEKAVQAW 263
           +Y+    E+ +D+ L   F P+G IT  ++  +      RGF FV +E  E A  A+   
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           N  E+ G+ + V  A+    +
Sbjct: 68  NESELFGRTIRVNLAKPMRIK 88

>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 = 58.5 bits (141), Expect = 9e-12
 Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 1/82 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKV 171
           +++  L + +D+K ++  F  FG I   ++  D +    +G+ FV FE  E A  +I+ +
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67

Query: 172 NGMLLNSKIVFVGKFIPRKERE 193
           N   L  + + V    P + +E
Sbjct: 68  NESELFGRTIRVNLAKPMRIKE 89

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 62.0 bits (150), Expect = 6e-13
 Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 2/85 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQ 261
             ++++N     ++E L+++F  YG ++           K +GF FV +  PE A KA  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQ 286
             +G+   G++L+V  +  K E +Q
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQ 93

>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 = 57.0 bits (137), Expect = 3e-11
 Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 1/88 (1%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANK 166
           SG G +F++NL  +   + +   FSA+G +       D      KG+ FV F   E A K
Sbjct: 6   SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 167 SIEKVNGMLLNSKIVFVGKFIPRKEREK 194
           +  +V+G +   +++ V     +KE  +
Sbjct: 66  AYAEVDGQVFQGRMLHVLPSTIKKEASQ 93

>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 = 34.7 bits (79), Expect = 0.003
 Identities = 6/34 (17%), Positives = 14/34 (41%)

Query: 76  DTERALDTMNFDALKGRPIRIMWSQRDPSLRKSG 109
              +A   ++    +GR + ++ S       +SG
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSG 95

>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 = 61.1 bits (148), Expect = 1e-12
 Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 2/85 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
             +Y+ N      +E++ E+F   G I    +  +     + GF FV Y S   AE A++
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQ 286
             NG  +D +I+         E  Q
Sbjct: 68  YINGTRLDDRIIRTDWDAGFKEGRQ 92

>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 = 52.3 bits (125), Expect = 1e-09
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 1/83 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSK-GYGFVHFETEEAANKSIEKV 171
           +++ NL      + +Y+ FS  G I    +  D+   +  G+ FV + +   A  ++  +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 172 NGMLLNSKIVFVGKFIPRKEREK 194
           NG  L+ +I+        KE  +
Sbjct: 70  NGTRLDDRIIRTDWDAGFKEGRQ 92

>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 = 60.9 bits (147), Expect = 1e-12
 Identities = 27/81 (33%), Positives = 48/81 (59%), Gaps = 2/81 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKS--RGFGFVAYESPEFAEKAVQAW 263
           +++     D N++ L+++F  YG I+   V+ +      RGFGFV +E+ + A+ A+ A 
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           NGK VDG+ + V +A K ++ 
Sbjct: 68  NGKSVDGRQIRVDQAGKSSDN 88

>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 = 49.4 bits (117), Expect = 2e-08
 Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 1/83 (1%)

Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIE 169
           G +F+  L    + +++   FS +G I    V +D +   S+G+GFV FE  + A  ++ 
Sbjct: 6   GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 65

Query: 170 KVNGMLLNSKIVFVGKFIPRKER 192
            +NG  ++ + + V +     + 
Sbjct: 66  AMNGKSVDGRQIRVDQAGKSSDN 88

>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 = 60.4 bits (146), Expect = 1e-12
 Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW 263
           ++I         E L+E F  +G +    VM      +SRGFGFV +      +K +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61

Query: 264 NGKEVDGKILYVGRA 278
           +  E+D K +    A
Sbjct: 62  SRHELDSKTIDPKVA 76

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.3 bits (125), Expect = 9e-10
 Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           +FI  L      + + + F  FG +  C V +D     S+G+GFV F  +   +K + + 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61

Query: 172 NGMLLNSKIVFV 183
           +   L+SK +  
Sbjct: 62  SRHELDSKTIDP 73

>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 = 60.4 bits (146), Expect = 2e-12
 Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 4/82 (4%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           + +++ N   D  +E+++++FE YG            K +GFGF+  E+   AE A    
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYG----KAGEVFIHKDKGFGFIRLETRTLAEIAKVEL 64

Query: 264 NGKEVDGKILYVGRAQKKAERT 285
           +   + GK L V  A   A  T
Sbjct: 65  DNMPLRGKQLRVRFACHSASLT 86

>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 = 46.9 bits (111), Expect = 1e-07
 Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
           +    +F+ NL   I  + M   F  +G      + +D+      +GF+  ET   A  +
Sbjct: 6   TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-----FGFIRLETRTLAEIA 60

Query: 168 IEKVNGMLLNSKIVFV 183
             +++ M L  K + V
Sbjct: 61  KVELDNMPLRGKQLRV 76

>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 = 60.6 bits (146), Expect = 2e-12
 Identities = 22/91 (24%), Positives = 40/91 (43%), Gaps = 10/91 (10%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND----------GKSRGFGFVAYESP 253
           + +Y++   +    + L + F+  G +   +               GK +G   V+YE P
Sbjct: 9   SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 68

Query: 254 EFAEKAVQAWNGKEVDGKILYVGRAQKKAER 284
             A+ AV+ ++GK+  G  L V  A+KK   
Sbjct: 69  PTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 99

>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 = 46.3 bits (109), Expect = 2e-07
 Identities = 16/90 (17%), Positives = 30/90 (33%), Gaps = 9/90 (10%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD---------EQGNSKGYGFVHFETEE 162
            ++++ L+ S+    + D F   G +   K             E G  KG   V +E   
Sbjct: 10  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 69

Query: 163 AANKSIEKVNGMLLNSKIVFVGKFIPRKER 192
            A  ++E  +G       + V     +   
Sbjct: 70  TAKAAVEWFDGKDFQGSKLKVSLARKKPPM 99

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.7 bits (144), Expect = 2e-12
 Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW 263
           ++I     +  DE L+  FE +GT+T   VM   N  +SRGFGFV Y + E  + A+ A 
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 67

Query: 264 NGKEVDGKILYVGRA 278
              +VDG+++   RA
Sbjct: 68  RPHKVDGRVVEPKRA 82

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 5e-08
 Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           +FI  L     ++++   F  +G++  C V +D     S+G+GFV + T E  + ++   
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 67

Query: 172 NGMLLNSKIVFVGK 185
               ++ ++V   +
Sbjct: 68  RPHKVDGRVVEPKR 81

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.1 bits (145), Expect = 2e-12
 Identities = 12/80 (15%), Positives = 30/80 (37%), Gaps = 8/80 (10%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND-------GKSRGFGFVAYESPEFAEK 258
           +Y+ N      +E + + F     +        +        + + F F+ + S +   +
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 259 AVQAWNGKEVDGKILYVGRA 278
           A+  ++G    G+ L + R 
Sbjct: 64  AMA-FDGIIFQGQSLKIRRP 82

>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 = 50.9 bits (121), Expect = 4e-09
 Identities = 13/86 (15%), Positives = 36/86 (41%), Gaps = 9/86 (10%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVA------QDEQGNSKGYGFVHFETEEAANK 166
           +++ N+   I  +AM D F+A   +     A        +    K + F+ F + +   +
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 167 SIEKVNGMLLNSKIVFVGKFIPRKER 192
           ++   +G++   + + + +  P   +
Sbjct: 64  AMAF-DGIIFQGQSLKIRR--PHDYQ 86

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.2 bits (145), Expect = 3e-12
 Identities = 16/90 (17%), Positives = 29/90 (32%), Gaps = 5/90 (5%)

Query: 201 KLF-TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKA 259
            L         F E     K + +F  Y   T+++   +         + + +P  A  A
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS----FKRVRINFSNPLSAADA 62

Query: 260 VQAWNGKEVDGKILYVGRAQKKAERTQELK 289
               +  E  GK + +  AQ     +  L 
Sbjct: 63  RLRLHKTEFLGKEMKLYFAQTLHIGSSHLA 92

>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 = 51.7 bits (123), Expect = 3e-09
 Identities = 7/94 (7%), Positives = 23/94 (24%), Gaps = 10/94 (10%)

Query: 108 SGVGNVFIKNLDKSI-----DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEE 162
           SG   +     +  +             F  +    + +  +           ++F    
Sbjct: 3   SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPL 57

Query: 163 AANKSIEKVNGMLLNSKIVFVGKFIPRKEREKEL 196
           +A  +  +++      K + +            L
Sbjct: 58  SAADARLRLHKTEFLGKEMKLYFAQTLHIGSSHL 91

>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 = 59.7 bits (144), Expect = 3e-12
 Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +YI N       + L+++F       + +V+       G+ FV Y    +A +A++  +G
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQVL----LKSGYAFVDYPDQNWAIRAIETLSG 59

Query: 266 K-EVDGKILYVGRAQKKAERT 285
           K E+ GKI+ V  +  K  R+
Sbjct: 60  KVELHGKIMEVDYSVSKKLRS 80

>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 = 52.4 bits (125), Expect = 1e-09
 Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 6/81 (7%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           ++I NL  ++    +   F      L+ +V         GY FV +  +  A ++IE ++
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETLS 58

Query: 173 GML-LNSKIVFVGKFIPRKER 192
           G + L+ KI+ V   + +K R
Sbjct: 59  GKVELHGKIMEVDYSVSKKLR 79

>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 = 59.2 bits (143), Expect = 3e-12
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEFAEKAVQAWN 264
           + + N     +D  ++E+F  +GT+    V  +  G+S G   V +E    A KA++ +N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 265 GKEVDGKILYVGRAQ 279
           G  +DG+ + +    
Sbjct: 63  GVPLDGRPMNIQLVT 77

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.4 bits (141), Expect = 6e-12
 Identities = 21/73 (28%), Positives = 40/73 (54%)

Query: 111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEK 170
           G + + NLD  + +  + + F+ FG++    V  D  G S G   VHFE +  A K++++
Sbjct: 1   GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 171 VNGMLLNSKIVFV 183
            NG+ L+ + + +
Sbjct: 61  YNGVPLDGRPMNI 73

>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 = 59.7 bits (144), Expect = 3e-12
 Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 5/83 (6%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           + V++     D  +++L+E F  YG +    +       R F FV +   + A+      
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF---RAFAFVTFADDQIAQSLCG-- 60

Query: 264 NGKEVDGKILYVGRAQKKAERTQ 286
               + G  +++  A+ K     
Sbjct: 61  EDLIIKGISVHISNAEPKHNSNS 83

>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 = 52.7 bits (126), Expect = 8e-10
 Identities = 13/87 (14%), Positives = 31/87 (35%), Gaps = 6/87 (6%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
           SG   VF+      +    + + FS +G ++   + +  +     + FV F  ++ A   
Sbjct: 3   SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR----AFAFVTFADDQIAQSL 58

Query: 168 IEKVNGMLLNSKIVFVGKFIPRKEREK 194
                 +++    V +    P+     
Sbjct: 59  CG--EDLIIKGISVHISNAEPKHNSNS 83

>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 = 58.9 bits (142), Expect = 5e-12
 Identities = 24/96 (25%), Positives = 43/96 (44%), Gaps = 10/96 (10%)

Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITS--YRVMNNDGKSRGF 245
           P +  +            + + N  ED  +  L+E+F P+G+I+          G+S+GF
Sbjct: 1   PNRRADDN--------ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGF 52

Query: 246 GFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK 281
            F+++   E A +A+   +G   D  IL V  A+  
Sbjct: 53  AFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS 88

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 1e-09
 Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 1/88 (1%)

Query: 103 PSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETE 161
           P+ R      + + NL +      + + F  FGSI    +A+D+  G SKG+ F+ F   
Sbjct: 1   PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 60

Query: 162 EAANKSIEKVNGMLLNSKIVFVGKFIPR 189
           E A ++I  V+G   +  I+ V    P 
Sbjct: 61  EDAARAIAGVSGFGYDHLILNVEWAKPS 88

>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 = 58.9 bits (142), Expect = 6e-12
 Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 4/80 (5%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +Y++N     ++E +++ F         RV     K R + FV + + E A +A++A NG
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKPGAVERV----KKIRDYAFVHFSNREDAVEAMKALNG 66

Query: 266 KEVDGKILYVGRAQKKAERT 285
           K +DG  + V  A+   + +
Sbjct: 67  KVLDGSPIEVTLAKPVDKDS 86

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 4e-09
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 5/85 (5%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
           S V  ++++NL  S   + +   F+        +V        + Y FVHF   E A ++
Sbjct: 6   SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEA 60

Query: 168 IEKVNGMLLNSKIVFVGKFIPRKER 192
           ++ +NG +L+   + V    P  + 
Sbjct: 61  MKALNGKVLDGSPIEVTLAKPVDKD 85

>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 = 59.4 bits (143), Expect = 6e-12
 Identities = 14/103 (13%), Positives = 35/103 (33%), Gaps = 5/103 (4%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESP-EFAEKAVQA 262
              +  +  +    E L  +F  +G I     +         G + ++   + A    + 
Sbjct: 12  LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG----AKEGIILFKEKAKEALGKAKD 67

Query: 263 WNGKEVDGKILYVGRAQKKAERTQELKRRFEMLKIERLNRYQG 305
            N   +  +   V     + E  +E  ++    + E LN+++ 
Sbjct: 68  ANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQESLNKWKS 110

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (107), Expect = 6e-07
 Identities = 20/95 (21%), Positives = 33/95 (34%), Gaps = 6/95 (6%)

Query: 106 RKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETE-EAA 164
            K G    F  +LD     + ++  FS  G I      +         G + F+ + + A
Sbjct: 7   EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEA 61

Query: 165 NKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEK 199
               +  N   L  +   V   +   E EKE  +K
Sbjct: 62  LGKAKDANNGNLQLRNKEVTWEVLEGEVEKEALKK 96

>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 = 58.9 bits (142), Expect = 7e-12
 Identities = 22/78 (28%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             +Y+ N   D   + ++++F  YG I    + N       F FV +E P  AE AV   
Sbjct: 15  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN-RRGGPPFAFVEFEDPRDAEDAVYGR 73

Query: 264 NGKEVDGKILYVGRAQKK 281
           +G + DG  L V   +  
Sbjct: 74  DGYDYDGYRLRVEFPRSG 91

>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 = 45.8 bits (108), Expect = 3e-07
 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 2/71 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +++ NL   I  K + D F  +G+I    +          + FV FE    A  ++   +
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG--GPPFAFVEFEDPRDAEDAVYGRD 74

Query: 173 GMLLNSKIVFV 183
           G   +   + V
Sbjct: 75  GYDYDGYRLRV 85

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.8 bits (142), Expect = 7e-12
 Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 4/83 (4%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN--DGKSRGFGFVAYESPEFAEKAVQ 261
           +++ +        ++ LKE F  +G +   +V  +   G S+GFGFV +   E   K + 
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
                 +DG+         K  +
Sbjct: 69  --QRHMIDGRWCDCKLPNSKQSQ 89

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 2e-10
 Identities = 18/83 (21%), Positives = 40/83 (48%), Gaps = 3/83 (3%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
           ++ +  L      + + + FS FG +L  +V +D + G+SKG+GFV F   E   K + +
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 171 VNGMLLNSKIVFVGKFIPRKERE 193
            +   ++ +         ++ ++
Sbjct: 70  RHM--IDGRWCDCKLPNSKQSQD 90

>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 = 58.9 bits (142), Expect = 7e-12
 Identities = 23/87 (26%), Positives = 46/87 (52%), Gaps = 3/87 (3%)

Query: 198 EKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAE 257
           +K +    +  KN   +  +++LKE+FE        R+++ DGKS+G  ++ ++S   AE
Sbjct: 11  KKVRAARTLLAKNLSFNITEDELKEVFEDA---LEIRLVSQDGKSKGIAYIEFKSEADAE 67

Query: 258 KAVQAWNGKEVDGKILYVGRAQKKAER 284
           K ++   G E+DG+ + +    +K   
Sbjct: 68  KNLEEKQGAEIDGRSVSLYYTGEKGGT 94

>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 = 46.2 bits (109), Expect = 2e-07
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 4/81 (4%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            +  KNL  +I    + + F     I        + G SKG  ++ F++E  A K++E+ 
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEK 73

Query: 172 NGMLLNSKIVFVGKFIPRKER 192
            G  ++ + V +     +   
Sbjct: 74  QGAEIDGRSVSLYYTGEKGGT 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 = 58.6 bits (141), Expect = 1e-11
 Identities = 26/90 (28%), Positives = 49/90 (54%), Gaps = 3/90 (3%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGK--SRGFGFVAYESPEFAEKAVQA 262
           +V++ N   +  +E+LK++F   G + S+R++ +      +G+GF  Y+  E A  A++ 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 263 WNGKEVDGKILYVGRAQKKAERTQELKRRF 292
            NG+E  G+ L V  A  +  + +ELK   
Sbjct: 70  LNGREFSGRALRVDNAASEKNK-EELKSLG 98

>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 = 55.1 bits (132), Expect = 2e-10
 Identities = 24/94 (25%), Positives = 49/94 (52%), Gaps = 2/94 (2%)

Query: 102 DPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFET 160
           DP++ +S + +VF+ N+      + + D FS  G ++S ++  D +    KGYGF  ++ 
Sbjct: 1   DPAVDRS-LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59

Query: 161 EEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREK 194
           +E A  ++  +NG   + + + V      K +E+
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKEE 93

>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 = 56.5 bits (136), Expect = 3e-11
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAW 263
           ++I     D   + LK+ F  +G +    +      G+SRGFGFV ++  E  +K +   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ- 60

Query: 264 NGKEVDGKILYVGRA 278
              +++GK++   RA
Sbjct: 61  KEHKLNGKVIDPKRA 75

>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 = 48.8 bits (116), Expect = 1e-08
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKV 171
           +FI  L      K + D FS FG ++ C +  D     S+G+GFV F+  E+ +K +++ 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ- 60

Query: 172 NGMLLNSKIVFVGK 185
               LN K++   +
Sbjct: 61  KEHKLNGKVIDPKR 74

>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 = 56.6 bits (136), Expect = 3e-11
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGK--SRGFGFVAYESPEFAEKAVQ 261
             + +        +  L+E+F  YG I    ++ +     SRGF FV +E+ + A++A +
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 262 AWNGKEVDGKILYV 275
             NG E+DG+ + V
Sbjct: 70  RANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (120), Expect = 4e-09
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEK 170
            + +  L      + + + FS +G I    +  D+Q   S+G+ FV+FE  + A ++ E+
Sbjct: 11  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 171 VNGMLLNSKIVFV 183
            NGM L+ + + V
Sbjct: 71  ANGMELDGRRIRV 83

>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 = 57.1 bits (137), Expect = 3e-11
 Identities = 25/82 (30%), Positives = 36/82 (43%), Gaps = 3/82 (3%)

Query: 203 FTNVYIKNFGEDFNDEKLKEMFEPYGTIT--SYRVMNNDGKSRGFGFVAYESPEFAEKAV 260
           FT +++        D  L++ FE +G I           GKSRG+GFV       AE+A 
Sbjct: 10  FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 69

Query: 261 QAWNGKEVDGKILYVGRAQKKA 282
           +  N   +DG+   V  A   A
Sbjct: 70  KDPNP-IIDGRKANVNLAYLGA 90

>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 = 49.0 bits (116), Expect = 3e-08
 Identities = 25/98 (25%), Positives = 41/98 (41%), Gaps = 9/98 (9%)

Query: 99  SQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVH 157
           SQ+D +  K     +F+  L     + ++   F  FG I    V  D + G S+GYGFV 
Sbjct: 4   SQKDTTFTK-----IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 58

Query: 158 FETEEAANKSIEKVNGMLLNSKI---VFVGKFIPRKER 192
                AA ++ +  N ++   K    +      PR  +
Sbjct: 59  MADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQ 96

>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 = 56.3 bits (135), Expect = 4e-11
 Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 2/80 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTIT--SYRVMNNDGKSRGFGFVAYESPEFAEKAVQ 261
             +++ +  E+  +++++E F  YG I      +    G S+G+  V YE+ + A  A +
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 262 AWNGKEVDGKILYVGRAQKK 281
           A NG E+ G+ + V     K
Sbjct: 68  ALNGAEIMGQTIQVDWCFVK 87

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 45.5 bits (107), Expect = 4e-07
 Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEK 170
            +F+ ++ +      + + F  +G I +  +  D +   SKGY  V +ET + A  + E 
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 171 VNGMLLNSKIVFVGKFIPR 189
           +NG  +  + + V     +
Sbjct: 69  LNGAEIMGQTIQVDWCFVK 87

>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 = 55.8 bits (134), Expect = 1e-10
 Identities = 11/80 (13%), Positives = 30/80 (37%), Gaps = 4/80 (5%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             + ++N       + L ++F  +GT+           ++    + Y  P  A+ A  + 
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK--NNQFQALLQYADPVSAQHAKLSL 65

Query: 264 NGKEV--DGKILYVGRAQKK 281
           +G+ +      L +  ++  
Sbjct: 66  DGQNIYNACCTLRIDFSKLT 85

>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 = 55.0 bits (132), Expect = 2e-10
 Identities = 15/105 (14%), Positives = 40/105 (38%), Gaps = 5/105 (4%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
           S V  + ++NL   +    ++  FS FG++L          N++    + +    +A  +
Sbjct: 5   SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHA 61

