Psyllid ID: psy3930

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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-------30
Protein Sequence
MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGNIIRHFLVPISMETEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSFGITPLGFESGGWWFKSSHEI
Secondary Structure (PSIPRED)
ccEEcccccccccHHHHHHHHccccccHHHHHcccccccccccHHHHHHHHHccccEEEEccccEEEcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccccccHHHHHHHcccccEEEEEEEcccccccccccHHHHHHHHHccccccccccccEEEccccccccccccccccccccccccccHHHHHHHHcccccEEEEEEcccccccccccEEEEEEccHHHHHHHHHHccccccccccccEEEEEccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEccccccHHHHHHHHHHccccccHHHEEEHHHHHHHcccHHHHHHHHHcccEEEEcccccEEEccccccccccccccccccccHcccccccccccccccccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHccccccHHHHEEHHHHHHHcccHHHHHHHHHcccEEEEcccccEEEEcccccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEccccccccccEEEEEEccHHHHHHHHHHHcccccccccccEHHHHHHHHcccccccccccEEEEEccccc
Coil and Loop (DISEMBL)
mefylsdsnlrkdrffsqllqespeieVSVFLKCNklarlthdpdDVVKALRKSKLLEVTEDGTKVKGNIIRHFLVPismeteasdnvdkdlsdlqrkdgggrhrKKQLYQQIMNLMEFylsdsnlrkdrffsqllqespeieVSVFLKCNklarlthdpdDVVKALRKSKLlevtedgtkVRRTVVvqdkpdvdectiyveklppeaehdYIESVFSKYgkvtyvslpkfkstgklkgfafVEFSTKEEAAKALElglnpcppdyqssiltttsrlsfgitplgfesggwwfksshei
Flexible Loop (DISEMBL)
mefylsdsnlrkdRFFSQLLQESPEIEVSVFLKCNKLarlthdpddvvKALRKskllevtedgtkvkgniIRHFLVPISmeteasdnvdkdlsdlqrkdgggrhrKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLarlthdpddvvKALRKskllevtedgtkvrrtvvvqdkpdvdecTIYVEklppeaehdyIESVFSKYGKVTYVSlpkfkstgkLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSFGITPLgfesggwwfksshei
Low Complexity Region (SEG)
MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGNIIRHFLVPISMETEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSFGITPLGFESGGWWFKSSHEI
Disordered region (IsUnstruct)
**************FFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGNIIRHFLVPIS*****************************LYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSFGITPLGFESGGWWF******
Disordered Region (DISOPRED)
MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGNIIRHFLVPISMETEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLN***************************************
Disordered Region (DISEMBL)
MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGNIIRHFLVPISMETEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSFGITPLGFESGGWWFKSSHEI
Disordered Region (DISPRO)
MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKG***********************************HRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSFGITPLGFESGGWWFKSS***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGNIIRHFLVPISMETEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSFGITPLGFESGGWWFKSSHEI
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	299	2.2.26 [Sep-21-2011]
Q28G87	593	La-related protein 7 OS=X	yes	N/A	0.612	0.308	0.428	6e-34
Q4R627	581	La-related protein 7 OS=M	N/A	N/A	0.531	0.273	0.444	6e-33
Q4G0J3	582	La-related protein 7 OS=H	yes	N/A	0.531	0.273	0.444	7e-33
Q7ZWE3	555	La-related protein 7 OS=D	yes	N/A	0.598	0.322	0.415	2e-32
Q5XI01	571	La-related protein 7 OS=R	yes	N/A	0.518	0.271	0.430	8e-31
Q05CL8	570	La-related protein 7 OS=M	yes	N/A	0.518	0.271	0.424	2e-30
P05455	408	Lupus La protein OS=Homo	no	N/A	0.525	0.384	0.303	1e-11
P10881	404	Lupus La protein homolog	no	N/A	0.525	0.388	0.297	2e-11
P32067	415	Lupus La protein homolog	no	N/A	0.494	0.356	0.295	3e-10
P38656	415	Lupus La protein homolog	no	N/A	0.481	0.346	0.296	1e-09

>sp|Q28G87|LARP7_XENTR La-related protein 7 OS=Xenopus tropicalis GN=larp7 PE=2 SV=1

 Score =  144 bits (364), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 81/189 (42%), Positives = 121/189 (64%), Gaps = 6/189 (3%)

Query: 79  SMETEA-SDNVDKDLSDLQRKD--GGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQL 135
           ++ET+  S+ V +D S   RKD     R R KQL   I   ++F+  D NL KDRF  + 
Sbjct: 3   AIETDTPSNKVKEDESTDLRKDREKKKRSRVKQLLADIAKQVDFWFGDVNLHKDRFLREQ 62

Query: 136 LQESPE--IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP- 192
           ++++ +  I++S+    NK+ ++T D   + +A++ S ++E+   GTK+RR   + +KP 
Sbjct: 63  IEKTRDGYIDISLLASFNKMKKITTDSKLIARAVKNSSVVEINLSGTKIRRRFPLGEKPQ 122

Query: 193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
           DVD  T+YVE LP    H +IE VF KYG V YVS+P++KSTG  KGFAF+EF T+E+AA
Sbjct: 123 DVDSRTVYVELLPKNVTHSWIERVFGKYGMVVYVSIPRYKSTGDPKGFAFIEFETQEQAA 182

Query: 253 KALELGLNP 261
           KA+E+  NP
Sbjct: 183 KAIEVLNNP 191

Xenopus tropicalis (taxid: 8364)

>sp|Q4R627|LARP7_MACFA La-related protein 7 OS=Macaca fascicularis GN=LARP7 PE=2 SV=1

 Score =  141 bits (355), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 72/162 (44%), Positives = 107/162 (66%), Gaps = 3/162 (1%)

Query: 103 RHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPE--IEVSVFLKCNKLARLTHDP 160
           R R KQ+   I   ++F+  D+NL KDRF  + +++S +  +++S+ +  NK+ +LT D 
Sbjct: 28  RSRVKQVLADIAKQVDFWFGDANLHKDRFLREQIEKSRDGYVDISLLVSFNKMKKLTTDG 87

Query: 161 DDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP-DVDECTIYVEKLPPEAEHDYIESVFSK 219
             + +ALR S ++E+  +GT++RR   + ++P D DE T+YVE LP    H +IE VF K
Sbjct: 88  KLIARALRSSAVVELDLEGTRIRRKKPLGERPKDEDERTVYVELLPKNVNHSWIERVFGK 147

Query: 220 YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNP 261
            G V Y+S+P +KSTG  KGFAFVEF TKE+AAKA+E   NP
Sbjct: 148 CGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIEFLNNP 189

Negative transcriptional regulator of polymerase II genes, acting by means of the 7SK RNP system. Within the 7SK RNP complex, the positive transcription elongation factor b (P-TEFb) is sequestered in an inactive form, preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation.

Macaca fascicularis (taxid: 9541)

>sp|Q4G0J3|LARP7_HUMAN La-related protein 7 OS=Homo sapiens GN=LARP7 PE=1 SV=1

 Score =  141 bits (355), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 72/162 (44%), Positives = 107/162 (66%), Gaps = 3/162 (1%)

Query: 103 RHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPE--IEVSVFLKCNKLARLTHDP 160
           R R KQ+   I   ++F+  D+NL KDRF  + +++S +  +++S+ +  NK+ +LT D 
Sbjct: 28  RSRVKQVLADIAKQVDFWFGDANLHKDRFLREQIEKSRDGYVDISLLVSFNKMKKLTTDG 87

Query: 161 DDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP-DVDECTIYVEKLPPEAEHDYIESVFSK 219
             + +ALR S ++E+  +GT++RR   + ++P D DE T+YVE LP    H +IE VF K
Sbjct: 88  KLIARALRSSAVVELDLEGTRIRRKKPLGERPKDEDERTVYVELLPKNVNHSWIERVFGK 147

Query: 220 YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNP 261
            G V Y+S+P +KSTG  KGFAFVEF TKE+AAKA+E   NP
Sbjct: 148 CGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIEFLNNP 189

Negative transcriptional regulator of polymerase II genes, acting by means of the 7SK RNP system. Within the 7SK RNP complex, the positive transcription elongation factor b (P-TEFb) is sequestered in an inactive form, preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation.