Query: 168 IEKVNGMLL--NSKIVFVGKFIPRKEREKELGEKAKLFTNVYIKN 210
              ++G  +      + +          K   +K++ +T   + +
Sbjct: 62  KLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPS 106

>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 = 56.5 bits (135), Expect = 1e-10
 Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 2/83 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGF--GFVAYESPEFAEKAVQ 261
            N+ +       ++ +L+++FE YG I S +++ +    +    GFV ++S   A++A+ 
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102

Query: 262 AWNGKEVDGKILYVGRAQKKAER 284
             NG  +  K L V  A    +R
Sbjct: 103 GLNGFNILNKRLKVALAASGHQR 125

>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 = 49.5 bits (117), Expect = 4e-08
 Identities = 24/118 (20%), Positives = 48/118 (40%), Gaps = 7/118 (5%)

Query: 92  RPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSK 151
           + I       +P + +    N+ +  +  ++D   +   F  +G I S K+  D +    
Sbjct: 28  QHIPPTQMNPEPDVLR----NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQS 83

Query: 152 GY-GFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRKEREKELGEKAKLFTNVYI 208
              GFV F++  +A ++I  +NG  + +K + V       +R    G       N Y+
Sbjct: 84  RGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVG--DGNGYL 139

>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 = 37.2 bits (85), Expect = 7e-04
 Identities = 7/44 (15%), Positives = 19/44 (43%), Gaps = 4/44 (9%)

Query: 76  DTERALDTMNFDALKGRPIRIMWS----QRDPSLRKSGVGNVFI 115
             ++A+  +N   +  + +++  +    QR       G GN ++
Sbjct: 96  SAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139

>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 = 55.1 bits (132), Expect = 1e-10
 Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM--NNDGKSRGFGFVAYESPEFAEKAVQ 261
           T + ++N     + +++ + F  Y  I     +  N  G   G   VA+ES + A  AV 
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 262 AWNGKEVDGKILYV 275
             N + +  + + +
Sbjct: 70  DLNDRPIGSRKVKL 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 = 49.7 bits (118), Expect = 1e-08
 Identities = 16/78 (20%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDEQGNSKGYGFVHFETEEAAN 165
           K G   + ++N+  ++    + D F  +  I     +  +E+G   G   V FE+ + A 
Sbjct: 6   KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 65

Query: 166 KSIEKVNGMLLNSKIVFV 183
            ++  +N   + S+ V +
Sbjct: 66  AAVIDLNDRPIGSRKVKL 83

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 1e-10
 Identities = 16/75 (21%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAW 263
           +++     D  +EK++E F  +G + S  +  ++   K RGF F+ ++  E  +K ++  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60

Query: 264 NGKEVDGKILYVGRA 278
               V      +  A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 8e-09
 Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
           +F+  L      + + + F  FG + S ++  D +    +G+ F+ F+ EE   K +EK 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 172 NGMLLNSKI 180
              +  SK 
Sbjct: 62  YHNVGLSKC 70

>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 = 55.0 bits (131), Expect = 2e-10
 Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 2/86 (2%)

Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVM-NNDGKSRGFGFVAYESPEF 255
           G ++    N++I N   + +  +LK             V+    G +R FG+V +ES E 
Sbjct: 7   GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED 66

Query: 256 AEKAVQAWNGKEVDGKILYVGRAQKK 281
            EKA++   G +V G  + + + + +
Sbjct: 67  LEKALE-LTGLKVFGNEIKLEKPKGR 91

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.5 bits (131), Expect = 2e-10
 Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 4/82 (4%)

Query: 202 LFTNVYIKNFGEDFND--EKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKA 259
           +F  +  ++     N+  E L+     +G I   +++  D    G   V++  PE A+  
Sbjct: 16  MFHPMDFEDDPLVLNEIREDLRVECSKFGQIR--KLLLFDRHPDGVASVSFRDPEEADYC 73

Query: 260 VQAWNGKEVDGKILYVGRAQKK 281
           +Q  +G+   G+ +        
Sbjct: 74  IQTLDGRWFGGRQITAQAWDGT 95

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.9 bits (93), Expect = 3e-05
 Identities = 14/85 (16%), Positives = 26/85 (30%), Gaps = 8/85 (9%)

Query: 113 VFIKNL--------DKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAA 164
           V IKN+        D  + N+   D           +       +  G   V F   E A
Sbjct: 11  VIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEA 70

Query: 165 NKSIEKVNGMLLNSKIVFVGKFIPR 189
           +  I+ ++G     + +    +   
Sbjct: 71  DYCIQTLDGRWFGGRQITAQAWDGT 95

>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 = 53.6 bits (128), Expect = 4e-10
 Identities = 13/76 (17%), Positives = 30/76 (39%), Gaps = 2/76 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTIT--SYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           +++ NF   +    ++++ +    +             SR F ++   S E A   V+  
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 264 NGKEVDGKILYVGRAQ 279
           NG +++G  L    + 
Sbjct: 64  NGLKIEGYTLVTKVSN 79

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.4 bits (104), Expect = 6e-07
 Identities = 11/72 (15%), Positives = 29/72 (40%), Gaps = 1/72 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEKV 171
           +++ N   S   + + D       +         + N S+ + ++   ++E A   +EK+
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 172 NGMLLNSKIVFV 183
           NG+ +    +  
Sbjct: 64  NGLKIEGYTLVT 75

>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 = 53.1 bits (127), Expect = 5e-10
 Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 6/78 (7%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             +Y+     D     L+  F P+G I    +       R   FV YE  E A++AV   
Sbjct: 6   NTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP----RNCAFVTYEKMESADQAVAEL 59

Query: 264 NGKEVDGKILYVGRAQKK 281
           NG +V+   L V  A+K+
Sbjct: 60  NGTQVESVQLKVNIARKQ 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 = 38.9 bits (90), Expect = 5e-05
 Identities = 15/72 (20%), Positives = 33/72 (45%), Gaps = 7/72 (9%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            +++   D  +    +   FS FG+I+            +   FV +E  E+A++++ ++
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNIIDLS-----MDPPRNCAFVTYEKMESADQAVAEL 59

Query: 172 NGMLLNSKIVFV 183
           NG  + S  + V
Sbjct: 60  NGTQVESVQLKV 71

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.6 bits (79), Expect = 0.002
 Identities = 4/32 (12%), Positives = 16/32 (50%)

Query: 72  PYMLDTERALDTMNFDALKGRPIRIMWSQRDP 103
             M   ++A+  +N   ++   +++  +++ P
Sbjct: 47  EKMESADQAVAELNGTQVESVQLKVNIARKQP 78

>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 = 54.0 bits (129), Expect = 5e-10
 Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 2/84 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGK--SRGFGFVAYESPEFAEKAVQ 261
             +Y+KN      +  L  +F  +       +         RG  F+ + + E A +A+ 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 262 AWNGKEVDGKILYVGRAQKKAERT 285
             NG ++ GKIL +   + K +R+
Sbjct: 79  LVNGYKLYGKILVIEFGKNKKQRS 102

>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 = 44.8 bits (105), Expect = 7e-07
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
            +++KNL   +  + +   F+ F       +      G  +G  F+ F  +E A +++  
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 171 VNGMLLNSKIVFVGKFIPRKER 192
           VNG  L  KI+ +     +K+R
Sbjct: 80  VNGYKLYGKILVIEFGKNKKQR 101

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.8 bits (126), Expect = 7e-10
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 3/75 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYR--VMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           +++     +   E +K  FE +G +            + RGFGFV +ES +  EK  +  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI- 60

Query: 264 NGKEVDGKILYVGRA 278
           +  E++ K++   +A
Sbjct: 61  HFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.0 bits (98), Expect = 4e-06
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 2/74 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVA-QDEQGNSKGYGFVHFETEEAANKSIEKV 171
           +F+  L  +   + +   F  FG +    +         +G+GFV FE+E+   K  E  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI- 60

Query: 172 NGMLLNSKIVFVGK 185
           +   +N+K+V   K
Sbjct: 61  HFHEINNKMVECKK 74

>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 = 52.8 bits (126), Expect = 7e-10
 Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           + + +KN  +D N +++ ++ + Y     Y        ++   FV   + E A+ A+Q +
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDR-----NKRTAFVTLLNGEQAQNAIQMF 60

Query: 264 NGKEVDGKILYVGRAQKKA 282
           +     GK L V      A
Sbjct: 61  HQYSFRGKDLIVQLQPTDA 79

>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 = 47.8 bits (113), Expect = 5e-08
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 7/85 (8%)

Query: 108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKS 167
           SG   + +KNL +  + + ++D    +               +K   FV     E A  +
Sbjct: 3   SGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCY------VDRNKRTAFVTLLNGEQAQNA 56

Query: 168 IEKVNGMLLNSKIVFVGKFIPRKER 192
           I+  +      K + V +  P    
Sbjct: 57  IQMFHQYSFRGKDLIV-QLQPTDAL 80

>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 = 52.9 bits (126), Expect = 1e-09
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDG-KSRGFGFVAYESPEFAEKAVQA 262
           TN+YI N     ++++L+ M +P+G + S R++ +    SRG GF   ES E  E  +  
Sbjct: 19  TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 78

Query: 263 WNGKEVDGKILYVGRAQ 279
           +NGK +          +
Sbjct: 79  FNGKFIKTPPGVSAPTE 95

>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 = 44.8 bits (105), Expect = 7e-07
 Identities = 21/77 (27%), Positives = 36/77 (46%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           N++I NL  S+D + + +    FG ++S ++ +D  G S+G GF   E+ E     I   
Sbjct: 20  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 79

Query: 172 NGMLLNSKIVFVGKFIP 188
           NG  + +         P
Sbjct: 80  NGKFIKTPPGVSAPTEP 96

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 5e-09
 Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 3/81 (3%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNND--GKSRGFGFVAYESPEFAEKAVQAW 263
            ++ N   D  +E +KE F                  + +GFG+  +E  +    A+   
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL- 76

Query: 264 NGKEVDGKILYVGRAQKKAER 284
           N + +  K + V  A +  ++
Sbjct: 77  NEESLGNKRIRVDVADQAQDK 97

>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 = 43.2 bits (101), Expect = 3e-06
 Identities = 13/83 (15%), Positives = 31/83 (37%), Gaps = 2/83 (2%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-GNSKGYGFVHFETEEAANKSIEKV 171
            F+ NL   +  +++ + F            +       KG+G+  FE  ++       +
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLS-ALSL 76

Query: 172 NGMLLNSKIVFVGKFIPRKEREK 194
           N   L +K + V      ++++ 
Sbjct: 77  NEESLGNKRIRVDVADQAQDKDS 99

>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 = 50.2 bits (119), Expect = 8e-09
 Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 8/89 (8%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGK--SRGFGFVAYESPEFAEKAVQ 261
             V+I+N   D  +E L E+ + +G +   RV+ +     S+G  F  + + E A+K + 
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 262 AWN------GKEVDGKILYVGRAQKKAER 284
           A +      G ++DG+ L V  A  + E 
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>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 = 41.7 bits (97), Expect = 1e-05
 Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 7/88 (7%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSIEK 170
            VFI+NL    + +A+ +    FG +   +V        SKG  F  F T+EAA K +  
Sbjct: 10  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 69

Query: 171 VN------GMLLNSKIVFVGKFIPRKER 192
            +      G+ L+ + + V   + R E 
Sbjct: 70  ASLEAEGGGLKLDGRQLKVDLAVTRDEA 97

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.7 bits (118), Expect = 9e-09
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 5/82 (6%)

Query: 204 TNVYIKNFGEDFNDEK-LKEMFEPYGTITSYRVM---NNDGKSRGFGFVAYESPEFAEKA 259
             + I+N   +  DE  L+E FE +G+I    +         +    F+ +E+ + AE+A
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 260 VQAWNGKEVDGKILYVGRAQKK 281
           +Q  N   +  + + V  A KK
Sbjct: 65  LQM-NRSLLGNREISVSLADKK 85

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 36.6 bits (84), Expect = 4e-04
 Identities = 18/81 (22%), Positives = 39/81 (48%), Gaps = 4/81 (4%)

Query: 112 NVFIKNLDKS-IDNKAMYDTFSAFGSILSCKVAQ--DEQGNSKGYGFVHFETEEAANKSI 168
            + I+NL    +D   + ++F  FGSI    +     E   +    F+ FE +++A +++
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 169 EKVNGMLLNSKIVFVGKFIPR 189
           + +N  LL ++ + V     +
Sbjct: 66  Q-MNRSLLGNREISVSLADKK 85

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.1 bits (116), Expect = 1e-08
 Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 1/75 (1%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           T V +KN  + +N  K+ + F+  G I    V ++  K+  F  + +        A    
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARY-DGALAAITK 59

Query: 264 NGKEVDGKILYVGRA 278
             K V    + V   
Sbjct: 60  THKVVGQNEIIVSHL 74

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 35.2 bits (80), Expect = 0.001
 Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            V +KNL KS +   +Y  F   G I+   VA   + N + +  + F   + A  +I K 
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR-FARIEFARYDGALAAITKT 60

Query: 172 NGMLLNSKI 180
           + ++  ++I
Sbjct: 61  HKVVGQNEI 69

>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 = 48.6 bits (115), Expect = 3e-08
 Identities = 13/82 (15%), Positives = 25/82 (30%), Gaps = 5/82 (6%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             V +       + + LK+     G +    V  +       G V Y   E  E A++  
Sbjct: 16  FRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-----MGMVEYLRKEDMEYALRKL 70

Query: 264 NGKEVDGKILYVGRAQKKAERT 285
           +  +           +   ER+
Sbjct: 71  DDTKFRSHEGETSYIRVYPERS 92

>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 = 40.5 bits (94), Expect = 2e-05
 Identities = 12/82 (14%), Positives = 21/82 (25%), Gaps = 6/82 (7%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           V +  L  S   + + D                      G G V +  +E    ++ K++
Sbjct: 18  VLVSGLPPSGSWQDLKDHMR------EAGDVCYADVQKDGMGMVEYLRKEDMEYALRKLD 71

Query: 173 GMLLNSKIVFVGKFIPRKEREK 194
                S            ER  
Sbjct: 72  DTKFRSHEGETSYIRVYPERSS 93

>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 = 47.5 bits (112), Expect = 4e-08
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITS--YRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           +YI+       D+ L ++ +PYG I S    +     K +G+GFV ++SP  A+KAV A 
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 264 NGKEVDGKIL 273
               V  ++ 
Sbjct: 61  KASGVQAQMA 70

>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 = 37.4 bits (86), Expect = 1e-04
 Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVA-QDEQGNSKGYGFVHFETEEAANKSIEKV 171
           ++I+ L     ++ +      +G I+S K          KGYGFV F++  AA K++  +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 172 NGMLLNSKIV 181
               + +++ 
Sbjct: 61  KASGVQAQMA 70

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 4e-08
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGK--SRGFGFVAYESPEFAEKAVQAW 263
           +++    ED  +  L++ FE YG I    +M + G    RGF FV ++  + +   +   
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD-SVDKIVIQ 63

Query: 264 NGKEVDGKILYVGRA 278
               V+G    V +A
Sbjct: 64  KYHTVNGHNCEVRKA 78

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 1e-05
 Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 2/77 (2%)

Query: 110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGN-SKGYGFVHFETEEAANKSI 168
           V  +F+  + +  +   + D F  +G I   ++  D      +G+ FV F+  ++ +K +
Sbjct: 2   VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 61

Query: 169 EKVNGMLLNSKIVFVGK 185
            +     +N     V K
Sbjct: 62  IQ-KYHTVNGHNCEVRK 77

>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 = 47.2 bits (111), Expect = 1e-07
 Identities = 16/95 (16%), Positives = 30/95 (31%), Gaps = 4/95 (4%)

Query: 197 GEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFA 256
           G   +  T +  KN        +++E F  +G++    +            V +  P  A
Sbjct: 4   GSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG----GITAIVEFLEPLEA 59

Query: 257 EKAVQAWNGKEVDGKILYVGRAQKKAERTQELKRR 291
            KA +     +     LY+  A          K+ 
Sbjct: 60  RKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKD 94

>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 = 2e-07
 Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 4/62 (6%)

Query: 218 EKLKEMFEPYGTITSYRVM----NNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKIL 273
           E +++    YG + S  +       +    G  FV + S    +KA+Q   G++   +++
Sbjct: 29  EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88

Query: 274 YV 275
             
Sbjct: 89  VT 90

>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 = 35.0 bits (80), Expect = 0.002
 Identities = 12/72 (16%), Positives = 29/72 (40%), Gaps = 3/72 (4%)

Query: 127 MYDTFSAFGSILSCKVAQD---EQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV 183
           + D  S +G + S ++ +     +    G  FV F +     K+++ + G    +++V  
Sbjct: 31  VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 90

Query: 184 GKFIPRKEREKE 195
               P     ++
Sbjct: 91  KYCDPDSYHRRD 102

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.7 bits (108), Expect = 2e-07
 Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           T V +  F +      L + F  YG I  + +      +  +  + Y+S   A KA+   
Sbjct: 5   TWVTVFGFPQASASYILLQ-FAQYGNILKHVMS----NTGNWMHIRYQSKLQARKALS-K 58

Query: 264 NGKEVDGK-ILYVGRAQKKA 282
           +G+      ++ V     K 
Sbjct: 59  DGRIFGESIMIGVKPCIDKN 78

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.5 bits (84), Expect = 5e-04
 Identities = 11/77 (14%), Positives = 33/77 (42%), Gaps = 6/77 (7%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           V +    ++  +  +   F+ +G+IL   ++         +  + ++++  A K++ K  
Sbjct: 7   VTVFGFPQASAS-YILLQFAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKALSKDG 60

Query: 173 GMLLNSKIVFVGKFIPR 189
            +   S ++ V   I +
Sbjct: 61  RIFGESIMIGVKPCIDK 77

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.4 bits (109), Expect = 2e-07
 Identities = 14/89 (15%), Positives = 37/89 (41%), Gaps = 3/89 (3%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITS--YRVMNNDGKSRGFGFVAYESPEFAEKAVQ 261
              +I N         + +  E      +  + +++N+G+  G   V +++ + A K+ +
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 68

Query: 262 AWNGKEVDGKILYVGRAQKKAERTQELKR 290
             + K+++G+  +V     +  R  E   
Sbjct: 69  -LHRKKLNGREAFVHVVTLEDMREIEKNP 96

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.5 bits (104), Expect = 1e-06
 Identities = 19/85 (22%), Positives = 26/85 (30%), Gaps = 2/85 (2%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQD-EQGNSKGYGFVHFETEEAANKSIEK 170
              I N+  SI    +           +         G   G   V F+ E+ A KS   
Sbjct: 10  CAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL 69

Query: 171 VNGMLLNSKIVFVGKFIPRKEREKE 195
            +   LN +  FV        RE E
Sbjct: 70  -HRKKLNGREAFVHVVTLEDMREIE 93

>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 = 45.9 bits (108), Expect = 3e-07
 Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 9/80 (11%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           V     G   +  +L  + E  G + +  +  N    + + F  Y + E +++A    NG
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN----KPYSFARYRTTEESKRAYVTLNG 78

Query: 266 KEV-DGK----ILYVGRAQK 280
           KEV D       LY+   +K
Sbjct: 79  KEVVDDLGQKITLYLNFVEK 98

>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 = 39.3 bits (91), Expect = 6e-05
 Identities = 15/100 (15%), Positives = 31/100 (31%), Gaps = 18/100 (18%)

Query: 101 RDPSLRKSGVGN---------VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSK 151
           +   LR  G+           V    L   +    +       G + +  +  ++     
Sbjct: 2   KHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP---- 57

Query: 152 GYGFVHFETEEAANKSIEKVNGMLL----NSKIVFVGKFI 187
            Y F  + T E + ++   +NG  +      KI     F+
Sbjct: 58  -YSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFV 96

>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 = 45.8 bits (108), Expect = 3e-07
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
           T +++   G + +   L   F+ +G+I +   +        F ++ YES + A+ A    
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG----DSFAYIQYESLDAAQAACAKM 73

Query: 264 NGKEVDG--KILYVGRAQKK 281
            G  + G  + L V  A+  
Sbjct: 74  RGFPLGGPDRRLRVDFAKSG 93

>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 = 37.7 bits (87), Expect = 2e-04
 Identities = 17/87 (19%), Positives = 38/87 (43%), Gaps = 11/87 (12%)

Query: 91  GRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNS 150
           G   +I + + +P+ R      +++  L  +    A+   F  FGSI +    + +    
Sbjct: 4   GSSGKIGYGKANPTTR------LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS--- 54

Query: 151 KGYGFVHFETEEAANKSIEKVNGMLLN 177
             + ++ +E+ +AA  +  K+ G  L 
Sbjct: 55  --FAYIQYESLDAAQAACAKMRGFPLG 79

>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 = 45.5 bits (107), Expect = 4e-07
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 7/82 (8%)