Homo sapiens (taxid: 9606)

>sp|Q7ZWE3|LARP7_DANRE La-related protein 7 OS=Danio rerio GN=larp7 PE=2 SV=1

 Score =  139 bits (351), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 76/183 (41%), Positives = 114/183 (62%), Gaps = 4/183 (2%)

Query: 86  DNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPE--IE 143
           D    DLS+ +  +   R R KQL   +   +EF+  D NL KDRF   ++++S +  I+
Sbjct: 19  DTACADLSEKKDNEKKKRSRVKQLLSDVKKQVEFWFGDVNLHKDRFMKSIIEQSRDGYID 78

Query: 144 VSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP-DVDECTIYVE 202
           ++V    N++  LT D   + +AL+ S ++EV ++GT++RR   + + P DVD  T+YVE
Sbjct: 79  IAVLTTFNRMKNLTADVKLIARALKNSTIVEVNDEGTRIRRKEPLGETPKDVDSRTVYVE 138

Query: 203 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPC 262
            LP    H ++E VFSK G V Y+S+P++KST   KGFAFVEF T+E+A KA+E+  NP 
Sbjct: 139 LLPKTVTHIWLERVFSKCGHVVYISIPRYKSTRHSKGFAFVEFETQEQAQKAVEMLNNP- 197

Query: 263 PPD 265
           P D
Sbjct: 198 PED 200

Danio rerio (taxid: 7955)

>sp|Q5XI01|LARP7_RAT La-related protein 7 OS=Rattus norvegicus GN=Larp7 PE=1 SV=2

 Score =  134 bits (337), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 68/158 (43%), Positives = 105/158 (66%), Gaps = 3/158 (1%)

Query: 107 KQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPE--IEVSVFLKCNKLARLTHDPDDVV 164
           KQ+   I   ++F+  D+NL KDRF  + +++S +  +++S+ +  NK+ +LT D   + 
Sbjct: 27  KQVLADIAKQVDFWFGDANLHKDRFLREQIEKSRDGYVDISLLVSFNKMKKLTTDGKLIA 86

Query: 165 KALRKSKLLEVTEDGTKVRRTVVVQDKP-DVDECTIYVEKLPPEAEHDYIESVFSKYGKV 223
           +AL+ S ++E+  +GT++RR   + ++P D +E T+YVE LP    H +IE VF K G V
Sbjct: 87  RALKSSSVVELDLEGTRIRRKKPLGERPKDEEERTVYVELLPKNVTHSWIERVFGKCGNV 146

Query: 224 TYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNP 261
            Y+S+P +KSTG  KGFAFVEF TKE+AAKA+E   NP
Sbjct: 147 VYISIPHYKSTGDPKGFAFVEFETKEQAAKAIEFLNNP 184

Negative transcriptional regulator of polymerase II genes, acting by means of the 7SK RNP system. Within the 7SK RNP complex, the positive transcription elongation factor b (P-TEFb) is sequestered in an inactive form, preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation.

Rattus norvegicus (taxid: 10116)

>sp|Q05CL8|LARP7_MOUSE La-related protein 7 OS=Mus musculus GN=Larp7 PE=1 SV=2

 Score =  132 bits (333), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 67/158 (42%), Positives = 105/158 (66%), Gaps = 3/158 (1%)

Query: 107 KQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPE--IEVSVFLKCNKLARLTHDPDDVV 164
           KQ+   I   ++F+  D+NL KD+F  + +++S +  +++S+ +  NK+ +LT D   + 
Sbjct: 26  KQVLADIAKQVDFWFGDANLHKDKFLREQIEKSRDGYVDISLLVSFNKMKKLTTDGKLIA 85

Query: 165 KALRKSKLLEVTEDGTKVRRTVVVQDKP-DVDECTIYVEKLPPEAEHDYIESVFSKYGKV 223
           +AL+ S ++E+  +GT++RR   + ++P D +E T+YVE LP    H +IE VF K G V
Sbjct: 86  RALKSSSVVELDLEGTRIRRKKPLGERPKDEEERTVYVELLPKNVTHSWIERVFGKCGNV 145

Query: 224 TYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNP 261
            Y+S+P +KSTG  KGFAFVEF TKE+AAKA+E   NP
Sbjct: 146 VYISIPHYKSTGDPKGFAFVEFETKEQAAKAIEFLNNP 183

Negative transcriptional regulator of polymerase II genes, acting by means of the 7SK RNP system. Within the 7SK RNP complex, the positive transcription elongation factor b (P-TEFb) is sequestered in an inactive form, preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation.

Mus musculus (taxid: 10090)

>sp|P05455|LA_HUMAN Lupus La protein OS=Homo sapiens GN=SSB PE=1 SV=2

 Score = 70.9 bits (172), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 51/168 (30%), Positives = 89/168 (52%), Gaps = 11/168 (6%)

Query: 99  DGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQ-ESPEIEVSVFLKCNKLARLT 157
           + G   +   L  +I + +E+Y  D NL +D+F  + ++ +   + + + +K N+L RLT
Sbjct: 3   ENGDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLT 62

Query: 158 HDPDDVVKALRKSK--LLEVTEDGTKVRRT-------VVVQDKPDVDECTIYVEKLPPEA 208
            D + +V+AL KSK  L+E++ED TK+RR+       V  + K DV   ++Y++  P +A
Sbjct: 63  TDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDA 122

Query: 209 EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             D I+      G+V  + + +       KG  FV F + E A K +E
Sbjct: 123 TLDDIKEWLEDKGQVLNIQMRRTLHKA-FKGSIFVVFDSIESAKKFVE 169

Binds to the 3' poly(U) terminii of nascent RNA polymerase III transcripts, protecting them from exonuclease digestion and facilitating their folding and maturation.

Homo sapiens (taxid: 9606)

>sp|P10881|LA_BOVIN Lupus La protein homolog OS=Bos taurus GN=SSB PE=2 SV=2

 Score = 69.7 bits (169), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 50/168 (29%), Positives = 88/168 (52%), Gaps = 11/168 (6%)

Query: 99  DGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQ-ESPEIEVSVFLKCNKLARLT 157
           + G   +   L  +I + +E+Y  D NL +D+F  + ++ +   + + + +K N+L RLT
Sbjct: 3   ENGDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLT 62

Query: 158 HDPDDVVKALRKSK--LLEVTEDGTKVRRT-------VVVQDKPDVDECTIYVEKLPPEA 208
            D + +V+AL KSK  L+E++ED TK+RR+       V  + K DV   ++Y++  P +A
Sbjct: 63  TDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDA 122

Query: 209 EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             D I+      G+V  + + +       KG  F  F + E A K +E
Sbjct: 123 ALDDIKEWLEDKGQVLNIQMRRTLHKA-FKGSIFAVFDSIESAKKFVE 169

Binds to the 3' poly(U) terminii of nascent RNA polymerase III transcripts, protecting them from exonuclease digestion and facilitating their folding and maturation.