Query: 206 VYIKNFGEDFNDEK-LKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA-- 262
           V+I +F    N    L ++ EP+G I+++ ++N         F+   + E A+ AV    
Sbjct: 11  VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK----INEAFIEMATTEDAQAAVDYYT 66

Query: 263 WNGKEVDGKILYVGRAQKKAER 284
                V GK + V  +QK    
Sbjct: 67  TTPALVFGKPVRVHLSQKYKRI 88

>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 = 45.1 bits (106), Expect = 7e-07
 Identities = 18/106 (16%), Positives = 43/106 (40%), Gaps = 8/106 (7%)

Query: 204 TNVYIKNFG-EDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQA 262
           + + + N   E    + L  +F  YG +   +++ N    +    V       A+ A+  
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK---KENALVQMADGNQAQLAMSH 59

Query: 263 WNGKEVDGKILYVGRAQKKAERT----QELKRRFEMLKIERLNRYQ 304
            NG ++ GK + +  ++ +  +     QE +   +      L+R++
Sbjct: 60  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFK 105

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 2e-06
 Identities = 10/81 (12%), Positives = 27/81 (33%), Gaps = 1/81 (1%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           V+++       +  +   F P   +  +  +  DG+  G   V + + E A  A+   + 
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDK 76

Query: 266 KEVDGKILYVGRAQKKAERTQ 286
             +  + + +           
Sbjct: 77  ANMQHRYVELFLNSTAGTSGS 97

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.6 bits (99), Expect = 3e-06
 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 5/77 (6%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           + I+    D  ++++ ++   Y             K +G  FV   + E AE A+  ++ 
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY-----ELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQ 55

Query: 266 KEVDGKILYVGRAQKKA 282
             +  + L V      A
Sbjct: 56  SRLRERELSVQLQPTDA 72

>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 = 14/71 (19%), Positives = 26/71 (36%), Gaps = 6/71 (8%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           + I+ L   + N+ ++D  S        ++        KG  FV     E A  +I   +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLS------DYELKYCFVDKYKGTAFVTLLNGEQAEAAINTFH 54

Query: 173 GMLLNSKIVFV 183
              L  + + V
Sbjct: 55  QSRLRERELSV 65

>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 = 42.9 bits (100), Expect = 3e-06
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 8/79 (10%)

Query: 205 NVYIKNFGEDFNDEKLKEMFE---PYGTITSYRVMNN-----DGKSRGFGFVAYESPEFA 256
            V++    +   D ++ +  E    +G I    + N+             +V Y   E A
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 257 EKAVQAWNGKEVDGKILYV 275
            +A+Q  N   VDG+ L  
Sbjct: 70  LRAIQCVNNVVVDGRTLKA 88

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.0 bits (82), Expect = 7e-04
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 7/77 (9%)

Query: 112 NVFIKNLDKSIDN---KAMYDTFSAFGSILSCKVAQDEQGN----SKGYGFVHFETEEAA 164
            VF+  L + + +       + F  FG I    +                +V +   E A
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 165 NKSIEKVNGMLLNSKIV 181
            ++I+ VN ++++ + +
Sbjct: 70  LRAIQCVNNVVVDGRTL 86

>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 = 42.9 bits (100), Expect = 4e-06
 Identities = 15/84 (17%), Positives = 31/84 (36%), Gaps = 6/84 (7%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW 263
             V+++   E   +  L E  E +GTI    +M      +    V +E+ + A++ V   
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF----KRQALVEFENIDSAKECVTFA 71

Query: 264 NGK--EVDGKILYVGRAQKKAERT 285
                 + G+  +   +  K    
Sbjct: 72  ADVPVYIAGQQAFFNYSTSKRITR 95

>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 = 34.8 bits (79), Expect = 0.003
 Identities = 11/73 (15%), Positives = 28/73 (38%), Gaps = 7/73 (9%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV- 171
           V ++ L +S+    + +    FG+I    +   ++        V FE  ++A + +    
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR-----QALVEFENIDSAKECVTFAA 72

Query: 172 -NGMLLNSKIVFV 183
              + +  +  F 
Sbjct: 73  DVPVYIAGQQAFF 85

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 4e-06
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV-MNNDGKSRGFGFVAYESPEFAEKAVQA 262
            +VYIK F  D   + +KE  E  G + + ++        +G  FV ++S E A+K V+ 
Sbjct: 7   RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 66

Query: 263 WNGKEVDGKILYV 275
             G++     L +
Sbjct: 67  -PGQKYKETDLLI 78

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 7e-05
 Identities = 14/70 (20%), Positives = 30/70 (42%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
           +V+IK          + +     G +L+ ++ +      KG  FV F++ E+A K +E  
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 67

Query: 172 NGMLLNSKIV 181
                 + ++
Sbjct: 68  GQKYKETDLL 77

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 40.2 bits (93), Expect = 2e-05
 Identities = 14/76 (18%), Positives = 32/76 (42%), Gaps = 4/76 (5%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           +++ N  E+ N+  L  +F  +      R++ N        FV + +   +  A +A  G
Sbjct: 11  LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFTTELQSNAAKEALQG 67

Query: 266 KEVD-GKILYVGRAQK 280
            ++     + +  A+K
Sbjct: 68  FKITPTHAMKITFAKK 83

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 35.2 bits (80), Expect = 0.001
 Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 4/65 (6%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           +F+ NL +  +   +   F+ F      ++  +         FV F TE  +N + E + 
Sbjct: 11  LFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRH----DIAFVEFTTELQSNAAKEALQ 66

Query: 173 GMLLN 177
           G  + 
Sbjct: 67  GFKIT 71

>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 = 40.3 bits (93), Expect = 2e-05
 Identities = 11/79 (13%), Positives = 23/79 (29%), Gaps = 5/79 (6%)

Query: 206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNG 265
           V +       + + LK+     G +    V  +       G V +   E    AV+  + 
Sbjct: 3   VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-----TGVVEFVRKEDMTYAVRKLDN 57

Query: 266 KEVDGKILYVGRAQKKAER 284
            +           + K + 
Sbjct: 58  TKFRSHEGETAYIRVKVDG 76

>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 = 34.5 bits (78), Expect = 0.002
 Identities = 11/82 (13%), Positives = 22/82 (26%), Gaps = 6/82 (7%)

Query: 113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN 172
           V +  L  S   + + D                      G G V F  +E    ++ K++
Sbjct: 3   VVVSGLPPSGSWQDLKDHMR------EAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLD 56

Query: 173 GMLLNSKIVFVGKFIPRKEREK 194
                S          + +  +
Sbjct: 57  NTKFRSHEGETAYIRVKVDGPR 78

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.4 bits (93), Expect = 3e-05
 Identities = 12/98 (12%), Positives = 31/98 (31%), Gaps = 5/98 (5%)

Query: 188 PRKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGF 247
           P  + +++  +K +L   +++ N       +                      + +   F
Sbjct: 3   PEGKPDQKFDQKQELGRVIHLSNLPHSGYSD---SAVLKLAEPYGKIKNYILMRMKSQAF 59

Query: 248 VAYESPEFAEKAVQAWN--GKEVDGKILYVGRAQKKAE 283
           +  E+ E A   V           G+ + V  ++K  +
Sbjct: 60  IEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKK 97

>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 = 39.4 bits (91), Expect = 5e-05
 Identities = 11/83 (13%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWN 264
            ++I+    +  + ++  +  P+G +T+  ++      +   F+   + E A   V  ++
Sbjct: 10  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG----KNQAFLELATEEAAITMVNYYS 65

Query: 265 GK--EVDGKILYVGRAQKKAERT 285
                +  + +Y+  +  K  +T
Sbjct: 66  AVTPHLRNQPIYIQYSNHKELKT 88

>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 = 37.0 bits (85), Expect = 3e-04
 Identities = 8/65 (12%), Positives = 25/65 (38%), Gaps = 3/65 (4%)

Query: 112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV 171
            + + N+  S+  + +   FS+ G ++       +         +   + E A +++  +
Sbjct: 12  TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK---MALIQMGSVEEAVQALIDL 68

Query: 172 NGMLL 176
           +   L
Sbjct: 69  HNHDL 73

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	336
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.98
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.97
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.81
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.81
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.81
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.81
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.81
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.8
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.8
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.8
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.8
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.8
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.8
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.79
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.79
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.79
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.78
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.78
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.78
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.78
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.78
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.78
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.78
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.78
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.78
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.78
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.78
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.78
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.78
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.77
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.77
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.77
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.77
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.77
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.76
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.76
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.76
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.76
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.76
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.75
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.75
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.75
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.75
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.75
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.75
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.75
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.75
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.75
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.75
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.75
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.75
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.74
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.74
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.74
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.74
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.74
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.73
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.73
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.73
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.73
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.73
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.73
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.73
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.73
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.72
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.72
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.72
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.72
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.72
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.72
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.72
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.72
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.72
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.71
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.71
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.71
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.71
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.71
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.7
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.7
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.7
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.7
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.7
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.7
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.7
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.7
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.7
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.69
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.69
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.69
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.69
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.69
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.69
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.69
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.68
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.68
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.68
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.68
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.68
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.68
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.68
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.68
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.68
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.67
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.67
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.67
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.67
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.66
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.66
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.66
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.66
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.66
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.66
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.66
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.66
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.65
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.65
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.65
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.65
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.65
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.65
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.65
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.64
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.64
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.64
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.64
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.64
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.63
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.63
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.63
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.63
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.63
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.62
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.62
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.62
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.61
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.61
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.6
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.59
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.58
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.58
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.54
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	99.54
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.51
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	99.51
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.51
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.49
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.48
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.43
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.43
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.4
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.38
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.37
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.33
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.32
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.32
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.22
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.78
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.76
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.73
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.57
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.51
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.48
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.44
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.07

>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=99.98  E-value=5.3e-31  Score=213.75  Aligned_cols=171  Identities=24%  Similarity=0.494  Sum_probs=150.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||+++|+++|+++|++||.|..+.++.+. +|.++|||||+|.+.++|.+|+. +++..+.++.+.+.+..+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            3789999999999999999999999999999999986 78899999999999999999999 577788888888877765


Q ss_pred             chhhhHhhhccccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCc
Q psy12549        189 RKEREKELGEKAKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGK  266 (336)
Q Consensus       189 ~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~  266 (336)
                      .......  ......++|||+|||..+++++|+++|+.||.|..+.+..  .+|.++|+|||+|.++++|.+|++ +++.
T Consensus        85 ~~~~~~~--~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~  161 (183)
T d1u1qa_          85 REDSQRP--GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYH  161 (183)
T ss_dssp             TTGGGST--TTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCE
T ss_pred             ccccccc--ccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCC
Confidence            5443322  2233447899999999999999999999999999998886  668899999999999999999997 7999


Q ss_pred             eecCEEEEEeecccchhh
Q psy12549        267 EVDGKILYVGRAQKKAER  284 (336)
Q Consensus       267 ~~~g~~l~v~~~~~~~~~  284 (336)
                      .+.|+.|+|.+|.++.+.
T Consensus       162 ~~~G~~i~V~~A~~k~e~  179 (183)
T d1u1qa_         162 TVNGHNCEVRKALSKQEM  179 (183)
T ss_dssp             EETTEEEEEEECCCHHHH
T ss_pred             eECCEEEEEEecCCcccc
Confidence            999999999999887544

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=1.1e-29  Score=205.98  Aligned_cols=169  Identities=16%  Similarity=0.216  Sum_probs=147.6

Q ss_pred             CceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeEE
Q psy12549         18 KHNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIRI   96 (336)
Q Consensus        18 ~~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~v   96 (336)
                      .|+|||+|||+++||++|+++| .+|.+.++.++++.   .+|.++|+|||+|.+.  ++|..|+. +.+..+.++.+.+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~---~~~~~~g~afv~f~~~--~~a~~a~~-~~~~~~~~~~~~~   79 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDP---NTKRSRGFGFVTYATV--EEVDAAMN-ARPHKVDGRVVEP   79 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT---TTCCEEEEEEEEESSH--HHHHHHHH-TCSCEETTEECEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecc---cCCCccCceecccCCH--HHHHHHHH-hcCCcccccchhh
Confidence            3889999999999999999999 77788899999877   3689999999999999  99999999 5667778888888


Q ss_pred             EeccCCCC----cCCCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHh
Q psy12549         97 MWSQRDPS----LRKSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKV  171 (336)
Q Consensus        97 ~~~~~~~~----~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l  171 (336)
                      .+......    ......++|||+|||..+|+++|+++|+.||.|..+.++.+. +|.++|||||+|.+.++|.+|++ +
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~  158 (183)
T d1u1qa_          80 KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-Q  158 (183)
T ss_dssp             EECCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-S
T ss_pred             hhhhhcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-h
Confidence            77544332    223445799999999999999999999999999999999987 68899999999999999999998 7


Q ss_pred             CCceeCCeEEEEeeccCchhhh
Q psy12549        172 NGMLLNSKIVFVGKFIPRKERE  193 (336)
Q Consensus       172 ~~~~~~~~~i~v~~~~~~~~~~  193 (336)
                      ++..+.|+.|.|.++.++.+..
T Consensus       159 ~~~~~~G~~i~V~~A~~k~e~~  180 (183)
T d1u1qa_         159 KYHTVNGHNCEVRKALSKQEMA  180 (183)
T ss_dssp             SCEEETTEEEEEEECCCHHHHH
T ss_pred             CCCeECCEEEEEEecCCccccc
Confidence            9999999999999988775543

>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=99.82  E-value=3.8e-20  Score=128.38  Aligned_cols=79  Identities=29%  Similarity=0.580  Sum_probs=75.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||+++++++|+++|++||.|..+.+.+++ +|.++|||||+|.++++|++|++.|||..+.|+.|.|.++.|
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            4679999999999999999999999999999999986 788999999999999999999999999999999999999876

>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=99.81  E-value=6.6e-20  Score=129.33  Aligned_cols=83  Identities=28%  Similarity=0.462  Sum_probs=78.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ....++|||+|||.++++++|+++|+.||.|.++.++.++ +|.++|||||+|.+.++|.+|++.|+|..++|+.|.|.+
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3456789999999999999999999999999999999987 788999999999999999999999999999999999999


Q ss_pred             ccCc
Q psy12549        186 FIPR  189 (336)
Q Consensus       186 ~~~~  189 (336)
                      +.|+
T Consensus        85 akp~   88 (90)
T d2cq0a1          85 AKPS   88 (90)
T ss_dssp             SSCC
T ss_pred             eeCC
Confidence            9875

>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=99.81  E-value=1.2e-19  Score=125.85  Aligned_cols=78  Identities=32%  Similarity=0.608  Sum_probs=74.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ++|||+|||.++++++|+++|++||+|..++++.+. .|.++|||||+|.++++|+.|++.|||..+.|+.|.|.++.|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            579999999999999999999999999999999886 788999999999999999999999999999999999999876

>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=99.81  E-value=9.5e-20  Score=127.85  Aligned_cols=82  Identities=22%  Similarity=0.377  Sum_probs=76.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      .+.++|||+|||.++|+++|+++|+.||.|.+++++.++ +|.++|||||+|.+.++|++|+..|||..+.|+.|.|.|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            345789999999999999999999999999999999986 7899999999999999999999999999999999999998


Q ss_pred             cCc
Q psy12549        187 IPR  189 (336)
Q Consensus       187 ~~~  189 (336)
                      .++
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            754

>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=99.81  E-value=9.9e-20  Score=125.39  Aligned_cols=77  Identities=25%  Similarity=0.464  Sum_probs=73.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ++|||+|||+.+|+++|+++|++||+|.++++++++ +|.++|||||+|.++++|..|++.|+|..+.|++|.|.++.
T Consensus         1 aslfV~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           1 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            369999999999999999999999999999999987 68899999999999999999999999999999999999875

>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=99.81  E-value=7.4e-20  Score=129.77  Aligned_cols=84  Identities=25%  Similarity=0.496  Sum_probs=78.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      ....++|||+|||..+|+++|+++|++||.|.+++++.++ +|.++|||||+|.+.++|..|++.|||..+.|+.|.|.+
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3445799999999999999999999999999999999987 789999999999999999999999999999999999999


Q ss_pred             ccCch
Q psy12549        186 FIPRK  190 (336)
Q Consensus       186 ~~~~~  190 (336)
                      +.++.
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            87764

>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=99.80  E-value=1.4e-19  Score=123.96  Aligned_cols=76  Identities=26%  Similarity=0.464  Sum_probs=73.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      +|||+|||+++++++|+++|++||+|.++++..+++|.++|||||+|.+.++|..|++.|||..+.|++|.|.++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            5999999999999999999999999999999999999999999999999999999999999999999999998875

>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=99.80  E-value=7.6e-20  Score=126.82  Aligned_cols=77  Identities=31%  Similarity=0.525  Sum_probs=73.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ++|||+|||.++++++|+++|++||+|.++++..  .+|.++|||||+|.++++|++|++.|||..+.|+.|+|.||+|
T Consensus         3 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           3 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            6799999999999999999999999999999876  6788999999999999999999999999999999999999976

>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=99.80  E-value=2.3e-19  Score=127.13  Aligned_cols=81  Identities=20%  Similarity=0.330  Sum_probs=76.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      .+++|||+|||.++|+++|+++|++||+|.++.++.++ +|.++|||||+|.+.++|..|++.|||..+.|+.|.|.|+.
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            45899999999999999999999999999999999987 78899999999999999999999999999999999999986


Q ss_pred             Cc
Q psy12549        188 PR  189 (336)
Q Consensus       188 ~~  189 (336)
                      +.
T Consensus        86 ~~   87 (93)
T d1h2vz_          86 GF   87 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.80  E-value=6.6e-20  Score=129.04  Aligned_cols=81  Identities=25%  Similarity=0.448  Sum_probs=76.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||.++++++|+++|++||+|.++.++.++ +|.++|||||+|.+.++|.+|+..||+..++|+.|.|.++.|
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            4789999999999999999999999999999999987 689999999999999999999999999999999999999876


Q ss_pred             ch
Q psy12549        189 RK  190 (336)
Q Consensus       189 ~~  190 (336)
                      ..
T Consensus        85 ~~   86 (89)
T d2cqba1          85 MR   86 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.80  E-value=1.5e-19  Score=125.30  Aligned_cols=77  Identities=31%  Similarity=0.572  Sum_probs=73.3

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ++|||+|||.++++++|+++|++||+|.+++++.  .++.++|||||+|.++++|++|++.|||..+.|+.|+|.||+|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            5799999999999999999999999999999986  6788999999999999999999999999999999999999976

>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=99.80  E-value=1.4e-19  Score=127.60  Aligned_cols=81  Identities=28%  Similarity=0.514  Sum_probs=76.0

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ..++|||+|||.++++++|+++|+.||+|.++.++.  .+|.++|||||+|.+.++|.+|++.|||..++|+.|+|.||.
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~ak   86 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK   86 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            347899999999999999999999999999999887  578899999999999999999999999999999999999998


Q ss_pred             cch
Q psy12549        280 KKA  282 (336)
Q Consensus       280 ~~~  282 (336)
                      ++.
T Consensus        87 p~~   89 (90)
T d2cq0a1          87 PST   89 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            763

>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=99.79  E-value=2e-19  Score=126.14  Aligned_cols=79  Identities=27%  Similarity=0.421  Sum_probs=74.8

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||..+++++|+++|+.||+|.+++++.  .+|.++|||||+|.+.++|.+|+..|||..+.|+.|+|+||.+
T Consensus         7 ~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~   86 (88)
T d1rk8a_           7 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV   86 (88)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecC
Confidence            37899999999999999999999999999999876  6788999999999999999999999999999999999999986


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      +
T Consensus        87 k   87 (88)
T d1rk8a_          87 K   87 (88)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.79  E-value=1.5e-19  Score=127.20  Aligned_cols=79  Identities=30%  Similarity=0.495  Sum_probs=74.9

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||.++++++|+++|++||+|.++.++.  .+|.++|||||+|.+.++|.+|++.+||..++|+.|+|.++.+
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            47899999999999999999999999999999986  6688999999999999999999999999999999999999987


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      +
T Consensus        85 ~   85 (89)
T d2cqba1          85 M   85 (89)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.79  E-value=3.4e-19  Score=128.54  Aligned_cols=84  Identities=26%  Similarity=0.457  Sum_probs=78.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||+++++++|+++|+.||.+.++.++.++ +|.++|||||+|.+.++|..|++.|||..+.|+.|.|.++
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            345789999999999999999999999999999999986 7889999999999999999999999999999999999998


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      .++..
T Consensus        96 ~~k~~  100 (102)
T d2cpza1          96 RSKND  100 (102)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            87653

>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=99.78  E-value=2.6e-19  Score=123.30  Aligned_cols=76  Identities=29%  Similarity=0.491  Sum_probs=72.3

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       205 ~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      +|||+|||..+++++|+++|++||+|.+++++.  .+|.++|+|||+|.++++|.+|++.|||..+.|+.|+|.|+..
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            599999999999999999999999999999987  6688999999999999999999999999999999999999853

>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=99.78  E-value=2.6e-19  Score=122.57  Aligned_cols=75  Identities=25%  Similarity=0.436  Sum_probs=72.1

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       205 ~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      +|||+|||.++++++|+++|++||+|.++++.. .+|.++|+|||+|.++++|.+|++.|||..+.|+.|+|+++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            599999999999999999999999999999987 788899999999999999999999999999999999999986

>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=99.78  E-value=6.4e-19  Score=124.90  Aligned_cols=81  Identities=28%  Similarity=0.526  Sum_probs=76.1

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ..++|||+|||..+++++|+++|+.||+|.++.++...+.++|||||+|.++++|.+|+..|||..+.|+.|+|.+|.++
T Consensus        10 ~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r   89 (93)
T d2cq3a1          10 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR   89 (93)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcC
Confidence            34789999999999999999999999999999999866678999999999999999999999999999999999999887


Q ss_pred             h
Q psy12549        282 A  282 (336)
Q Consensus       282 ~  282 (336)
                      .
T Consensus        90 ~   90 (93)
T d2cq3a1          90 V   90 (93)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.78  E-value=6.7e-19  Score=122.18  Aligned_cols=75  Identities=25%  Similarity=0.430  Sum_probs=71.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      ..++|||+|||.++|+++|+++|++||.|.++.++.++ +|.++|||||+|.+.++|..|+..||+..+.|+.|.|
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            35789999999999999999999999999999999987 6889999999999999999999999999999999986

>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=99.78  E-value=4.3e-19  Score=125.73  Aligned_cols=80  Identities=25%  Similarity=0.310  Sum_probs=75.1

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ..++|||+|||..+++++|+++|++||+|.++.++.  .++.++|||||+|.+.++|..|++.|||..+.|+.|+|.|+.
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            448999999999999999999999999999999886  678889999999999999999999999999999999999987


Q ss_pred             cc
Q psy12549        280 KK  281 (336)
Q Consensus       280 ~~  281 (336)
                      +.
T Consensus        86 ~~   87 (93)
T d1h2vz_          86 GF   87 (93)
T ss_dssp             CC
T ss_pred             CC
Confidence            55

>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=99.78  E-value=2.8e-19  Score=123.56  Aligned_cols=78  Identities=14%  Similarity=0.269  Sum_probs=68.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ++|||+|||+++|+++|+++|++||.|..+.+..+. .|.++|||||+|.+.++|++|++.|||..+.|++|.|.++.|
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            689999999999999999999999999888777665 788999999999999999999999999999999999999876

>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=99.78  E-value=1.8e-19  Score=125.48  Aligned_cols=79  Identities=24%  Similarity=0.485  Sum_probs=75.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      .+|||+|||.++|+++|+++|++||+|.++++++++ +|.++|||||+|.++++|..|+..||+..+.|+.|.|.++.+.
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            369999999999999999999999999999999987 6999999999999999999999999999999999999998764

>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=99.78  E-value=8.2e-19  Score=123.60  Aligned_cols=82  Identities=22%  Similarity=0.358  Sum_probs=75.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||.++|+++|+++|+.||+|..+.++.++.+ .+|||||+|.+.++|..|+..++|..+.|+.|.|.++.
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            34579999999999999999999999999999999988644 47899999999999999999999999999999999987


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      ++.
T Consensus        85 ~~~   87 (90)
T d2cqia1          85 TPS   87 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            654

>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=99.78  E-value=5.6e-19  Score=122.98  Aligned_cols=77  Identities=26%  Similarity=0.512  Sum_probs=71.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEeec
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNS--KIVFVGKF  186 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~--~~i~v~~~  186 (336)
                      .++|||+|||+++|+++|+++|++||+|.+++++.++ +|.++|||||+|.++++|..|++.|||..+.|  ++|.|.|+
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            4789999999999999999999999999999999987 78999999999999999999999999999987  55888774

>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=99.78  E-value=4.9e-19  Score=125.70  Aligned_cols=83  Identities=18%  Similarity=0.420  Sum_probs=76.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC--CCCcccEEEEEeCCHHHHHHHHHHh-CCceeCCeEEEEe
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE--QGNSKGYGFVHFETEEAANKSIEKV-NGMLLNSKIVFVG  184 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~--~~~~~g~afV~F~~~~~a~~a~~~l-~~~~~~~~~i~v~  184 (336)
                      ...++|||+|||.++++++|+++|+.||.|.++.++++.  +|.++|||||+|.+.++|.+|++.| |+..+.|++|.|.
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            345789999999999999999999999999999998874  6889999999999999999999998 8999999999999


Q ss_pred             eccCch
Q psy12549        185 KFIPRK  190 (336)
Q Consensus       185 ~~~~~~  190 (336)
                      |+.+..
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            987653

>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=99.78  E-value=2.1e-19  Score=126.42  Aligned_cols=80  Identities=33%  Similarity=0.694  Sum_probs=75.3

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccchh
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKAE  283 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~~  283 (336)
                      .+|||+|||.++++++|+++|+.||.|..++++...+.++|||||+|.+.++|.+|++.|||..++|+.|.|.++.++.+
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~~   88 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE   88 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTTT
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            57999999999999999999999999999999986677899999999999999999999999999999999999987643

>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=99.78  E-value=6.5e-19  Score=126.52  Aligned_cols=84  Identities=29%  Similarity=0.490  Sum_probs=78.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+|||+++++++|+++|++||.|.++.++.++ +|.++|||||+|.+.++|..|++.||+..+.|+.|.|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            345789999999999999999999999999999999986 7899999999999999999999999999999999999998


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      .++..
T Consensus        86 ~~~~~   90 (99)
T d1whwa_          86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCCc
Confidence            87653

>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=99.78  E-value=2.8e-19  Score=123.56  Aligned_cols=77  Identities=17%  Similarity=0.342  Sum_probs=68.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ++|||+|||.++++++|+++|+.||+|..+.++.  ..|.++|+|||+|.+.++|.+|++.|||..+.|++|+|.++.|
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            6899999999999999999999999998887765  6788899999999999999999999999999999999999876

>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=99.78  E-value=7e-19  Score=122.62  Aligned_cols=79  Identities=23%  Similarity=0.465  Sum_probs=73.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEe
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNS--KIVFVG  184 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~--~~i~v~  184 (336)
                      ...++|||+|||.++++++|+++|++||.|..+++++++ +|.++|||||+|.+.++|.+|++.||+..+.|  ++|.|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            345789999999999999999999999999999999986 78999999999999999999999999999876  889998


Q ss_pred             ec
Q psy12549        185 KF  186 (336)
Q Consensus       185 ~~  186 (336)
                      |+
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            75

>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=99.78  E-value=5.3e-19  Score=124.58  Aligned_cols=81  Identities=21%  Similarity=0.357  Sum_probs=75.0

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ..++|||+|||..+++++|+++|+.||+|.++.+.......+|||||+|.+.++|.+|+..++|..+.|+.|+|.||.+.
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~   86 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTP   86 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCT
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCC
Confidence            34789999999999999999999999999999998865666899999999999999999999999999999999999865


Q ss_pred             h
Q psy12549        282 A  282 (336)
Q Consensus       282 ~  282 (336)
                      .
T Consensus        87 ~   87 (90)
T d2cqia1          87 S   87 (90)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.78  E-value=9.3e-19  Score=121.44  Aligned_cols=78  Identities=21%  Similarity=0.480  Sum_probs=73.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+|||.++|+++|+++|+.||.|..+.++.++ +|.++|||||+|.++++|++|++ +++..+.|+.|.|..+.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            34789999999999999999999999999999999997 69999999999999999999998 69999999999998764

>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=99.78  E-value=1.8e-19  Score=126.77  Aligned_cols=82  Identities=79%  Similarity=1.252  Sum_probs=75.5

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      .+..+|||+|||+++++++|+++|+.||.|..+.++.+..+ ++|||||+|.+.++|++|++.|||..+.|+.|.|.++.
T Consensus         6 s~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~-~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           6 SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTB-CCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34568999999999999999999999999999999988644 78999999999999999999999999999999999988


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      ++.
T Consensus        85 ~~~   87 (89)
T d1cvja2          85 SRK   87 (89)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            764

>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=99.78  E-value=2.4e-19  Score=127.05  Aligned_cols=80  Identities=25%  Similarity=0.404  Sum_probs=75.6

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||..+++++|+++|++||+|.++.++.  .+|.++|||||+|.+.++|++|++.|||..+.|+.|+|.+|.+
T Consensus         9 ~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~   88 (93)
T d1x5ua1           9 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASA   88 (93)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTT
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            37899999999999999999999999999999876  6788999999999999999999999999999999999999987


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      +.
T Consensus        89 ~~   90 (93)
T d1x5ua1          89 HN   90 (93)
T ss_dssp             TS
T ss_pred             CC
Confidence            64

>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=4e-19  Score=128.21  Aligned_cols=82  Identities=33%  Similarity=0.560  Sum_probs=76.3

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      +.++|||+|||.++++++|+++|+.||.+.++.++.  .+|.++|||||+|.++++|..|++.|||..+.|+.|+|+|+.
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            347899999999999999999999999999998876  678899999999999999999999999999999999999998


Q ss_pred             cchh
Q psy12549        280 KKAE  283 (336)
Q Consensus       280 ~~~~  283 (336)
                      ++.+
T Consensus        97 ~k~~  100 (102)
T d2cpza1          97 SKND  100 (102)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            8754

>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=99.77  E-value=2e-18  Score=122.28  Aligned_cols=83  Identities=29%  Similarity=0.534  Sum_probs=76.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ....++|||+|||+++++++|+++|+.||+|..|.++.++.+ ++|||||+|.+.++|.+|+..||+..+.|+.|.|.++
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            345678999999999999999999999999999999988755 6899999999999999999999999999999999999


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .++.
T Consensus        87 ~~r~   90 (93)
T d2cq3a1          87 TARV   90 (93)
T ss_dssp             CSSC
T ss_pred             CcCC
Confidence            8764

>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=99.77  E-value=1.3e-18  Score=122.19  Aligned_cols=80  Identities=23%  Similarity=0.405  Sum_probs=73.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+|||+++|+++|+++|+.||.|..+.++.++ +|.++|||||+|.++++|.+|++  ++..++|+.|.|.++.
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 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh--cCCccCCEEeEEEeCC
Confidence            45789999999999999999999999999999999997 79999999999999999999998  4558999999999987


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      ++.
T Consensus        85 ~k~   87 (90)
T d2cqga1          85 SKQ   87 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            754

>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=99.77  E-value=4.9e-19  Score=125.70  Aligned_cols=81  Identities=25%  Similarity=0.493  Sum_probs=75.0

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC---CCCccceEEEEEeCCHHHHHHHHHHh-CCceecCEEEEEee
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN---NDGKSRGFGFVAYESPEFAEKAVQAW-NGKEVDGKILYVGR  277 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~---~~~~~~g~afV~F~~~~~a~~a~~~l-~g~~~~g~~l~v~~  277 (336)
                      ..++|||+|||..+++++|+++|+.||.|.++.++.   .+|.++|||||+|.++++|.+|+..| ||..+.|++|+|.|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            347899999999999999999999999999999976   46889999999999999999999998 89999999999999


Q ss_pred             cccch
Q psy12549        278 AQKKA  282 (336)
Q Consensus       278 ~~~~~  282 (336)
                      |..+.
T Consensus        87 A~~~~   91 (94)
T d2cpha1          87 ADSEV   91 (94)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98764

>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=99.77  E-value=1.3e-18  Score=120.73  Aligned_cols=74  Identities=28%  Similarity=0.454  Sum_probs=69.7

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEE
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYV  275 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v  275 (336)
                      +.++|||+|||..+|+++|+++|++||.|.++.++.  .++.++|||||+|.+.++|.+|+..|||..+.|+.|+|
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            347899999999999999999999999999999876  66889999999999999999999999999999999987

>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=99.77  E-value=6e-19  Score=124.46  Aligned_cols=82  Identities=24%  Similarity=0.469  Sum_probs=76.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      +.++|||+|||+++++++|+++|++||.|..+.+..++ +|.++|||||+|.++++|..|+..|+|..+.|+.|.|.++.
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            45789999999999999999999999999999988876 78899999999999999999999999999999999999987


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      +..
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.76  E-value=2.3e-19  Score=122.18  Aligned_cols=75  Identities=25%  Similarity=0.443  Sum_probs=70.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ++|||+|||+++|+++|+++|++||.|.+++++.++ +|.++|||||+|.++++|++|++ ++++.++|+.|.|..+
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            579999999999999999999999999999999987 68999999999999999999998 7999999999999764

>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=99.76  E-value=4.3e-19  Score=123.50  Aligned_cols=79  Identities=25%  Similarity=0.562  Sum_probs=74.6

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      .+|||+|||..+++++|+++|+.||+|.+++++.  .+|.++|||||+|.++++|..|++.|||..+.|+.|.|.+|.+.
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            4699999999999999999999999999999987  67899999999999999999999999999999999999999865


Q ss_pred             h
Q psy12549        282 A  282 (336)
Q Consensus       282 ~  282 (336)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=1.3e-18  Score=124.93  Aligned_cols=81  Identities=27%  Similarity=0.474  Sum_probs=75.8

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||+.+++++|+++|++||+|.++.++.  .++.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.+
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            46799999999999999999999999999999986  6788999999999999999999999999999999999999987


Q ss_pred             chh
Q psy12549        281 KAE  283 (336)
Q Consensus       281 ~~~  283 (336)
                      +..
T Consensus        88 ~~~   90 (99)
T d1whwa_          88 KKE   90 (99)
T ss_dssp             CST
T ss_pred             CCc
Confidence            643

>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=99.76  E-value=9.6e-19  Score=126.86  Aligned_cols=83  Identities=25%  Similarity=0.528  Sum_probs=77.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||.++++++|+++|++||.|.++.++.++ +|.++|||||+|.+.++|..|++.||+..+.|+.|.|.++.+
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            3689999999999999999999999999999999987 788999999999999999999999999999999999999877


Q ss_pred             chhh
Q psy12549        189 RKER  192 (336)
Q Consensus       189 ~~~~  192 (336)
                      ....
T Consensus        88 ~~~~   91 (104)
T d1p1ta_          88 EKNK   91 (104)
T ss_dssp             TTHH
T ss_pred             CCCc
Confidence            6543

>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=99.76  E-value=5.3e-19  Score=126.97  Aligned_cols=77  Identities=18%  Similarity=0.399  Sum_probs=72.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ++|||+|||.++++++|+++|+.||.|.++.++.  .+|.++|||||+|.+.++|.+|++ |||..|.|+.|.|.++.++
T Consensus        19 ~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~~   97 (101)
T d2cq4a1          19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQAE   97 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCCC
Confidence            7899999999999999999999999999999987  578999999999999999999995 9999999999999998654

>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=99.76  E-value=1e-18  Score=118.58  Aligned_cols=74  Identities=31%  Similarity=0.592  Sum_probs=69.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      +|||+|||+++|+++|+++|++||+|..+.++.++ +|.++|||||+|.++++|++|++ +++..+.|+.|.|..+
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            48999999999999999999999999999999987 78899999999999999999998 7999999999998653

>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=99.76  E-value=8.6e-19  Score=121.66  Aligned_cols=78  Identities=45%  Similarity=0.764  Sum_probs=71.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEE-EEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCch
Q psy12549        113 VFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPRK  190 (336)
Q Consensus       113 l~v~nlp~~~t~~~l~~~f~~~G~v~~~-~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~~  190 (336)
                      |||+|||+++++++|+++|++||.|.++ .++.++ +|.++|||||+|.+.++|.+|++.++|..+.|++|.|.++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999998764 677776 78899999999999999999999999999999999999987654

>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=99.75  E-value=1.3e-18  Score=121.24  Aligned_cols=77  Identities=38%  Similarity=0.615  Sum_probs=70.2

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCC---ccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDG---KSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       206 l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~---~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      |||+|||.++++++|+++|++||+|.++.++.  .++   .++|||||+|.++++|.+|++.|||..++|+.|+|.++.+
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            79999999999999999999999999999886  222   4689999999999999999999999999999999999875


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            53

>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=99.75  E-value=1.3e-18  Score=124.90  Aligned_cols=79  Identities=24%  Similarity=0.338  Sum_probs=74.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||.++++++|+++|+.||.|.++.++.+. +|.++|||||+|.+.++|.+|++ |||..+.|+.|.|.++.+
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            4689999999999999999999999999999999986 79999999999999999999996 999999999999988754


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      +
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=99.75  E-value=1.7e-18  Score=120.60  Aligned_cols=75  Identities=33%  Similarity=0.581  Sum_probs=70.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecC--EEEEEeec
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG--KILYVGRA  278 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g--~~l~v~~~  278 (336)
                      ++|||+|||..+++++|+++|++||+|.+++++.  .+|.++|||||+|.++++|.+|++.|||..+.|  ++|+|.||
T Consensus         7 t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2           7 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            6799999999999999999999999999999886  678899999999999999999999999999987  88999986

>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=99.75  E-value=1.5e-18  Score=125.90  Aligned_cols=80  Identities=31%  Similarity=0.636  Sum_probs=75.3

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ++|||+|||.++++++|+++|+.||.|.++.++.  .+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.++.++
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            6899999999999999999999999999999886  67899999999999999999999999999999999999999876


Q ss_pred             hh
Q psy12549        282 AE  283 (336)
Q Consensus       282 ~~  283 (336)
                      ..
T Consensus        89 ~~   90 (104)
T d1p1ta_          89 KN   90 (104)
T ss_dssp             TH
T ss_pred             CC
Confidence            43

>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=99.75  E-value=3.4e-18  Score=118.79  Aligned_cols=77  Identities=19%  Similarity=0.216  Sum_probs=72.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      .++|||+|||.++|+++|+++|+.||+|..+.+..+++|.++|||||+|.++++|.+|++ +++..+.|+.|.|.+..
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            478999999999999999999999999999999999899999999999999999999997 79999999999998754

>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=99.75  E-value=3.4e-18  Score=123.44  Aligned_cols=80  Identities=24%  Similarity=0.422  Sum_probs=73.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+|||..+++++|+++|+.||.|.++.++.++ +|.++|||||+|.+.++|.+|++.+++ .+.|+.|.|.++.
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            34679999999999999999999999999999999987 689999999999999999999998776 7999999999876


Q ss_pred             Cc
Q psy12549        188 PR  189 (336)
Q Consensus       188 ~~  189 (336)
                      ..
T Consensus        88 ~~   89 (103)
T d2cqda1          88 LG   89 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=2.9e-18  Score=131.18  Aligned_cols=83  Identities=25%  Similarity=0.469  Sum_probs=77.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ..++|||+|||.++|+++|+++|+.||.|.++.+++++ +|.++|||||+|.+.++|..|++.|||..+.|+.|.|.++.
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            34689999999999999999999999999999999987 68899999999999999999999999999999999999987


Q ss_pred             Cchh
Q psy12549        188 PRKE  191 (336)
Q Consensus       188 ~~~~  191 (336)
                      +...
T Consensus       121 ~~~~  124 (139)
T d1u6fa1         121 SGHQ  124 (139)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.75  E-value=2.2e-18  Score=124.03  Aligned_cols=81  Identities=20%  Similarity=0.471  Sum_probs=75.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .++|||+|||+++++++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|.+|++ +++..+.|+.|.|.++.+
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            3689999999999999999999999999999999987 67899999999999999999997 799999999999999887


Q ss_pred             chh
Q psy12549        189 RKE  191 (336)
Q Consensus       189 ~~~  191 (336)
                      +..
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            643

>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=99.75  E-value=3.4e-18  Score=119.98  Aligned_cols=80  Identities=23%  Similarity=0.391  Sum_probs=72.9

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ..++|||+|||+++|+++|+++|+.||.|.++.++.  .+|.++|||||+|.++++|.+|++.  +..++|+.|.|.++.
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            347899999999999999999999999999999987  6799999999999999999999985  558999999999998


Q ss_pred             cchh
Q psy12549        280 KKAE  283 (336)
Q Consensus       280 ~~~~  283 (336)
                      ++..
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            7643

>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=99.75  E-value=2.6e-18  Score=119.76  Aligned_cols=77  Identities=29%  Similarity=0.513  Sum_probs=70.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCC-C---CcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQ-G---NSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       113 l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~-~---~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      |||+|||.++|+++|+++|+.||.|.++.+++++. +   .++|||||+|.+.++|.+|++.|||..++|+.|.|.++.+
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            79999999999999999999999999999998763 2   4689999999999999999999999999999999999754


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=8.3e-19  Score=123.72  Aligned_cols=81  Identities=35%  Similarity=0.620  Sum_probs=75.3

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||..+++++|+++|++||.|..+.++.  .++.++|||||+|.++++|++|++.|||..+.|+.|+|.++.+
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~   84 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGK   84 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEEC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            36799999999999999999999999999998876  7788999999999999999999999999999999999999987


Q ss_pred             chh
Q psy12549        281 KAE  283 (336)
Q Consensus       281 ~~~  283 (336)
                      +.+
T Consensus        85 ~~~   87 (90)
T d1x5sa1          85 SSD   87 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=1.2e-18  Score=120.99  Aligned_cols=77  Identities=26%  Similarity=0.556  Sum_probs=70.8