Bos taurus (taxid: 9913)

>sp|P32067|LA_MOUSE Lupus La protein homolog OS=Mus musculus GN=Ssb PE=2 SV=1

 Score = 65.9 bits (159), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 47/159 (29%), Positives = 84/159 (52%), Gaps = 11/159 (6%)

Query: 109 LYQQIMNLMEFYLSDSNLRKDRFFSQLLQ-ESPEIEVSVFLKCNKLARLTHDPDDVVKAL 167
           L  +I + +E+Y  D NL +D+F  + ++ +   + +   +K N+L RLT D + +V+AL
Sbjct: 13  LEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLETMIKFNRLNRLTTDFNVIVQAL 72

Query: 168 RKS--KLLEVTEDGTKVRRT-------VVVQDKPDVDECTIYVEKLPPEAEHDYIESVFS 218
            KS  KL+EV+ D TK+RR+       V  + K DV   ++Y++  P +A  D I+    
Sbjct: 73  SKSKAKLMEVSADKTKIRRSPSRPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLD 132

Query: 219 KYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
             G++  + + +       KG  F  F + + A K +E+
Sbjct: 133 DKGQILNIQMRRTLHK-TFKGSIFAVFDSIQSAKKFVEI 170

Binds to the 3' poly(U) terminii of nascent RNA polymerase III transcripts, protecting them from exonuclease digestion and facilitating their folding and maturation.

Mus musculus (taxid: 10090)

>sp|P38656|LA_RAT Lupus La protein homolog OS=Rattus norvegicus GN=Ssb PE=2 SV=1

 Score = 63.9 bits (154), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 46/155 (29%), Positives = 81/155 (52%), Gaps = 11/155 (7%)

Query: 109 LYQQIMNLMEFYLSDSNLRKDRFFSQLLQ-ESPEIEVSVFLKCNKLARLTHDPDDVVKAL 167
           L  +I + +E+Y  D NL +D+F  + ++ +   + +   +K N+L RLT D + +V+AL
Sbjct: 13  LEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLETMIKFNRLNRLTTDFNVIVQAL 72

Query: 168 RKSK--LLEVTEDGTKVRRT-------VVVQDKPDVDECTIYVEKLPPEAEHDYIESVFS 218
            KSK  L+EV+ D TK+RR+       V  + K DV   ++Y++  P +A  D I+    
Sbjct: 73  SKSKANLMEVSADKTKIRRSPSRPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLD 132

Query: 219 KYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
             G++  + + +       KG  F  F + + A K
Sbjct: 133 DKGQILNIQMRRTLHK-TFKGSIFAVFDSIQSAKK 166

Binds to the 3' poly(U) terminii of nascent RNA polymerase III transcripts, protecting them from exonuclease digestion and facilitating their folding and maturation.

Rattus norvegicus (taxid: 10116)

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	299
189235300	504	PREDICTED: similar to multi-sex-combs [T	0.578	0.343	0.517	2e-46
242024527	527	lupus la ribonucleoprotein, putative [Pe	0.515	0.292	0.564	2e-43
383859770	612	PREDICTED: uncharacterized protein LOC10	0.521	0.254	0.506	1e-41
307212601	625	La-related protein 7 [Harpegnathos salta	0.525	0.251	0.525	3e-41
380025220	609	PREDICTED: la-related protein 7-like [Ap	0.521	0.256	0.493	8e-41
345492037	638	PREDICTED: la-related protein 7-like [Na	0.602	0.282	0.470	9e-41
328790716	624	PREDICTED: la-related protein 7-like [Ap	0.521	0.25	0.493	9e-41
322795732	764	hypothetical protein SINV_08003 [Solenop	0.521	0.204	0.540	9e-41
332026973	835	La-related protein 7 [Acromyrmex echinat	0.521	0.186	0.528	2e-40
340727580	597	PREDICTED: LOW QUALITY PROTEIN: la-relat	0.521	0.261	0.512	2e-40

>gi|189235300|ref|XP_974730.2| PREDICTED: similar to multi-sex-combs [Tribolium castaneum] gi|270004171|gb|EFA00619.1| hypothetical protein TcasGA2_TC003495 [Tribolium castaneum]