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCceeEE-EEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        206 VYIKNFGEDFNDEKLKEMFEPYGTITSY-RVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       206 l~V~nlp~~~t~~~l~~~f~~~g~i~~~-~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      |||+|||.++++++|+++|++||.|..+ .++.  .+|+++|||||+|.+.++|.+|++.|+|..++|++|+|.++.++.
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            7999999999999999999999998664 5655  678899999999999999999999999999999999999998764

>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=99.75  E-value=5e-18  Score=116.58  Aligned_cols=75  Identities=20%  Similarity=0.432  Sum_probs=70.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ++|||+|||+++|+++|+++|++||.+..+.+..++ ++.++|||||+|.++++|.+|++ +++..++|+.|.|..+
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            689999999999999999999999999999999987 78899999999999999999997 8999999999999865

>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=99.75  E-value=1.9e-18  Score=120.25  Aligned_cols=75  Identities=29%  Similarity=0.592  Sum_probs=70.2

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecC--EEEEEeec
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG--KILYVGRA  278 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g--~~l~v~~~  278 (336)
                      ++|||+|||..+++++|+++|++||+|.+++++.  .+|.++|||||+|.++++|.+|++.|||..+.|  ++|+|.||
T Consensus         7 ~~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           7 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            6799999999999999999999999999999986  578899999999999999999999999999998  55999886

>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=99.75  E-value=1.3e-18  Score=121.38  Aligned_cols=78  Identities=24%  Similarity=0.401  Sum_probs=68.9

Q ss_pred             cceEEEcCCCCCCc-HHHHHHhhccCCceeEEEEeC---CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        203 FTNVYIKNFGEDFN-DEKLKEMFEPYGTITSYRVMN---NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       203 ~~~l~V~nlp~~~t-~~~l~~~f~~~g~i~~~~i~~---~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      .++|||+|||.+++ +++|+++|++||.|.++++..   .++.++|+|||+|.+.++|.+|++ +||..++|+.|+|.++
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            37899999999976 556999999999999999865   577889999999999999999996 9999999999999999


Q ss_pred             ccc
Q psy12549        279 QKK  281 (336)
Q Consensus       279 ~~~  281 (336)
                      .++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            876

>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=99.74  E-value=1.8e-18  Score=120.64  Aligned_cols=80  Identities=20%  Similarity=0.387  Sum_probs=70.7

Q ss_pred             CCceEEEcCCCCCCC-HHHHHHHhhccCCeeEEEEeeCC--CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        109 GVGNVFIKNLDKSID-NKAMYDTFSAFGSILSCKVAQDE--QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t-~~~l~~~f~~~G~v~~~~~~~~~--~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      +.++|||+|||.+++ +++|+++|++||.|.++.++.+.  +|.++|||||+|.+.++|.+|++ +|+..++|+.|.|.+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            457899999999876 56699999999999999987753  78899999999999999999996 999999999999999


Q ss_pred             ccCc
Q psy12549        186 FIPR  189 (336)
Q Consensus       186 ~~~~  189 (336)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8764

>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=99.74  E-value=5.5e-18  Score=117.47  Aligned_cols=75  Identities=36%  Similarity=0.606  Sum_probs=70.7

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ++|||+|||.++++++|+++|+.||.|..+.++.  .+|.++|||||+|.++++|++|++ +++..+.|+.|+|..|.
T Consensus         7 ~~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           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            6899999999999999999999999999999886  678999999999999999999997 69999999999998875

>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=99.74  E-value=2e-18  Score=124.28  Aligned_cols=81  Identities=26%  Similarity=0.505  Sum_probs=75.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||+++++++|+++|+.||.|..+.+..+..+.++|||||+|.+.++|++|++.|||..+.|+++.+.++.
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            34578999999999999999999999999999999999888999999999999999999999999999999998887665


Q ss_pred             C
Q psy12549        188 P  188 (336)
Q Consensus       188 ~  188 (336)
                      |
T Consensus        96 P   96 (101)
T d1x5oa1          96 P   96 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=9.1e-19  Score=119.22  Aligned_cols=74  Identities=27%  Similarity=0.444  Sum_probs=69.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ++|||+|||.++++++|+++|++||.|.++.++.  .+|.++|||||+|.++++|++|++ +++..++|+.|.|..|
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            5799999999999999999999999999999987  668899999999999999999997 6999999999999875

>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=99.74  E-value=4.8e-18  Score=120.87  Aligned_cols=78  Identities=23%  Similarity=0.508  Sum_probs=72.6

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      +..++|||+|||..+++++|+++|++||+|.++++.+.    +|+|||+|.++++|.+|+..|||..+.|+.|+|.|+.+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~----kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            34478999999999999999999999999999999865    88999999999999999999999999999999999987


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      +.
T Consensus        92 ~p   93 (96)
T d1x4ga1          92 SP   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.73  E-value=5.3e-18  Score=122.06  Aligned_cols=79  Identities=28%  Similarity=0.532  Sum_probs=73.7

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ++|||+|||+++++++|+++|++||.|..+.+..  .++.++|||||+|.+.++|.+|++ ++|..|.|+.|.|.+|.++
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECccc
Confidence            6899999999999999999999999999999987  567889999999999999999996 7999999999999999887


Q ss_pred             hh
Q psy12549        282 AE  283 (336)
Q Consensus       282 ~~  283 (336)
                      .+
T Consensus       100 e~  101 (103)
T d1x4ba1         100 EE  101 (103)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.73  E-value=1.6e-18  Score=117.18  Aligned_cols=74  Identities=19%  Similarity=0.365  Sum_probs=68.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      +|||+|||+++|+++|+++|++||+|..+.++.++ +|.++|||||+|.+.++|++|++ .+++.+.|+.+.|..+
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            48999999999999999999999999999999997 78999999999999999999998 5788899999888653

>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=99.73  E-value=3.3e-18  Score=115.94  Aligned_cols=73  Identities=27%  Similarity=0.556  Sum_probs=68.4

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       205 ~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      .|||+|||+++++++|+++|++||+|..+.++.  .+++++|||||+|.++++|++|++ +++..+.|+.|.|..|
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            489999999999999999999999999999987  678899999999999999999997 7999999999999764

>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=99.73  E-value=3.9e-18  Score=130.46  Aligned_cols=80  Identities=29%  Similarity=0.517  Sum_probs=75.2

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||.++++++|+++|+.||.|.++.++.  .+|.++|||||+|.+.++|.+|++.|||..|+|+.|+|.++.+
T Consensus        42 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~  121 (139)
T d1u6fa1          42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS  121 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            36899999999999999999999999999999886  6788999999999999999999999999999999999999976


Q ss_pred             ch
Q psy12549        281 KA  282 (336)
Q Consensus       281 ~~  282 (336)
                      +.
T Consensus       122 ~~  123 (139)
T d1u6fa1         122 GH  123 (139)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=5.3e-18  Score=122.40  Aligned_cols=78  Identities=32%  Similarity=0.509  Sum_probs=72.1

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||..+++++|+++|+.||.|.++.++.  .+|.++|||||+|.+.++|.+|++.+++ .+.|+.|.|.++..
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~   88 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYL   88 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTT
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCC
Confidence            36799999999999999999999999999999987  5688999999999999999999998876 79999999999875


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      +
T Consensus        89 ~   89 (103)
T d2cqda1          89 G   89 (103)
T ss_dssp             T
T ss_pred             C
Confidence            5

>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=1e-17  Score=123.61  Aligned_cols=78  Identities=28%  Similarity=0.382  Sum_probs=72.5

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      .++|||+|||.++++++|+++|+.||.|.+|.+.. ++.++|||||+|.+.++|..|++.|||..|.|+.|+|.++...
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 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN-TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNAN   84 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC-STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc-cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            47899999999999999999999999999998875 4667999999999999999999999999999999999998654

>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=99.73  E-value=1e-18  Score=123.10  Aligned_cols=80  Identities=21%  Similarity=0.290  Sum_probs=74.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ....+|||+|||.++++++|+++|+.||.|..+.++.+.+|.++|||||+|.+.++|++|++ +|+..+.|+.|.|.++.
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecC
Confidence            34568999999999999999999999999998888877789999999999999999999996 99999999999999886


Q ss_pred             C
Q psy12549        188 P  188 (336)
Q Consensus       188 ~  188 (336)
                      .
T Consensus        90 ~   90 (91)
T d1fjeb1          90 G   90 (91)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.73  E-value=1.4e-17  Score=119.35  Aligned_cols=83  Identities=28%  Similarity=0.451  Sum_probs=75.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhC------CceeCCeE
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVN------GMLLNSKI  180 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~------~~~~~~~~  180 (336)
                      .+.++|||+|||.++|+++|+++|++||.+..+.+..++ .+.++|||||+|.+.++|.+|++.++      |..+.|+.
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            345789999999999999999999999999999998887 67899999999999999999999886      56789999


Q ss_pred             EEEeeccCch
Q psy12549        181 VFVGKFIPRK  190 (336)
Q Consensus       181 i~v~~~~~~~  190 (336)
                      |.|.++.++.
T Consensus        86 l~v~~a~~k~   95 (98)
T d1x4ha1          86 LKVDLAVTRD   95 (98)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEECCCCC
Confidence            9999987754

>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=99.72  E-value=1.4e-17  Score=114.37  Aligned_cols=74  Identities=30%  Similarity=0.582  Sum_probs=69.3

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ++|||+|||+++|+++|+++|++||.|..+.+..  .++.++|+|||+|.++++|.+|++ ++|..++|+.|.|..|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            6899999999999999999999999999998876  677889999999999999999996 8999999999999876

>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=1.6e-17  Score=122.57  Aligned_cols=79  Identities=22%  Similarity=0.400  Sum_probs=72.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      .+++|||+|||.++++++|+++|+.||.|.+|.+..+  +.++|||||+|.+.++|..|++.|||..+.|+.|.|.++.+
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~--~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc--CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4578999999999999999999999999999998764  56789999999999999999999999999999999998764


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      .
T Consensus        84 ~   84 (114)
T d2f9da1          84 N   84 (114)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=99.72  E-value=1e-17  Score=113.36  Aligned_cols=74  Identities=23%  Similarity=0.286  Sum_probs=68.4

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ++|||+|||+++++++|+++|+.||+|..+.+....+..+++|||+|.++++|.+|+. +++..|+|+.|.|+.+
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            4799999999999999999999999999999988556667899999999999999995 8999999999999875

>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=99.72  E-value=6.9e-18  Score=117.50  Aligned_cols=76  Identities=28%  Similarity=0.497  Sum_probs=71.2

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      .++|||+|||.++++++|+++|++||+|.++.+.+.    +++|||+|.+.++|.+|+..|||..+.|+.|+|+||....
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 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   83 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCcC
Confidence            367999999999999999999999999999999864    7899999999999999999999999999999999998763

>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=99.72  E-value=1.5e-17  Score=118.29  Aligned_cols=76  Identities=30%  Similarity=0.467  Sum_probs=71.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      .++|||+|||.++++++|+++|++||.|.+++++++     +|||||+|.+.++|.+|+..|+|..+.|+.|.|.|+.+.
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 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            478999999999999999999999999999999975     689999999999999999999999999999999998764


Q ss_pred             h
Q psy12549        190 K  190 (336)
Q Consensus       190 ~  190 (336)
                      .
T Consensus        93 p   93 (96)
T d1x4ga1          93 P   93 (96)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.72  E-value=5.4e-18  Score=115.24  Aligned_cols=74  Identities=26%  Similarity=0.448  Sum_probs=69.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      +|||+|||+++|+++|+++|+.||.+..+.+..++ +|.+++||||+|.+.++|++|++ +|+..++|++|.|.++
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            48999999999999999999999999999998887 68899999999999999999997 9999999999999764

>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=99.72  E-value=1.9e-17  Score=114.96  Aligned_cols=75  Identities=27%  Similarity=0.321  Sum_probs=70.7

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ++|||+|||.++|+++|+++|+.||+|..+.+.. .+|.++|+|||+|.++++|.+|++ ++|..+.|+.|.|.+..
T Consensus         7 rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           7 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            7899999999999999999999999999999977 778899999999999999999996 79999999999998864

>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=99.72  E-value=1.2e-17  Score=119.79  Aligned_cols=82  Identities=29%  Similarity=0.462  Sum_probs=74.3

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhC------CceecCEEE
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWN------GKEVDGKIL  273 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~------g~~~~g~~l  273 (336)
                      ..++|||+|||..+++++|+++|++||++..+.+..  ..+.++|||||+|.+.++|.+|++.++      |..+.|+.|
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l   86 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL   86 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEE
Confidence            347899999999999999999999999999998876  567789999999999999999999886      677899999


Q ss_pred             EEeecccchh
Q psy12549        274 YVGRAQKKAE  283 (336)
Q Consensus       274 ~v~~~~~~~~  283 (336)
                      +|.++.++.+
T Consensus        87 ~v~~a~~k~~   96 (98)
T d1x4ha1          87 KVDLAVTRDE   96 (98)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEECCCCCc
Confidence            9999988753

>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=99.72  E-value=7.3e-19  Score=123.85  Aligned_cols=79  Identities=25%  Similarity=0.374  Sum_probs=72.6

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ...+|||+|||.++++++|+++|+.||.|..+.++. .+|.++|||||+|.+.++|++|++ +||..+.|+.|+|.++..
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            346899999999999999999999999998887765 678899999999999999999996 999999999999999876


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      +
T Consensus        91 k   91 (91)
T d1fjeb1          91 R   91 (91)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.71  E-value=2.1e-17  Score=117.49  Aligned_cols=80  Identities=28%  Similarity=0.439  Sum_probs=72.5

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.+.. ++.++++|||+|.+.++|..|++.|||..+.|+.|+|+|+++
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~-~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN-RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC-SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc-cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            3447899999999999999999999999999988764 345689999999999999999999999999999999999875


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      .
T Consensus        91 ~   91 (95)
T d1x4aa1          91 G   91 (95)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.71  E-value=3.8e-17  Score=116.11  Aligned_cols=80  Identities=19%  Similarity=0.279  Sum_probs=72.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...++|||+|||+++++++|+++|+.||.|..+.+..+  +.+++||||+|.+.++|..|++.||+..+.|++|.|.++.
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~   89 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   89 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecc
Confidence            44578999999999999999999999999999887654  3468999999999999999999999999999999999987


Q ss_pred             Cc
Q psy12549        188 PR  189 (336)
Q Consensus       188 ~~  189 (336)
                      +.
T Consensus        90 ~~   91 (95)
T d1x4aa1          90 SG   91 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.71  E-value=6.2e-18  Score=121.68  Aligned_cols=78  Identities=31%  Similarity=0.545  Sum_probs=72.5

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .++|||+|||.++++++|+++|+.||.|..+.+.. .++.++|||||+|.+.++|.+|++.|||..+.|+++.|.++.|
T Consensus        18 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            47899999999999999999999999999998877 6788899999999999999999999999999999998877765

>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=99.71  E-value=1.9e-17  Score=119.32  Aligned_cols=83  Identities=19%  Similarity=0.303  Sum_probs=74.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCee--------EEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCC
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSIL--------SCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNS  178 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~--------~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~  178 (336)
                      ...++|||+|||.++|+++|+++|+.||.|.        .+.+..++ +|.++|||||+|.+.++|.+|++.|||..+.|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            3457999999999999999999999999874        45566665 68899999999999999999999999999999


Q ss_pred             eEEEEeeccCch
Q psy12549        179 KIVFVGKFIPRK  190 (336)
Q Consensus       179 ~~i~v~~~~~~~  190 (336)
                      +.|.|.++.++.
T Consensus        86 r~i~V~~a~~~~   97 (101)
T d2cpea1          86 SKLKVSLARKKP   97 (101)
T ss_dssp             EECEEECSSCCC
T ss_pred             EEEEEEEcCCCC
Confidence            999999987754

>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=99.71  E-value=7.9e-18  Score=114.40  Aligned_cols=73  Identities=26%  Similarity=0.543  Sum_probs=68.3

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       205 ~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      .|||+|||.++|+++|+++|+.||.+..+.+..  .++.++++|||+|.+.++|.+|++ +||..++|+.|+|.+|
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            489999999999999999999999999998876  567889999999999999999997 9999999999999875

>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=99.70  E-value=1e-17  Score=119.39  Aligned_cols=82  Identities=18%  Similarity=0.285  Sum_probs=73.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCC-eeEEEEeeCC--CCCcccEEEEEeCCHHHHHHHHHHhCC--ceeCCeEEEEee
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGS-ILSCKVAQDE--QGNSKGYGFVHFETEEAANKSIEKVNG--MLLNSKIVFVGK  185 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~-v~~~~~~~~~--~~~~~g~afV~F~~~~~a~~a~~~l~~--~~~~~~~i~v~~  185 (336)
                      ++|||+|||.++++++|+++|++||+ +..+.++.+.  .|.++|||||+|.+.++|..|++.|++  ..++|+.|.|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            68999999999999999999999996 8999999875  578999999999999999999998864  456899999999


Q ss_pred             ccCchhh
Q psy12549        186 FIPRKER  192 (336)
Q Consensus       186 ~~~~~~~  192 (336)
                      +.+....
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9876544

>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=99.70  E-value=2.8e-17  Score=114.60  Aligned_cols=77  Identities=26%  Similarity=0.353  Sum_probs=70.6

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      .++|||+|||..+++++|+++|+.||.+..+.+..    ++|+|||+|.++++|.+|+..|||..+.|+.|.|.|+.|+.
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~----~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc----ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            36899999999999999999999999998887743    58899999999999999999999999999999999998764


Q ss_pred             h
Q psy12549        283 E  283 (336)
Q Consensus       283 ~  283 (336)
                      +
T Consensus        84 ~   84 (86)
T d2cpda1          84 K   84 (86)
T ss_dssp             C
T ss_pred             C
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=99.70  E-value=4.8e-18  Score=116.67  Aligned_cols=76  Identities=26%  Similarity=0.478  Sum_probs=68.8

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCc-eecCEEEEEeecccch
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGK-EVDGKILYVGRAQKKA  282 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~-~~~g~~l~v~~~~~~~  282 (336)
                      ++|||+|||.++++++|+++|++||.+..+.+..    ++|||||+|.++++|.+|++.|||. .+.|+.|+|.|+.++.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~----~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~   77 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL----KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   77 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE----ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec----ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcC
Confidence            5799999999999999999999999987766653    4899999999999999999999996 6999999999999875


Q ss_pred             h
Q psy12549        283 E  283 (336)
Q Consensus       283 ~  283 (336)
                      +
T Consensus        78 ~   78 (80)
T d2cqha1          78 L   78 (80)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=1.9e-17  Score=113.43  Aligned_cols=74  Identities=30%  Similarity=0.438  Sum_probs=68.6

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ..++|||+|++  +|+++|+++|++||.|.++.+.+.    +++|||+|.+.++|.+|+..|||..+.|+.|+|.|+.++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP----RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            34789999986  899999999999999999999754    789999999999999999999999999999999999876

>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=99.70  E-value=2.3e-17  Score=117.52  Aligned_cols=80  Identities=28%  Similarity=0.445  Sum_probs=72.3

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ...++|||+|||.++++++|+++|+.||.|..+.   .++.+++||||+|.+.++|.+|++.|||..+.|+.|+|.|+.+
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~---~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~   90 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS---QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE---ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee---ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            3458899999999999999999999999887664   3677899999999999999999999999999999999999988


Q ss_pred             chh
Q psy12549        281 KAE  283 (336)
Q Consensus       281 ~~~  283 (336)
                      +..
T Consensus        91 k~~   93 (96)
T d1fjca_          91 KGG   93 (96)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            743

>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=99.70  E-value=2.7e-17  Score=115.23  Aligned_cols=74  Identities=24%  Similarity=0.363  Sum_probs=66.3

Q ss_pred             cceEEEcCCCCCCcHHHH---HHhhccCCceeEEEEeC--CCC---ccceEEEEEeCCHHHHHHHHHHhCCceecCEEEE
Q psy12549        203 FTNVYIKNFGEDFNDEKL---KEMFEPYGTITSYRVMN--NDG---KSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILY  274 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l---~~~f~~~g~i~~~~i~~--~~~---~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~  274 (336)
                      .++|||+|||+++++++|   +++|++||+|..+.+.+  .++   ..+|+|||+|.++++|.+|++.|||..++|+.|+
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            367999999999999999   77899999999999987  222   3458999999999999999999999999999999


Q ss_pred             Ee
Q psy12549        275 VG  276 (336)
Q Consensus       275 v~  276 (336)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>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=99.70  E-value=2.6e-17  Score=114.56  Aligned_cols=75  Identities=25%  Similarity=0.390  Sum_probs=70.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      .++|||+|||.++++++|+++|++||.|.++.+.++     ++||||+|.+.++|..|+..|||..+.|+.|.|.++.+.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCc
Confidence            467999999999999999999999999999999864     679999999999999999999999999999999998765

>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=99.70  E-value=1.5e-17  Score=117.27  Aligned_cols=82  Identities=24%  Similarity=0.394  Sum_probs=72.8

Q ss_pred             cceEEEcCCCCCCcHHHHHH----hhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        203 FTNVYIKNFGEDFNDEKLKE----MFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~----~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      .++|||+|||..+++++|++    +|++||+|.++.+.. ++.++|+|||+|.+.++|.+|++.+||..+.|+.|+|.|+
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~-~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~a   81 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA   81 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH-HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee-eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            47899999999999998864    689999999988754 4567899999999999999999999999999999999999


Q ss_pred             ccchhhH
Q psy12549        279 QKKAERT  285 (336)
Q Consensus       279 ~~~~~~~  285 (336)
                      .++.+..
T Consensus        82 k~~~~~~   88 (91)
T d1nu4a_          82 KTDSDII   88 (91)
T ss_dssp             SSCCTHH
T ss_pred             CCCchhh
Confidence            8875543

>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=99.70  E-value=2.6e-17  Score=118.62  Aligned_cols=82  Identities=27%  Similarity=0.485  Sum_probs=71.9

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeE--------EEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCE
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITS--------YRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK  271 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~--------~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~  271 (336)
                      ..++|||+|||..+++++|+++|+.||+|..        +.+..  .+|.++|+|||+|.++++|.+|++.|||..|.|+
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr   86 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGS   86 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCE
Confidence            3478999999999999999999999998853        33333  4578899999999999999999999999999999


Q ss_pred             EEEEeecccchh
Q psy12549        272 ILYVGRAQKKAE  283 (336)
Q Consensus       272 ~l~v~~~~~~~~  283 (336)
                      .|+|+++.++..
T Consensus        87 ~i~V~~a~~~~p   98 (101)
T d2cpea1          87 KLKVSLARKKPP   98 (101)
T ss_dssp             ECEEECSSCCCC
T ss_pred             EEEEEEcCCCCC
Confidence            999999987643

>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=99.69  E-value=4.2e-17  Score=114.23  Aligned_cols=79  Identities=18%  Similarity=0.217  Sum_probs=70.3

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCcee-cCEEEEEeecc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEV-DGKILYVGRAQ  279 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~-~g~~l~v~~~~  279 (336)
                      ++.++|||+|||.++++++|+++|+.||.|..+.+..  +.++++|||+|.+.++|.+|+..|||..+ +|+.|+|+|++
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~--~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk   85 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF--QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK   85 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC--SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee--ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCC
Confidence            4457899999999999999999999999998877654  34578999999999999999999999998 58999999987


Q ss_pred             cc
Q psy12549        280 KK  281 (336)
Q Consensus       280 ~~  281 (336)
                      +.
T Consensus        86 ~~   87 (88)
T d2adca2          86 ST   87 (88)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>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=99.69  E-value=3.8e-17  Score=113.03  Aligned_cols=76  Identities=17%  Similarity=0.295  Sum_probs=69.3

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCcee-cCEEEEEeecc
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEV-DGKILYVGRAQ  279 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~-~g~~l~v~~~~  279 (336)
                      ++.++|||+|||..+++++|+++|+.||+|..+++.+.   .+|+|||+|.+.++|.+|+..|||..+ +|+.|+|+||+
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 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN---RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT---TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc---cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            34589999999999999999999999999999999763   368999999999999999999999998 46899999986

>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=99.69  E-value=4.2e-18  Score=123.07  Aligned_cols=83  Identities=22%  Similarity=0.337  Sum_probs=76.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      .+++|||+|||.++++++|+++|+.||.|..+.+..+. +|.++|||||+|.+.++|..|++.|||..+.|+.|.|.++.
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            35789999999999999999999999999988888775 78899999999999999999999999999999999999998


Q ss_pred             Cchh
Q psy12549        188 PRKE  191 (336)
Q Consensus       188 ~~~~  191 (336)
                      ++.+
T Consensus        97 ~k~~  100 (102)
T d2cpxa1          97 NKKQ  100 (102)
T ss_dssp             CCSC
T ss_pred             Cccc
Confidence            7653

>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=99.69  E-value=6.5e-18  Score=114.13  Aligned_cols=73  Identities=22%  Similarity=0.407  Sum_probs=67.5

Q ss_pred             eEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        205 NVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       205 ~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      .|||+|||+++|+++|+++|++||+|.++.++.  .++.++|||||+|.+.++|++|++. ++..++|+.+.|..|
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 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            489999999999999999999999999999887  6788999999999999999999974 788999999998765

>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=99.69  E-value=6.3e-17  Score=109.41  Aligned_cols=74  Identities=23%  Similarity=0.380  Sum_probs=68.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ++|||+|||+++++++|+++|+.||.|..+.+..++.+. ++||||+|.++++|.+|+. +++..++|+.|.|...
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            479999999999999999999999999999999987654 5799999999999999996 8999999999999754

>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=99.69  E-value=2.5e-18  Score=124.27  Aligned_cols=82  Identities=23%  Similarity=0.385  Sum_probs=75.6

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      +.++|||+|||.++++++|+++|+.||.|..+.+..  .+|.++|||||+|.+.++|.+|++.|||..+.|+.|+|.|+.
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            347899999999999999999999999998877765  678899999999999999999999999999999999999999


Q ss_pred             cchh
Q psy12549        280 KKAE  283 (336)
Q Consensus       280 ~~~~  283 (336)
                      ++.+
T Consensus        97 ~k~~  100 (102)
T d2cpxa1          97 NKKQ  100 (102)
T ss_dssp             CCSC
T ss_pred             Cccc
Confidence            8754

>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=2e-17  Score=121.47  Aligned_cols=77  Identities=18%  Similarity=0.163  Sum_probs=70.6

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ..++|||+|||..+++++|+++|+.||+|..+.+.+    ++++|||+|.+.++|.+|++.|||..|.|+.|.|+|+...
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~----~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec----cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            347899999999999999999999999999998854    4789999999999999999999999999999999998654


Q ss_pred             h
Q psy12549        282 A  282 (336)
Q Consensus       282 ~  282 (336)
                      .
T Consensus        85 ~   85 (111)
T d1whxa_          85 V   85 (111)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=99.68  E-value=1.2e-16  Score=111.38  Aligned_cols=76  Identities=24%  Similarity=0.373  Sum_probs=69.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      .++|||+|||+++++++|+++|+.||.+..+.+..     ++|||||+|.+.++|..|+..|||..+.|+.|.|.++.|.
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~-----~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~   82 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   82 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc-----ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCC
Confidence            47899999999999999999999999988777754     4789999999999999999999999999999999998865


Q ss_pred             h
Q psy12549        190 K  190 (336)
Q Consensus       190 ~  190 (336)
                      .
T Consensus        83 ~   83 (86)
T d2cpda1          83 D   83 (86)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.68  E-value=7.7e-17  Score=111.46  Aligned_cols=75  Identities=17%  Similarity=0.273  Sum_probs=68.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcee-CCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLL-NSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~-~~~~i~v~~~~  187 (336)
                      .+++|||+|||.++++++|.++|+.||+|..+++.++    .+|||||+|.+.++|..|+..|+|..+ +|+.|.|.|+.
T Consensus         7 P~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1           7 PNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            4579999999999999999999999999999999865    367999999999999999999999888 57899999875

>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=99.68  E-value=1.1e-17  Score=112.62  Aligned_cols=69  Identities=25%  Similarity=0.546  Sum_probs=65.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEE
Q psy12549        113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIV  181 (336)
Q Consensus       113 l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i  181 (336)
                      |||+|||.++|+++|+++|++||.|..+++..++ ++.++|+|||+|.+.++|++|++.|||..+.|+.+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            7999999999999999999999999999999887 78899999999999999999999999999999865

>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=99.68  E-value=6.5e-17  Score=112.76  Aligned_cols=78  Identities=19%  Similarity=0.270  Sum_probs=71.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeE-EEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILS-CKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~-~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ....|||+|||.++++++|+++|+.||.+.. +.+..+++|.++|+|||+|.+.++|.+|+..||+..+.|++|.|.++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3467999999999999999999999999876 56777778999999999999999999999999999999999999753

>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=99.68  E-value=4.2e-17  Score=114.21  Aligned_cols=75  Identities=17%  Similarity=0.346  Sum_probs=67.5

Q ss_pred             CceEEEcCCCCCCCHHHH---HHHhhccCCeeEEEEeeCC-CC---CcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEE
Q psy12549        110 VGNVFIKNLDKSIDNKAM---YDTFSAFGSILSCKVAQDE-QG---NSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVF  182 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l---~~~f~~~G~v~~~~~~~~~-~~---~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~  182 (336)
                      ..+|||+|||+++++++|   +++|++||.|..+.+++++ ++   ..+|||||+|.++++|.+|++.|||..++|+.|+
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            457999999999999999   7789999999999999886 33   3458999999999999999999999999999998


Q ss_pred             Ee
Q psy12549        183 VG  184 (336)
Q Consensus       183 v~  184 (336)
                      +.
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            73

>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=99.68  E-value=2.2e-17  Score=113.27  Aligned_cols=75  Identities=25%  Similarity=0.391  Sum_probs=67.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCc-eeCCeEEEEeeccCch
Q psy12549        112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGM-LLNSKIVFVGKFIPRK  190 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~-~~~~~~i~v~~~~~~~  190 (336)
                      +|||+|||+++|+++|+++|++||.+..+.+..     ++|||||+|.+.++|..|++.|||. .+.|+.|.|.++.++.
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~-----~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~   77 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK   77 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-----ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec-----ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcC
Confidence            599999999999999999999999988766665     4789999999999999999999986 6999999999998764


Q ss_pred             h
Q psy12549        191 E  191 (336)
Q Consensus       191 ~  191 (336)
                      .
T Consensus        78 ~   78 (80)
T d2cqha1          78 L   78 (80)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.68  E-value=1.5e-17  Score=111.98  Aligned_cols=69  Identities=32%  Similarity=0.629  Sum_probs=64.8

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEE
Q psy12549        206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILY  274 (336)
Q Consensus       206 l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~  274 (336)
                      |||+|||.++++++|+++|+.||+|..+++..  .++.++|+|||+|.++++|.+|++.|||..+.|+.|+
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            79999999999999999999999999998887  6788899999999999999999999999999998763

>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=99.68  E-value=1.4e-16  Score=107.72  Aligned_cols=71  Identities=20%  Similarity=0.338  Sum_probs=64.4

Q ss_pred             EEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        206 VYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       206 l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      |||+|||.++++++|+++|++|| +..+.+.    .++|+|||+|.+.++|.+|++.|||..+.|++|+|++++..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~----~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD----KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE----TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec----ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 5555553    45899999999999999999999999999999999999754

>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=99.68  E-value=4.6e-17  Score=113.55  Aligned_cols=76  Identities=20%  Similarity=0.243  Sum_probs=68.8

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeE-EEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITS-YRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~-~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ...|+|+|||.++++++|+++|+.||.+.. +.+.. .++.++|+|||+|.+.++|.+|++.|||..+.|+.|+|+++
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            367999999999999999999999999865 34444 78899999999999999999999999999999999999875

>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=7e-17  Score=114.97  Aligned_cols=81  Identities=21%  Similarity=0.314  Sum_probs=72.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        107 KSGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ....++|||+|||.++|+++|+++|+.||.|..+.    .++.++|||||+|.+.++|.+|++.||+..+.|+.|.|.++
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            34468999999999999999999999999876554    25678999999999999999999999999999999999998


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      .++..
T Consensus        89 ~~k~~   93 (96)
T d1fjca_          89 GEKGG   93 (96)
T ss_dssp             SSSCC
T ss_pred             CCCCC
Confidence            87653

>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=99.67  E-value=2.2e-17  Score=117.71  Aligned_cols=81  Identities=22%  Similarity=0.259  Sum_probs=71.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCc-eeEEEEeC---CCCccceEEEEEeCCHHHHHHHHHHhCCc--eecCEEEEEee
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGT-ITSYRVMN---NDGKSRGFGFVAYESPEFAEKAVQAWNGK--EVDGKILYVGR  277 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~-i~~~~i~~---~~~~~~g~afV~F~~~~~a~~a~~~l~g~--~~~g~~l~v~~  277 (336)
                      ++|||+|||.++++++|+++|+.||+ |..+.++.   .++.++|||||+|.++++|.+|++.|++.  .++|+.|+|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            57999999999999999999999996 88998876   45788999999999999999999998654  45799999999


Q ss_pred             cccchhh
Q psy12549        278 AQKKAER  284 (336)
Q Consensus       278 ~~~~~~~  284 (336)
                      |.++.+.
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9887544

>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=99.67  E-value=9.7e-17  Score=114.37  Aligned_cols=73  Identities=27%  Similarity=0.497  Sum_probs=67.5

Q ss_pred             cceEEEcCCC-CCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        203 FTNVYIKNFG-EDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       203 ~~~l~V~nlp-~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      .++|||+||| ..+++++|+++|++||.|.++.+.      +|||||+|.+.++|.+|++.|||..+.|+.|+|.++.++
T Consensus        15 ~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          15 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             CCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            3679999997 578889999999999999999984      899999999999999999999999999999999999754

>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=99.67  E-value=1.1e-16  Score=111.83  Aligned_cols=74  Identities=22%  Similarity=0.345  Sum_probs=65.7

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      .++|||+|||.++++++|+++|++|| +..+.+    +.++++|||+|.+.++|.+|++.|||..+.|++|+|+++..+
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~----~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV----DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE----EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee----eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            36899999999999999999999999 333433    345899999999999999999999999999999999998765

>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=99.66  E-value=1.7e-16  Score=114.81  Aligned_cols=80  Identities=18%  Similarity=0.313  Sum_probs=71.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC--CCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE--QGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~--~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ..++|||+|||.++|+++|+++|+.|| +..+.++.++  ++.++|||||+|.+.++|++|++ ||+..+.|+.|.|.++
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-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEEC
Confidence            458999999999999999999999999 6777777764  67889999999999999987775 9999999999999998


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .+..
T Consensus        92 ~~~~   95 (104)
T d1wi8a_          92 DQAQ   95 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.66  E-value=1.1e-16  Score=117.09  Aligned_cols=76  Identities=16%  Similarity=0.317  Sum_probs=69.8

Q ss_pred             CceEEEcCCCC-CCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDK-SIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~-~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      +++|||+|||+ .+|+++|+++|+.||.|..+.+++++    +|||||+|.+.++|.+|++.|+|..+.|+.|.|.++..
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~~   77 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   77 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            57899999965 69999999999999999999999874    67999999999999999999999999999999999864


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      .
T Consensus        78 ~   78 (109)
T d2adca1          78 Q   78 (109)
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=99.66  E-value=1.1e-16  Score=115.76  Aligned_cols=79  Identities=23%  Similarity=0.392  Sum_probs=69.4

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC---CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN---NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~---~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      +.++|||+|||.++++++|+++|+.|| +..+.++.   .++.++|||||+|.+.++|++|+ .+|+..|.|+.|+|.++
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            347899999999999999999999999 66666654   46788999999999999998777 59999999999999999


Q ss_pred             ccch
Q psy12549        279 QKKA  282 (336)
Q Consensus       279 ~~~~  282 (336)
                      .++.
T Consensus        92 ~~~~   95 (104)
T d1wi8a_          92 DQAQ   95 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>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=99.66  E-value=2.2e-16  Score=110.50  Aligned_cols=77  Identities=12%  Similarity=0.157  Sum_probs=68.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcee-CCeEEEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLL-NSKIVFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~-~~~~i~v~~~~~  188 (336)
                      +++|||+|||.++++++|+++|++||.+..+.+...   .++|+|||+|.+.++|.+|+..|+|..+ +|+.|.|.++++
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~---~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS---SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee---cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            478999999999999999999999999988776654   3578999999999999999999999988 589999999865


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      .
T Consensus        87 ~   87 (88)
T d2adca2          87 T   87 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.66  E-value=2e-17  Score=115.47  Aligned_cols=74  Identities=16%  Similarity=0.141  Sum_probs=68.3

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      ++|||+|||..+++++|+++|+.||+|.++.+..     .|+|||+|.+.++|.+|+..|||..|.|+.|+|.++..+.
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 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-----DGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT-----TSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc-----cceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            3699999999999999999999999999999864     4899999999999999999999999999999999886554

>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=99.66  E-value=1.9e-16  Score=113.93  Aligned_cols=82  Identities=15%  Similarity=0.142  Sum_probs=72.6

Q ss_pred             ccCceeeeecCchhhhhhhHHhhhcccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeE
Q psy12549         16 IPKHNVATRELSAKVVEGVSRSLSSLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIR   95 (336)
Q Consensus        16 ~p~~~v~v~~lp~~~~e~~l~~~f~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~   95 (336)
                      .+..+|+|+|||+++||++|+++|..+++..+.++.+.    +|+++|||||+|.++  ++|++|++ +|+..|.||.|+
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~~~v~~~~~~----~g~~~G~afVeF~~~--~~a~~Al~-~~~~~i~gR~I~   85 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGP----DGRVTGEADVEFATH--EDAVAAMA-KDKANMQHRYVE   85 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCSEEEEEESS----SSCEEEEEEEECSSS--HHHHHHHT-TSSCCSSSSCCE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCcceeeeEEec----CCcceEEEEEEECCH--HHHHHHHH-cCCCEECCEEEE
Confidence            34457999999999999999999977778888888765    488999999999999  99999997 899999999999


Q ss_pred             EEeccCCCC
Q psy12549         96 IMWSQRDPS  104 (336)
Q Consensus        96 v~~~~~~~~  104 (336)
                      |.++...+.
T Consensus        86 V~~s~~~~~   94 (102)
T d1weza_          86 LFLNSTAGT   94 (102)
T ss_dssp             EEEECCCCC
T ss_pred             EEEcCCCCC
Confidence            999876554

>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=99.66  E-value=1.1e-16  Score=115.18  Aligned_cols=81  Identities=16%  Similarity=0.194  Sum_probs=73.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ....+|||+|||+++|+++|+++|+.+|. ..+.++.+..|.++|||||+|.+.++|++|++ +|+..+.||.|.|.++.
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEcC
Confidence            44568999999999999999999999984 57888888889999999999999999999987 89999999999999887


Q ss_pred             Cch
Q psy12549        188 PRK  190 (336)
Q Consensus       188 ~~~  190 (336)
                      +..
T Consensus        91 ~~~   93 (102)
T d1weza_          91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=3.8e-16  Score=109.23  Aligned_cols=79  Identities=13%  Similarity=0.257  Sum_probs=70.9

Q ss_pred             ccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHh--CCceecCEEEEEee
Q psy12549        200 AKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW--NGKEVDGKILYVGR  277 (336)
Q Consensus       200 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l--~g~~~~g~~l~v~~  277 (336)
                      ..+.++|||+|||.++++++|+++|++||.|.++.+.+.    +++|||+|.+.++|.+|++.+  ++..+.|++|+|.|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~   80 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQY   80 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEE
Confidence            345689999999999999999999999999999998864    689999999999999999865  67899999999999


Q ss_pred             cccch
Q psy12549        278 AQKKA  282 (336)
Q Consensus       278 ~~~~~  282 (336)
                      ++.+.
T Consensus        81 sk~~~   85 (88)
T d2cq1a1          81 SNHKE   85 (88)
T ss_dssp             CSCSS
T ss_pred             CCCCC
Confidence            98663

>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=99.66  E-value=1e-16  Score=112.93  Aligned_cols=80  Identities=23%  Similarity=0.393  Sum_probs=71.1

Q ss_pred             CceEEEcCCCCCCCHHHHH----HHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEee
Q psy12549        110 VGNVFIKNLDKSIDNKAMY----DTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGK  185 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~----~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~  185 (336)
                      .++|||+|||+++++++|+    ++|++||+|.+|.+..  ++.++|||||+|.+.++|..|++.+||..+.|+.|.|.+
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4789999999999999886    4689999999988754  455789999999999999999999999999999999999


Q ss_pred             ccCchh
Q psy12549        186 FIPRKE  191 (336)
Q Consensus       186 ~~~~~~  191 (336)
                      +.+..+
T Consensus        81 ak~~~~   86 (91)
T d1nu4a_          81 AKTDSD   86 (91)
T ss_dssp             CSSCCT
T ss_pred             eCCCch
Confidence            987654

>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=99.65  E-value=1.1e-16  Score=117.50  Aligned_cols=75  Identities=17%  Similarity=0.141  Sum_probs=69.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      .++|||+|||..+++++|+++|+.||.|..|.+..     ++|||||+|.+.++|.+|++.|||..+.|+.|.|.|+...
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~-----~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec-----cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            46899999999999999999999999999998753     4789999999999999999999999999999999987654

>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=99.65  E-value=1.4e-16  Score=108.90  Aligned_cols=74  Identities=20%  Similarity=0.376  Sum_probs=68.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..++|||+|+|  +|+++|+++|++||.|.++.+.++     ++||||+|.+.++|..|+..|||..+.|+.|.|.|+.+
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   76 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   76 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCS
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            35789999996  899999999999999999998754     67999999999999999999999999999999999875


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      .
T Consensus        77 ~   77 (79)
T d2bz2a1          77 Q   77 (79)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.65  E-value=2e-16  Score=112.70  Aligned_cols=77  Identities=22%  Similarity=0.392  Sum_probs=70.4