 Score =  192 bits (488), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 91/176 (51%), Positives = 132/176 (75%), Gaps = 3/176 (1%)

Query: 80  METEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQES 139
           ME E  +N +     + +K   GRHRKKQLY  I+  MEFY SDSNL KDRF SQL++E+
Sbjct: 1   MENETKENANAHDDSILKK---GRHRKKQLYNSILQQMEFYFSDSNLTKDRFLSQLIKEN 57

Query: 140 PEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTI 199
           P ++++VFLK NK+ +LT   DD+ KA++KS+L+E++ED +++RRT  V++K +VD+CTI
Sbjct: 58  PFVDLNVFLKFNKITKLTTSIDDIQKAVQKSQLIELSEDRSRIRRTKPVKEKANVDDCTI 117

Query: 200 YVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           YVE+L  +A H+++ SVFS++G V YVS+PK+K+   +KGFAFVEF  ++EA  AL
Sbjct: 118 YVERLKSDATHEWLNSVFSEFGNVVYVSIPKYKNNSAIKGFAFVEFEKEKEAQNAL 173

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242024527|ref|XP_002432679.1| lupus la ribonucleoprotein, putative [Pediculus humanus corporis] gi|212518149|gb|EEB19941.1| lupus la ribonucleoprotein, putative [Pediculus humanus corporis]

 Score =  182 bits (461), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 87/154 (56%), Positives = 119/154 (77%)

Query: 103 RHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDD 162
           R RKKQLY+ I   MEFY SDSNL+KDRF SQL+++ PE+++ +FLK NK+ +LT    D
Sbjct: 21  RRRKKQLYELIRERMEFYFSDSNLQKDRFLSQLIKDDPEVDLEIFLKFNKIHQLTTSLHD 80

Query: 163 VVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGK 222
           + KAL+KS+ L +TED +KV R   V++K +VD CTIYVE+L  +A+HD+++ +FS+YGK
Sbjct: 81  LKKALKKSQFLSLTEDKSKVFRNTPVKEKLNVDACTIYVEQLSYDADHDWLKLIFSRYGK 140

Query: 223 VTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           V Y+S+PK+K TGK+KGFAFVEF T E A  AL+
Sbjct: 141 VDYISIPKYKGTGKIKGFAFVEFETPESAKAALD 174

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383859770|ref|XP_003705365.1| PREDICTED: uncharacterized protein LOC100883293 [Megachile rotundata]

 Score =  176 bits (446), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 79/156 (50%), Positives = 114/156 (73%)

Query: 100 GGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHD 159
           G  R RKK L+  I+  MEFY SD+NL KDRF S L++E P +++ +F++CNK+  LT D
Sbjct: 43  GKPRLRKKALHAAILKQMEFYFSDANLNKDRFLSNLIKEDPYVDLMIFMRCNKIRELTTD 102

Query: 160 PDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSK 219
            + V KAL+ S +L +++DGTKV R   +  K ++D+CT+YV+ LPP+A+H+ + ++FS+
Sbjct: 103 VNRVTKALQASTILSLSKDGTKVCRVTPIVQKENIDDCTVYVQNLPPDADHEMLSTIFSQ 162

Query: 220 YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           YG+V YVS+PKFK   K+KGFAFVEF+  EEA K L
Sbjct: 163 YGQVVYVSVPKFKINKKIKGFAFVEFNAPEEANKCL 198

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307212601|gb|EFN88316.1| La-related protein 7 [Harpegnathos saltator]

 Score =  175 bits (443), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 84/160 (52%), Positives = 115/160 (71%), Gaps = 3/160 (1%)

Query: 100 GGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHD 159
           G  R RKK L+  I+  MEFY SD+NL KDR+ S+LL++SP + + VF   NKL+ LT D
Sbjct: 41  GKPRLRKKALHAAILKQMEFYFSDANLSKDRYLSELLKKSPYVALDVFTNFNKLSTLTTD 100