Q ss_pred             cccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecC--EEEEEeec
Q psy12549        201 KLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDG--KILYVGRA  278 (336)
Q Consensus       201 ~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g--~~l~v~~~  278 (336)
                      .+.++|||+|||.++++++|+++|++||+|..+++.+.    +++|||+|.+.++|.+|++.|||..+.|  ++|+|+|+
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~----~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~a   90 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA   90 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEEC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc----ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeC
Confidence            34589999999999999999999999999999999754    7899999999999999999999999976  58999999


Q ss_pred             ccc
Q psy12549        279 QKK  281 (336)
Q Consensus       279 ~~~  281 (336)
                      ++.
T Consensus        91 k~~   93 (97)
T d1whya_          91 KSG   93 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            865

>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=99.65  E-value=2.7e-16  Score=111.99  Aligned_cols=75  Identities=25%  Similarity=0.490  Sum_probs=67.8

Q ss_pred             CCCceEEEcCCC-CCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLD-KSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp-~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ...++|||+||| ..+++++|+++|++||.|.++.+.       +|||||+|.+.++|.+|+..|||..+.|+.|.|.++
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 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA   85 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEET
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            344679999997 568899999999999999999983       689999999999999999999999999999999998


Q ss_pred             cCc
Q psy12549        187 IPR  189 (336)
Q Consensus       187 ~~~  189 (336)
                      .+.
T Consensus        86 ~~~   88 (98)
T d1wf2a_          86 AEP   88 (98)
T ss_dssp             TSC
T ss_pred             CCC
Confidence            654

>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=99.65  E-value=2.2e-16  Score=113.98  Aligned_cols=82  Identities=22%  Similarity=0.235  Sum_probs=72.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeE-EEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILS-CKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~-~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      ...+|||+|||+++|+++|+++|+.||.+.. +.+..+.+|.++|+|||+|.+.++|++|++ +|+..+.|+.|.|.++.
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            3467999999999999999999999998876 556666789999999999999999999997 89999999999998875


Q ss_pred             Cchh
Q psy12549        188 PRKE  191 (336)
Q Consensus       188 ~~~~  191 (336)
                      ....
T Consensus        86 ~~~~   89 (103)
T d2cpya1          86 LEDM   89 (103)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            5433

>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=99.65  E-value=1.2e-16  Score=116.87  Aligned_cols=75  Identities=19%  Similarity=0.355  Sum_probs=68.9

Q ss_pred             ceEEEcCCC-CCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccc
Q psy12549        204 TNVYIKNFG-EDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKK  281 (336)
Q Consensus       204 ~~l~V~nlp-~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~  281 (336)
                      ++|||+||| ..+++++|+++|+.||.|..+.+++.   .+|+|||+|.++++|.+|++.|||..+.|+.|+|.|+...
T Consensus         3 ~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~---~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~   78 (109)
T d2adca1           3 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN---KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             SEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT---TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CEEEEeCCCcccCCHHHHHHHHhhccccceEEEEec---ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            689999995 56999999999999999999999864   3789999999999999999999999999999999998644

>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=2.9e-16  Score=109.66  Aligned_cols=75  Identities=20%  Similarity=0.289  Sum_probs=65.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..++|||+|||+++++++|+++|++||. ..+.+.     .+++||||+|.+.++|++|++.||+..+.|+.|.|.++.+
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~~-----~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcCc-eeeeee-----ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4578999999999999999999999993 223332     3688999999999999999999999999999999999865


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      .
T Consensus        78 ~   78 (88)
T d1wg1a_          78 D   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.64  E-value=1.3e-16  Score=113.67  Aligned_cols=75  Identities=16%  Similarity=0.127  Sum_probs=69.7

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      ..+|||+|||+.+++++|+++|+.||.|.++.+..     +|+|||+|.+.++|.+|++.|||..|.|+.|+|.++..+.
T Consensus        15 ~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-----~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          15 DFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-----DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             SCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-----TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-----cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            36799999999999999999999999999999864     6899999999999999999999999999999999987653

>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=99.64  E-value=4.4e-16  Score=112.47  Aligned_cols=82  Identities=21%  Similarity=0.276  Sum_probs=72.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEE-EEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSC-KVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~-~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      .....|||+|||+++|+++|+++|+.+|.+... .+..+.++.++|+|||+|.++++|++|++ +|+..+.|+.|.|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            345679999999999999999999999988774 44445588999999999999999999997 8999999999999988


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .+..
T Consensus        92 ~~~~   95 (104)
T d1wg5a_          92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7654

>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=99.64  E-value=2.3e-16  Score=113.85  Aligned_cols=78  Identities=17%  Similarity=0.231  Sum_probs=69.8

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeE-EEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITS-YRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~-~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      ..+|||+|||+++++++|+++|+.||.+.. +.+.. .+|.++|+|||+|.+.++|++|++ +||..|.|+.|.|.++..
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEECH
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECCH
Confidence            367999999999999999999999999876 44444 788999999999999999999996 899999999999998764


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      +
T Consensus        87 ~   87 (103)
T d2cpya1          87 E   87 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=1.1e-16  Score=111.93  Aligned_cols=76  Identities=20%  Similarity=0.425  Sum_probs=68.5

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      .++|||+|||.++++++|+++|++||.|.++++..   .+++||||+|.+.++|++|+.  ++..+.|+.|.|.++.++.
T Consensus         5 s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~---~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~   79 (88)
T d1wf0a_           5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK---PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEPKH   79 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS---SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCCCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee---ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCCCC
Confidence            47899999999999999999999999999987753   458899999999999999985  7889999999999998764


Q ss_pred             h
Q psy12549        283 E  283 (336)
Q Consensus       283 ~  283 (336)
                      .
T Consensus        80 ~   80 (88)
T d1wf0a_          80 N   80 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.64  E-value=7.3e-16  Score=104.04  Aligned_cols=71  Identities=23%  Similarity=0.322  Sum_probs=63.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        113 VFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       113 l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      |||+|||+++++++|+++|++|| +..+.+.     .++|||||+|.+.++|.+|+..|||..+.|++|.|.++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~-----~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-----KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE-----TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec-----ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 4444443     46789999999999999999999999999999999998654

>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=99.63  E-value=1.3e-16  Score=111.47  Aligned_cols=76  Identities=16%  Similarity=0.426  Sum_probs=68.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ..++|||+|||.++|+++|+++|++||.|..+++..+    +++||||+|.+.++|++|+.  +++.+.|+.|.|.++.+
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~----~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec----cCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCCC
Confidence            4578999999999999999999999999999887643    57899999999999999986  78899999999999876


Q ss_pred             ch
Q psy12549        189 RK  190 (336)
Q Consensus       189 ~~  190 (336)
                      +.
T Consensus        78 k~   79 (88)
T d1wf0a_          78 KH   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.63  E-value=6.3e-17  Score=112.91  Aligned_cols=72  Identities=19%  Similarity=0.234  Sum_probs=66.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccCc
Q psy12549        112 NVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIPR  189 (336)
Q Consensus       112 ~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~~  189 (336)
                      +|||+|||+++++++|+++|++||.|.++.+..+      |||||+|.+.++|.+|+..|||..+.|+.+.+.+..+.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            5999999999999999999999999999998753      79999999999999999999999999999988776544

>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=99.63  E-value=4.3e-16  Score=112.50  Aligned_cols=80  Identities=18%  Similarity=0.260  Sum_probs=71.0

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC--CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN--NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~--~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ....|||+|||+++++++|+++|+.+|.+....++.  .++.++|+|||+|.++++|++|++ +|+..|.||.|+|.++.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEEC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEECC
Confidence            336799999999999999999999999987754444  778889999999999999999996 89999999999999987


Q ss_pred             cch
Q psy12549        280 KKA  282 (336)
Q Consensus       280 ~~~  282 (336)
                      ++.
T Consensus        93 ~~~   95 (104)
T d1wg5a_          93 RAE   95 (104)
T ss_dssp             TTT
T ss_pred             HHH
Confidence            663

>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=99.63  E-value=1.9e-16  Score=113.10  Aligned_cols=79  Identities=23%  Similarity=0.340  Sum_probs=70.1

Q ss_pred             ccccceEEEcCCCCC-CcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHH--HhCCceecCEEEEEe
Q psy12549        200 AKLFTNVYIKNFGED-FNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQ--AWNGKEVDGKILYVG  276 (336)
Q Consensus       200 ~~~~~~l~V~nlp~~-~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~--~l~g~~~~g~~l~v~  276 (336)
                      ....++|||+|||.+ +|+++|.++|+.||.|.++.+.+.    +|+|||+|.+.++|.+|++  .+++..+.|+.|+|.
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~   90 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   90 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec----CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEE
Confidence            344578999999975 899999999999999999999864    7899999999999999997  578889999999999


Q ss_pred             ecccch
Q psy12549        277 RAQKKA  282 (336)
Q Consensus       277 ~~~~~~  282 (336)
                      |+..+.
T Consensus        91 ~s~~~~   96 (99)
T d1x4fa1          91 LSEKYK   96 (99)
T ss_dssp             EECSCS
T ss_pred             EcCCcc
Confidence            997653

>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=99.63  E-value=7.8e-16  Score=109.60  Aligned_cols=75  Identities=19%  Similarity=0.342  Sum_probs=68.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCC--eEEEEeecc
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNS--KIVFVGKFI  187 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~--~~i~v~~~~  187 (336)
                      .++|||+|||+++++++|+++|++||.|..+++.++     ++||||+|.+.++|..|++.||+..+.|  ++|.|.|+.
T Consensus        17 s~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak   91 (97)
T d1whya_          17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCC
Confidence            478999999999999999999999999999998764     6799999999999999999999999976  589999987


Q ss_pred             Cc
Q psy12549        188 PR  189 (336)
Q Consensus       188 ~~  189 (336)
                      +.
T Consensus        92 ~~   93 (97)
T d1whya_          92 SG   93 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.62  E-value=3.2e-16  Score=114.01  Aligned_cols=77  Identities=14%  Similarity=0.254  Sum_probs=69.8

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCcee--cCEEEEEeeccc
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEV--DGKILYVGRAQK  280 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~--~g~~l~v~~~~~  280 (336)
                      ..+|||+|||+.+|+++|+++|++||.|..+.+...  +++|+|||+|.++++|..|+..|||..+  .|+.|++.|+.+
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~--~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~   84 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK--NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL   84 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE--TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee--CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCC
Confidence            367999999999999999999999999999988763  3589999999999999999999999998  578999999876


Q ss_pred             c
Q psy12549        281 K  281 (336)
Q Consensus       281 ~  281 (336)
                      +
T Consensus        85 ~   85 (108)
T d2adba1          85 T   85 (108)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.62  E-value=1.9e-15  Score=105.61  Aligned_cols=77  Identities=16%  Similarity=0.192  Sum_probs=69.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHh--CCceeCCeEEEEee
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV--NGMLLNSKIVFVGK  185 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l--~~~~~~~~~i~v~~  185 (336)
                      ..+++|||+|||.++++++|+++|++||.|..+++.++     +++|||+|.+.++|.+|++.+  ++..+.|++|.|.+
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~   80 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQY   80 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEE
Confidence            45689999999999999999999999999999998854     579999999999999999865  67889999999999


Q ss_pred             ccCc
Q psy12549        186 FIPR  189 (336)
Q Consensus       186 ~~~~  189 (336)
                      +..+
T Consensus        81 sk~~   84 (88)
T d2cq1a1          81 SNHK   84 (88)
T ss_dssp             CSCS
T ss_pred             CCCC
Confidence            8754

>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=99.62  E-value=1e-15  Score=106.86  Aligned_cols=77  Identities=26%  Similarity=0.283  Sum_probs=68.9

Q ss_pred             cccceEEEcCCCCC-CcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHh--CCceecCEEEEEee
Q psy12549        201 KLFTNVYIKNFGED-FNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW--NGKEVDGKILYVGR  277 (336)
Q Consensus       201 ~~~~~l~V~nlp~~-~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l--~g~~~~g~~l~v~~  277 (336)
                      ...++|||+|||.. +|++||.++|++||.|.++.+.+.    +++|||+|.+.++|..|+..+  ++..+.|++|+|.|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~----k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~   81 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHL   81 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc----ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEE
Confidence            44588999999986 899999999999999999999764    678999999999999999965  78889999999999


Q ss_pred             cccc
Q psy12549        278 AQKK  281 (336)
Q Consensus       278 ~~~~  281 (336)
                      +...
T Consensus        82 s~~~   85 (89)
T d1x4da1          82 SQKY   85 (89)
T ss_dssp             ECCC
T ss_pred             CCCc
Confidence            9754

>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=99.61  E-value=6.1e-16  Score=112.51  Aligned_cols=79  Identities=13%  Similarity=0.163  Sum_probs=70.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcee--CCeEEEEeec
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLL--NSKIVFVGKF  186 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~--~~~~i~v~~~  186 (336)
                      ...+|||+|||.++|+++|+++|++||.|..+.+..++   ++|+|||+|.+.++|..|+..|||..+  .++.|.+.++
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~---~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s   82 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS   82 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEEC
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC---CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEec
Confidence            34679999999999999999999999999999998764   578999999999999999999999988  5788999887


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .+..
T Consensus        83 ~~~~   86 (108)
T d2adba1          83 KLTS   86 (108)
T ss_dssp             SSCS
T ss_pred             CCcc
Confidence            6643

>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=99.61  E-value=5.4e-16  Score=110.41  Aligned_cols=75  Identities=16%  Similarity=0.170  Sum_probs=68.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeeccC
Q psy12549        109 GVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFIP  188 (336)
Q Consensus       109 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~~  188 (336)
                      ...+|||+|||.++++++|+++|++||.|..+.+.+      +|||||+|.+.++|.+|++.||+..+.|+.|.|.+...
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~   87 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRV   87 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEec
Confidence            456899999999999999999999999999999864      47999999999999999999999999999999988755


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      .
T Consensus        88 ~   88 (98)
T d1wg4a_          88 Y   88 (98)
T ss_dssp             E
T ss_pred             C
Confidence            4

>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=1.9e-15  Score=105.52  Aligned_cols=79  Identities=18%  Similarity=0.146  Sum_probs=69.9

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHh--CCceeCCeEEEE
Q psy12549        107 KSGVGNVFIKNLDKS-IDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV--NGMLLNSKIVFV  183 (336)
Q Consensus       107 ~~~~~~l~v~nlp~~-~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l--~~~~~~~~~i~v  183 (336)
                      ...+++|||+|||.. +|++||.++|++||.|.++.+..+     +++|||+|.+.++|..|++.+  ++..+.|++|.|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            455688999999986 789999999999999999999865     568999999999999999966  677899999999


Q ss_pred             eeccCch
Q psy12549        184 GKFIPRK  190 (336)
Q Consensus       184 ~~~~~~~  190 (336)
                      .++.+..
T Consensus        80 ~~s~~~~   86 (89)
T d1x4da1          80 HLSQKYK   86 (89)
T ss_dssp             EEECCCT
T ss_pred             EECCCcc
Confidence            9987543

>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=99.60  E-value=1.9e-15  Score=108.97  Aligned_cols=78  Identities=19%  Similarity=0.247  Sum_probs=69.9

Q ss_pred             ccccceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHh--CCceecCEEEEEee
Q psy12549        200 AKLFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW--NGKEVDGKILYVGR  277 (336)
Q Consensus       200 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l--~g~~~~g~~l~v~~  277 (336)
                      ..+.++|||+|||..+++++|+++|+.||.|..+.+.+.    +++|||+|.+.++|..|+..+  ++..+.|++|+|.|
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~   87 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec----ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEE
Confidence            345578999999999999999999999999999999764    789999999999999999977  56678899999999


Q ss_pred             cccc
Q psy12549        278 AQKK  281 (336)
Q Consensus       278 ~~~~  281 (336)
                      +..+
T Consensus        88 s~~~   91 (104)
T d1wexa_          88 STSK   91 (104)
T ss_dssp             CSSS
T ss_pred             cCCC
Confidence            9765

>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=99.59  E-value=3.5e-16  Score=114.49  Aligned_cols=80  Identities=18%  Similarity=0.265  Sum_probs=70.6

Q ss_pred             ccceEEEcCCCCCCcHHHHHHhhccCCceeEEEE--eCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        202 LFTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRV--MNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       202 ~~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i--~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      ..++|||+|||+++|+++|+++|+.||.+..+.+  ...+|.++|+|||+|.+.++|++|+. +||..|+|+.|.|..+.
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            3478999999999999999999999999865433  33889999999999999999999996 89999999999999887


Q ss_pred             cch
Q psy12549        280 KKA  282 (336)
Q Consensus       280 ~~~  282 (336)
                      ++.
T Consensus        96 ~~~   98 (112)
T d1wela1          96 KKG   98 (112)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            664

>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=99.58  E-value=5.1e-15  Score=106.70  Aligned_cols=78  Identities=17%  Similarity=0.245  Sum_probs=69.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHh--CCceeCCeEEEEee
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKV--NGMLLNSKIVFVGK  185 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l--~~~~~~~~~i~v~~  185 (336)
                      ...++|||+|||..+++++|.++|+.||.|..+.+.++     +++|||+|.+.++|..|+..+  ++..+.|++|.|.+
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~   87 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEE
Confidence            44678999999999999999999999999999998753     689999999999999999977  56778999999999


Q ss_pred             ccCch
Q psy12549        186 FIPRK  190 (336)
Q Consensus       186 ~~~~~  190 (336)
                      +....
T Consensus        88 s~~~~   92 (104)
T d1wexa_          88 STSKR   92 (104)
T ss_dssp             CSSSS
T ss_pred             cCCCc
Confidence            87643

>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=99.58  E-value=1.7e-15  Score=108.01  Aligned_cols=77  Identities=18%  Similarity=0.204  Sum_probs=68.9

Q ss_pred             CCCceEEEcCCCCC-CCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHH--HhCCceeCCeEEEEe
Q psy12549        108 SGVGNVFIKNLDKS-IDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIE--KVNGMLLNSKIVFVG  184 (336)
Q Consensus       108 ~~~~~l~v~nlp~~-~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~--~l~~~~~~~~~i~v~  184 (336)
                      ..+++|||+|||.+ +|+++|.++|+.||.|.++.+.++     +|+|||+|.+.++|..|++  .+++..+.|+.|.|.
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~   90 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   90 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEE
Confidence            44578999999985 899999999999999999999864     6899999999999999997  478889999999999


Q ss_pred             eccCc
Q psy12549        185 KFIPR  189 (336)
Q Consensus       185 ~~~~~  189 (336)
                      ++..+
T Consensus        91 ~s~~~   95 (99)
T d1x4fa1          91 LSEKY   95 (99)
T ss_dssp             EECSC
T ss_pred             EcCCc
Confidence            98654

>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=99.58  E-value=7.3e-16  Score=112.76  Aligned_cols=82  Identities=20%  Similarity=0.303  Sum_probs=72.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeE-EEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILS-CKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~-~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ....+|||+|||+++|+++|.++|+.+|.+.. +.+..+.+|.++|+|||+|.+.++|++|+. +|+..|+|+.|.|..+
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            34568999999999999999999999998876 445556689999999999999999999997 8999999999999887


Q ss_pred             cCch
Q psy12549        187 IPRK  190 (336)
Q Consensus       187 ~~~~  190 (336)
                      .+..
T Consensus        95 ~~~~   98 (112)
T d1wela1          95 TKKG   98 (112)
T ss_dssp             CHHH
T ss_pred             ChHH
Confidence            6554

>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=99.54  E-value=3.3e-15  Score=107.26  Aligned_cols=77  Identities=18%  Similarity=0.140  Sum_probs=68.6

Q ss_pred             cceEEEcCCCCCCcH-----HHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEee
Q psy12549        203 FTNVYIKNFGEDFND-----EKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGR  277 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~-----~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~  277 (336)
                      .++|||+||+.++..     ++|+++|+.||.|.++++.+    ++++|||+|.+.++|.+|+..|||..+.|+.|+|.|
T Consensus         5 ~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   80 (104)
T d1weya_           5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK----SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYF   80 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET----TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEEC
T ss_pred             CceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec----CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEee
Confidence            478999999988633     56999999999999999985    478999999999999999999999999999999999


Q ss_pred             cccchh
Q psy12549        278 AQKKAE  283 (336)
Q Consensus       278 ~~~~~~  283 (336)
                      +.++..
T Consensus        81 a~~~~~   86 (104)
T d1weya_          81 AQTLHI   86 (104)
T ss_dssp             CCCSSC
T ss_pred             cccCCC
Confidence            976643

>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=99.54  E-value=9.4e-16  Score=110.19  Aligned_cols=75  Identities=25%  Similarity=0.347  Sum_probs=70.3

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeec
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRA  278 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~  278 (336)
                      ..++|.+++.++++++|+++|++||+|.++.|++ .++.++|+|||+|.+.++|.+|+..|||+.++|++|.|+|+
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            3477889999999999999999999999999987 77889999999999999999999999999999999999986

>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=99.51  E-value=2.9e-14  Score=104.17  Aligned_cols=92  Identities=13%  Similarity=0.091  Sum_probs=73.8

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCH-HHHHHHHHHhCCceecCEEEEEeecccch
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESP-EFAEKAVQAWNGKEVDGKILYVGRAQKKA  282 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~-~~a~~a~~~l~g~~~~g~~l~v~~~~~~~  282 (336)
                      ..+||+|||..+|+++|+++|++||+|.++.++..    +|+|||+|.++ ++|..|+..+++..+.++.+.|.++..+.
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~~   87 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEG   87 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECCH
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC----CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeeccc
Confidence            34699999999999999999999999999999864    88999999985 78999999999999988777777776665


Q ss_pred             hhHHHHHHHHHHHHHHh
Q psy12549        283 ERTQELKRRFEMLKIER  299 (336)
Q Consensus       283 ~~~~~~~~~~~~~~~~~  299 (336)
                      +................
T Consensus        88 ~~e~~~~~k~~~~~q~~  104 (113)
T d1owxa_          88 EVEKEALKKIIEDQQES  104 (113)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHH
Confidence            55544444444333333

>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=99.51  E-value=1.5e-15  Score=109.14  Aligned_cols=76  Identities=16%  Similarity=0.230  Sum_probs=71.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      ..++|++++..+++++|+++|++||.|.+|.|+++.+|.++|+|||+|.+.++|.+|+..|||..+.|+.|.|.++
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            3588888999999999999999999999999998889999999999999999999999999999999999999875

>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=99.51  E-value=1.7e-15  Score=106.31  Aligned_cols=79  Identities=6%  Similarity=0.043  Sum_probs=65.2

Q ss_pred             ceeeeecCchhhhhhhHHhhh-cccCCceEEEeCCCC--cccccCCceEEEEEeCCcchhhHHHHHhhcCccccCCeeeE
Q psy12549         19 HNVATRELSAKVVEGVSRSLS-SLIDGNTVKYDWDSG--YTCHQLGSGAILVQLGQPYMLDTERALDTMNFDALKGRPIR   95 (336)
Q Consensus        19 ~~v~v~~lp~~~~e~~l~~~f-~~~~~~~v~~~~~~~--~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~~~~~~g~~i~   95 (336)
                      |.|||+|||.++||++|+++| .++.+..+.+.....  ...+++++|||||+|.++  ++|++|+. +||..+.|++|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~--e~a~~a~~-l~g~~~~Gr~l~   78 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV--DETTQAMA-FDGIIFQGQSLK   78 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSC--TTTTTGGG-GSSCCSSSSCCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCH--HHHHHHHh-hCCcEECCEEEE
Confidence            689999999999999999999 666666655543321  123678999999999999  99999996 999999999999


Q ss_pred             EEecc
Q psy12549         96 IMWSQ  100 (336)
Q Consensus        96 v~~~~  100 (336)
                      |..+.
T Consensus        79 V~r~k   83 (90)
T d1u2fa_          79 IRRPH   83 (90)
T ss_dssp             CBCTT
T ss_pred             ECCCC
Confidence            97643

>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=99.49  E-value=1.4e-14  Score=103.99  Aligned_cols=78  Identities=8%  Similarity=-0.007  Sum_probs=69.0

Q ss_pred             CCceEEEcCCCCCC-C----HHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEE
Q psy12549        109 GVGNVFIKNLDKSI-D----NKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFV  183 (336)
Q Consensus       109 ~~~~l~v~nlp~~~-t----~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v  183 (336)
                      +..+|||+||+.++ +    +++|+++|+.||.|.++.+.+     +++||||+|.+.++|.+|+..|||..+.|+.|.|
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k-----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v   78 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-----TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec-----CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEE
Confidence            45789999999875 3    357999999999999999985     4689999999999999999999999999999999


Q ss_pred             eeccCchh
Q psy12549        184 GKFIPRKE  191 (336)
Q Consensus       184 ~~~~~~~~  191 (336)
                      .|+.+...
T Consensus        79 ~~a~~~~~   86 (104)
T d1weya_          79 YFAQTLHI   86 (104)
T ss_dssp             ECCCCSSC
T ss_pred             eecccCCC
Confidence            99876644

>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=99.48  E-value=1.9e-16  Score=111.31  Aligned_cols=76  Identities=16%  Similarity=0.355  Sum_probs=66.5

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeC-------CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEe
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMN-------NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVG  276 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~-------~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~  276 (336)
                      ++|||+|||.++++++|+++|+.||.+..+.+..       ..+.++|||||+|.++++|++|++ |||..+.|+.|+|.
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            6799999999999999999999999877655432       456679999999999999999985 99999999999998


Q ss_pred             eccc
Q psy12549        277 RAQK  280 (336)
Q Consensus       277 ~~~~  280 (336)
                      +++.
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6554

>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=99.43  E-value=1.5e-13  Score=98.01  Aligned_cols=66  Identities=23%  Similarity=0.403  Sum_probs=58.9

Q ss_pred             cccccceEEEcC--CCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCcee
Q psy12549        199 KAKLFTNVYIKN--FGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEV  268 (336)
Q Consensus       199 ~~~~~~~l~V~n--lp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~  268 (336)
                      ...+.++++|.|  ||..+|+++|+++|++||.|..+.+.+.    +++|||+|.+.++|.+|+..|||..+
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~----k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN----KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT----CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC----ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            344557888855  9999999999999999999999988764    67999999999999999999999987

>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=99.43  E-value=2.8e-13  Score=96.19  Aligned_cols=80  Identities=23%  Similarity=0.347  Sum_probs=68.4

Q ss_pred             cccceEEEcCC--CCCC---------cHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceec
Q psy12549        201 KLFTNVYIKNF--GEDF---------NDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVD  269 (336)
Q Consensus       201 ~~~~~l~V~nl--p~~~---------t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~  269 (336)
                      ...++|+|.|+  |.++         .+++|++.|++||.|..+.+...  ..+|+|||+|.+.++|.+|+..|||..|+
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~--~~~G~~fV~f~~~e~A~~A~~~lng~~~~   83 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR--HPDGVASVSFRDPEEADYCIQTLDGRWFG   83 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT--CTTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC--CCccEEEEEECCHHHHHHHHHHhCCcEEC
Confidence            34578999998  5543         23689999999999999988753  45799999999999999999999999999


Q ss_pred             CEEEEEeecccch
Q psy12549        270 GKILYVGRAQKKA  282 (336)
Q Consensus       270 g~~l~v~~~~~~~  282 (336)
                      |++|.|.+..++.
T Consensus        84 gr~i~v~~~~g~~   96 (99)
T d2dita1          84 GRQITAQAWDGTT   96 (99)
T ss_dssp             TEECEEEECCSCC
T ss_pred             CEEEEEEEeCCcC
Confidence            9999999987664

>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=99.40  E-value=2.7e-13  Score=98.92  Aligned_cols=79  Identities=19%  Similarity=0.118  Sum_probs=66.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCH-HHHHHHHHHhCCceeCCeEEEEeec
Q psy12549        108 SGVGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETE-EAANKSIEKVNGMLLNSKIVFVGKF  186 (336)
Q Consensus       108 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~-~~a~~a~~~l~~~~~~~~~i~v~~~  186 (336)
                      .+...+||+|||+++|+++|+++|++||+|..|.++.+     +|+|||.|.++ ++|..|+..+++..+.++.+.+.+.
T Consensus         9 ~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_           9 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            33446799999999999999999999999999999864     68999999996 6788999999998887777777666


Q ss_pred             cCchh
Q psy12549        187 IPRKE  191 (336)
Q Consensus       187 ~~~~~  191 (336)
                      ....+
T Consensus        84 ~~~~~   88 (113)
T d1owxa_          84 VLEGE   88 (113)
T ss_dssp             ECCHH
T ss_pred             eccch
Confidence            55544

>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=99.38  E-value=5.5e-13  Score=90.57  Aligned_cols=73  Identities=23%  Similarity=0.246  Sum_probs=62.7

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCE-EEEEeecccch
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGK-ILYVGRAQKKA  282 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~-~l~v~~~~~~~  282 (336)
                      +.|+|.|+|++.+++.| +.|++||+|.++++.+    +++||||+|.++++|++|++ +||..++|+ .+.|..+..+.
T Consensus         5 ~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~----~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~k~   78 (81)
T d1wwha1           5 TWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN----TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCIDKN   78 (81)
T ss_dssp             GEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS----SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCCHH
T ss_pred             cEEEEECCChHHHHHHH-HHHHhhhhhheEEecC----CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCChh
Confidence            67999999999987655 5799999999998854    47999999999999999996 899999997 46788877653

>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=99.37  E-value=6.4e-13  Score=94.63  Aligned_cols=62  Identities=15%  Similarity=0.346  Sum_probs=56.2

Q ss_pred             CceEEE--cCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcee
Q psy12549        110 VGNVFI--KNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLL  176 (336)
Q Consensus       110 ~~~l~v--~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~  176 (336)
                      ..+++|  +|||.++|+++|+++|++||.|..+.+.++     ++||||+|.+.++|..|+..|||..+
T Consensus        18 t~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            467888  559999999999999999999999988764     57999999999999999999999876

>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=99.33  E-value=7e-13  Score=95.10  Aligned_cols=80  Identities=18%  Similarity=0.251  Sum_probs=66.9

Q ss_pred             ccceEEEcCC--CCCC--------cHHHHHHhhccCCceeEEEEeCC----CCccceEEEEEeCCHHHHHHHHHHhCCce
Q psy12549        202 LFTNVYIKNF--GEDF--------NDEKLKEMFEPYGTITSYRVMNN----DGKSRGFGFVAYESPEFAEKAVQAWNGKE  267 (336)
Q Consensus       202 ~~~~l~V~nl--p~~~--------t~~~l~~~f~~~g~i~~~~i~~~----~~~~~g~afV~F~~~~~a~~a~~~l~g~~  267 (336)
                      +++.|.+.|+  |.++        ..++|++.|++||.|.++.+.+.    .....|++||+|.+.++|.+|+..|||+.
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            3477899998  4443        34679999999999999998762    22346899999999999999999999999


Q ss_pred             ecCEEEEEeecccc
Q psy12549        268 VDGKILYVGRAQKK  281 (336)
Q Consensus       268 ~~g~~l~v~~~~~~  281 (336)
                      ++||.|.+.|..+.
T Consensus        83 f~gR~v~v~f~~~~   96 (104)
T d1o0pa_          83 FANRVVVTKYCDPD   96 (104)
T ss_dssp             SSSSCCEEEEECHH
T ss_pred             ECCeEEEEEEcCHH
Confidence            99999999998743

>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=2.2e-12  Score=91.51  Aligned_cols=79  Identities=19%  Similarity=0.239  Sum_probs=67.4

Q ss_pred             CCCceEEEcCC--CCCC---------CHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCcee
Q psy12549        108 SGVGNVFIKNL--DKSI---------DNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLL  176 (336)
Q Consensus       108 ~~~~~l~v~nl--p~~~---------t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~  176 (336)
                      ...++|+|+||  |.++         .+++|++.|++||.|..+.+..+   ..+|+|||+|.++++|.+|+..|||..+
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            34578999999  5432         23689999999999999988765   3568999999999999999999999999


Q ss_pred             CCeEEEEeeccCc
Q psy12549        177 NSKIVFVGKFIPR  189 (336)
Q Consensus       177 ~~~~i~v~~~~~~  189 (336)
                      .|++|.|.++.++
T Consensus        83 ~gr~i~v~~~~g~   95 (99)
T d2dita1          83 GGRQITAQAWDGT   95 (99)
T ss_dssp             TTEECEEEECCSC
T ss_pred             CCEEEEEEEeCCc
Confidence            9999999987654

>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=99.32  E-value=1.6e-12  Score=88.18  Aligned_cols=73  Identities=15%  Similarity=0.287  Sum_probs=61.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeE-EEEeeccC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKI-VFVGKFIP  188 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~-i~v~~~~~  188 (336)
                      .+.|+|.|+|++.+++.| .+|++||+|.++.+.+     .++||||+|.++++|++|++ +||..+.|+. +.|.++..
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~-----~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN-----TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS-----SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC-----CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            467999999999886555 5799999999998754     46899999999999999997 9999999975 56877665


Q ss_pred             c
Q psy12549        189 R  189 (336)
Q Consensus       189 ~  189 (336)
                      +
T Consensus        77 k   77 (81)
T d1wwha1          77 K   77 (81)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.22  E-value=6.7e-12  Score=89.85  Aligned_cols=79  Identities=16%  Similarity=0.246  Sum_probs=67.4

Q ss_pred             CceEEEcCC--CCCC--------CHHHHHHHhhccCCeeEEEEeeCCC---CCcccEEEEEeCCHHHHHHHHHHhCCcee
Q psy12549        110 VGNVFIKNL--DKSI--------DNKAMYDTFSAFGSILSCKVAQDEQ---GNSKGYGFVHFETEEAANKSIEKVNGMLL  176 (336)
Q Consensus       110 ~~~l~v~nl--p~~~--------t~~~l~~~f~~~G~v~~~~~~~~~~---~~~~g~afV~F~~~~~a~~a~~~l~~~~~  176 (336)
                      ++.|.|+|+  |...        ..+||++.|++||.|.++.++++..   ....|++||+|.+.++|.+|+..|||..+
T Consensus         4 s~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f   83 (104)
T d1o0pa_           4 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF   83 (104)
T ss_dssp             CSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCS
T ss_pred             CcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEE
Confidence            467999999  4443        2357899999999999999988653   34568999999999999999999999999


Q ss_pred             CCeEEEEeeccC
Q psy12549        177 NSKIVFVGKFIP  188 (336)
Q Consensus       177 ~~~~i~v~~~~~  188 (336)
                      +||.|.+.++.+
T Consensus        84 ~gR~v~v~f~~~   95 (104)
T d1o0pa_          84 ANRVVVTKYCDP   95 (104)
T ss_dssp             SSSCCEEEEECH
T ss_pred             CCeEEEEEEcCH
Confidence            999999999764

>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=97.78  E-value=4.8e-05  Score=47.51  Aligned_cols=62  Identities=23%  Similarity=0.213  Sum_probs=53.6

Q ss_pred             HHHHHHhhccCCceeEEEEeC-CCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeeccc
Q psy12549        217 DEKLKEMFEPYGTITSYRVMN-NDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQK  280 (336)
Q Consensus       217 ~~~l~~~f~~~g~i~~~~i~~-~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~~  280 (336)
                      .+.|.+.|.++|.|.++.+.. .+|..  .|-|...+..+|.-|+..|+-..+++++|.|+++..
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            355678899999999999987 44443  489999999999999999999999999999999763

>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=97.76  E-value=0.00013  Score=48.90  Aligned_cols=76  Identities=14%  Similarity=0.159  Sum_probs=61.9

Q ss_pred             ceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCC---CC-ccceEEEEEeCCHHHHHHHHHHhCCceecC-----EEEE
Q psy12549        204 TNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNN---DG-KSRGFGFVAYESPEFAEKAVQAWNGKEVDG-----KILY  274 (336)
Q Consensus       204 ~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~---~~-~~~g~afV~F~~~~~a~~a~~~l~g~~~~g-----~~l~  274 (336)
                      ++|.|+.||+.+|++++.+.++..|.+........   .+ ..-..|||.|.+.++...-.+.++|..|.+     .+-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            56899999999999999999999999988877761   11 123579999999999999999999999853     3456


Q ss_pred             Eeecc
Q psy12549        275 VGRAQ  279 (336)
Q Consensus       275 v~~~~  279 (336)
                      |++|.
T Consensus        82 VE~AP   86 (91)
T d1uw4a_          82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66664

>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=97.73  E-value=9e-05  Score=49.67  Aligned_cols=66  Identities=9%  Similarity=0.229  Sum_probs=56.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCC-C-C-CcccEEEEEeCCHHHHHHHHHHhCCcee
Q psy12549        111 GNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDE-Q-G-NSKGYGFVHFETEEAANKSIEKVNGMLL  176 (336)
Q Consensus       111 ~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~-~-~-~~~g~afV~F~~~~~a~~a~~~l~~~~~  176 (336)
                      ++|.|+.||+++|++++.+.+...|.+........+ + + ..-.-|||.|.+.++.....+..+|..+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F   70 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            469999999999999999999999998887777765 2 2 2234699999999999999999999876

>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=97.57  E-value=0.00036  Score=43.46  Aligned_cols=60  Identities=15%  Similarity=0.232  Sum_probs=52.1

Q ss_pred             HHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhCCceeCCeEEEEeecc
Q psy12549        126 AMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVNGMLLNSKIVFVGKFI  187 (336)
Q Consensus       126 ~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~~~~~~~~~i~v~~~~  187 (336)
                      -|.+.|.++|.|.++.+....+|..  .|-|..++.++|.-|+..|+...++++.|.|.++.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            3556789999999999988766633  59999999999999999999999999999998764

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.51  E-value=0.0002  Score=47.05  Aligned_cols=70  Identities=19%  Similarity=0.102  Sum_probs=54.4

Q ss_pred             ccCceeeeecCchhhhh---------hhHHhhh-cccCCceEEEeCCCCcccccCCceEEEEEeCCcchhhHHHHHhhcC
Q psy12549         16 IPKHNVATRELSAKVVE---------GVSRSLS-SLIDGNTVKYDWDSGYTCHQLGSGAILVQLGQPYMLDTERALDTMN   85 (336)
Q Consensus        16 ~p~~~v~v~~lp~~~~e---------~~l~~~f-~~~~~~~v~~~~~~~~~~~g~~~g~afV~f~~~~~~~A~~A~~~~~   85 (336)
                      .|+-+|.|.-..++..+         .+|.+-| .+|.+.-++++.+.           .+|+|.+-  +.|..|++ ++
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d~-----------mwVTF~dG--~SAL~al~-l~   78 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-----------MLVTFADS--HSALSVLD-VD   78 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-----------EEEECSCS--HHHHHHHH-GG
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCCe-----------EEEEECCc--HHHHHHhc-cC
Confidence            35556777555434333         2444445 88899999999977           89999999  99999999 99


Q ss_pred             ccccCCeeeEEEec
Q psy12549         86 FDALKGRPIRIMWS   99 (336)
Q Consensus        86 ~~~~~g~~i~v~~~   99 (336)
                      +..+.|+.|.|...
T Consensus        79 g~~v~G~~l~It~~   92 (95)
T d1ufwa_          79 GMKVKGRAVKISGP   92 (95)
T ss_dssp             GSEETTEEEEEECC
T ss_pred             CeEEcceEEEEecC
Confidence            99999999998754

>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=97.48  E-value=9.1e-05  Score=48.74  Aligned_cols=55  Identities=22%  Similarity=0.395  Sum_probs=48.9

Q ss_pred             HHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHhCCceecCEEEEEeecc
Q psy12549        218 EKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAWNGKEVDGKILYVGRAQ  279 (336)
Q Consensus       218 ~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l~g~~~~g~~l~v~~~~  279 (336)
                      .+|.+.|..||+|.-+++.      .+..+|+|.+-++|.+|+. ++|..+.|+.|.++...
T Consensus        39 ~~Llq~l~~~GeViLvRFv------~d~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRIN------QGQMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEE------TTEEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             HHHHHHHhhCCeEEEEEEe------CCeEEEEECCcHHHHHHhc-cCCeEEcceEEEEecCC
Confidence            5788899999999999998      5569999999999999997 79999999999997654

>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=95.44  E-value=0.031  Score=37.09  Aligned_cols=55  Identities=22%  Similarity=0.350  Sum_probs=45.0

Q ss_pred             cceEEEcCCCCCCcHHHHHHhhccCCceeEEEEeCCCCccceEEEEEeCCHHHHHHHHHHh
Q psy12549        203 FTNVYIKNFGEDFNDEKLKEMFEPYGTITSYRVMNNDGKSRGFGFVAYESPEFAEKAVQAW  263 (336)
Q Consensus       203 ~~~l~V~nlp~~~t~~~l~~~f~~~g~i~~~~i~~~~~~~~g~afV~F~~~~~a~~a~~~l  263 (336)
                      ...||.-.+|..+...||.++|++||.|.---|-      -..|||...+.++|..++..+
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswId------dTSa~V~L~~~e~~~~v~~~~   69 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWID------DTSAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEE------TTEEEEECSCHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEEEEec------CceEEEEecCHHHHHHHHHHh
Confidence            3679999999999999999999999987533332      235999999999998888754

>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=95.07  E-value=0.05  Score=36.03  Aligned_cols=56  Identities=23%  Similarity=0.373  Sum_probs=46.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhhccCCeeEEEEeeCCCCCcccEEEEEeCCHHHHHHHHHHhC
Q psy12549        110 VGNVFIKNLDKSIDNKAMYDTFSAFGSILSCKVAQDEQGNSKGYGFVHFETEEAANKSIEKVN  172 (336)
Q Consensus       110 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~g~afV~F~~~~~a~~a~~~l~  172 (336)
                      ...||.-..|..+...||.++|+.||.|. |..+.+.      -|||...+.++|..++..++
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT------EEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc------eEEEEecCHHHHHHHHHHhc
Confidence            35799999999999999999999999877 3334332      59999999999999988543