Query: 160 PDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSK 219
            + + KAL KS +L+V+EDGTKV R   +  K ++DECT+YV+ LPP+++HD++ S FSK
Sbjct: 101 TNRIAKALEKSTMLKVSEDGTKVCRLTPINKKENIDECTVYVQNLPPDSDHDWLISAFSK 160

Query: 220 YGKVTYVSLPKFKSTGKLKGFAFVEFST---KEEAAKALE 256
           YGKV YVS+P+++S  K+KGFAFVEF T    EE  KA +
Sbjct: 161 YGKVVYVSIPRYQSNKKIKGFAFVEFDTPAGAEECIKAFQ 200

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380025220|ref|XP_003696375.1| PREDICTED: la-related protein 7-like [Apis florea]

 Score =  173 bits (439), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 77/156 (49%), Positives = 113/156 (72%)

Query: 100 GGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHD 159
           G  R RKK L+  I+  MEFY SD+NL KDRF S LL+E P I+++VFL  N++  LT D
Sbjct: 43  GKPRLRKKALHAAILKQMEFYFSDANLSKDRFLSNLLKEDPYIDLNVFLSFNRIKELTTD 102

Query: 160 PDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSK 219
            + + KA+  SK+L ++EDGTK+RR   +  + ++DECT+YV+ LPP+++H+ + S+FS+
Sbjct: 103 SNRIAKAVETSKMLSLSEDGTKIRRITPIISRENIDECTVYVQNLPPDSDHETLSSIFSQ 162

Query: 220 YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           YG+V Y+S+P+FK+  K+KGFAFVEF   + A K L
Sbjct: 163 YGQVVYISIPRFKNNKKIKGFAFVEFDIPQSAKKCL 198

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345492037|ref|XP_001600355.2| PREDICTED: la-related protein 7-like [Nasonia vitripennis]

 Score =  173 bits (438), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 87/185 (47%), Positives = 123/185 (66%), Gaps = 5/185 (2%)

Query: 76  VPISMETEASDNVDKDLSDLQRK-----DGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDR 130
           VP   + E    V KD ++  +K      G  R RKK  +  I+  MEFY  DSNL KDR
Sbjct: 19  VPQVHQPEVEAPVPKDTNETNQKANDIPHGKPRLRKKAFHAAILKQMEFYFGDSNLSKDR 78

Query: 131 FFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD 190
           F S+L++E P++ +  F+K NK+  LT D   + KAL KS +L+V+E+G  VRR   + +
Sbjct: 79  FLSELIKECPDVPLDTFIKFNKIRSLTTDIGRIAKALSKSTMLQVSENGKTVRRITPIVE 138

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
           K ++DECT+YV++LP +A+H+++ S+FS+YG V YVS+PKFK+T K+KGFAFVEF T E 
Sbjct: 139 KQNIDECTVYVQRLPSDADHEWLSSLFSEYGPVAYVSIPKFKATQKIKGFAFVEFETPEG 198

Query: 251 AAKAL 255
           A K L
Sbjct: 199 AKKCL 203

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328790716|ref|XP_001120336.2| PREDICTED: la-related protein 7-like [Apis mellifera]

 Score =  173 bits (438), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 77/156 (49%), Positives = 113/156 (72%)

Query: 100 GGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHD 159
           G  R RKK L+  I+  MEFY SD+NL KDRF S LL+E P I+++VFL  N++  LT D
Sbjct: 43  GKPRLRKKALHAAILKQMEFYFSDANLSKDRFLSNLLKEDPYIDLNVFLSFNRIKELTTD 102

Query: 160 PDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSK 219
            + + KA+  SK+L ++EDGTK+RR   +  + ++DECT+YV+ LPP+++H+ + S+FS+
Sbjct: 103 SNRIAKAVETSKMLSLSEDGTKIRRITPIISRENIDECTVYVQNLPPDSDHETLSSIFSQ 162

Query: 220 YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           YG+V Y+S+P+FK+  K+KGFAFVEF   + A K L
Sbjct: 163 YGQVVYISIPRFKNNKKIKGFAFVEFDIPQSAKKCL 198

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322795732|gb|EFZ18411.1| hypothetical protein SINV_08003 [Solenopsis invicta]

 Score =  173 bits (438), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 87/161 (54%), Positives = 114/161 (70%), Gaps = 5/161 (3%)

Query: 100 GGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHD 159
           G  R RKK L+  I   MEFY SDSNL KDRF S+LL+E+  I++ VF KCNKL  LT D
Sbjct: 38  GKPRLRKKALHALIRKQMEFYFSDSNLSKDRFLSKLLKENSYIDLEVFTKCNKLQELTTD 97

Query: 160 -----PDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIE 214
                 + + KAL+ S +L+V+EDGTKV R   +Q K +VD+CTIYV+ LPP+A+H+++ 
Sbjct: 98  EHMITTNRIAKALQGSTMLKVSEDGTKVCRVTPIQTKENVDQCTIYVQNLPPDADHEWLI 157

Query: 215 SVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           SVFSKYG V YVS+P++K+  K+KGFAFVEF T   A + L
Sbjct: 158 SVFSKYGTVDYVSIPRYKNNRKIKGFAFVEFDTPNHAQECL 198

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332026973|gb|EGI67069.1| La-related protein 7 [Acromyrmex echinatior]

 Score =  172 bits (436), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 84/159 (52%), Positives = 115/159 (72%), Gaps = 3/159 (1%)

Query: 100 GGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHD 159
           G  R RKK L+  I+  MEFY SD+NL KDR+ S LL+E+P +++ VF + NKL  LT D
Sbjct: 39  GKPRLRKKALHASILKQMEFYFSDANLNKDRYLSGLLKENPYVDLEVFTRFNKLRELTTD 98

Query: 160 PDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSK 219
            + + KAL+ S +L+V+EDGTKV R   +Q K D+D+CTIYV+ LPP+A+HD++ S+FSK
Sbjct: 99  INRIAKALQGSTMLKVSEDGTKVCRLTPIQKKRDIDQCTIYVQNLPPDADHDWLISIFSK 158

Query: 220 YGKVTYVSLPKFKSTGKLKGFAFVEF---STKEEAAKAL 255
           YG V YVS+P+++S  K+KGFAFVEF   S+ EE  K  
Sbjct: 159 YGLVEYVSIPRYRSNRKIKGFAFVEFDKPSSAEECIKTF 197

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340727580|ref|XP_003402119.1| PREDICTED: LOW QUALITY PROTEIN: la-related protein 7-like [Bombus terrestris]

 Score =  172 bits (436), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 80/156 (51%), Positives = 112/156 (71%)

Query: 100 GGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHD 159
           G  R RKK L+  I+  MEFY SD+NL KDRF S L++E P +++SVFLK NK+  LT D
Sbjct: 43  GKPRLRKKALHAAILKQMEFYFSDANLSKDRFLSNLVKEDPYVDLSVFLKFNKIRELTTD 102

Query: 160 PDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSK 219
            + + K ++ S +L ++EDG KVRR   +  K + DECT+YV+ LPP+A+H+ + S+FS+
Sbjct: 103 INRISKGIQASTILSLSEDGMKVRRITPIVPKENTDECTVYVQNLPPDADHETLSSIFSQ 162

Query: 220 YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           YG+V YVS+P+FK+  K+KGFAFVEF+T E A   L
Sbjct: 163 YGQVVYVSIPRFKNNKKIKGFAFVEFNTIESAKNCL 198

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

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	299
FB|FBgn0260771	595	Larp7 "La related protein 7" [	0.581	0.292	0.426	3.5e-34
UNIPROTKB|F1NJ86	233	LARP7 "Uncharacterized protein	0.608	0.781	0.420	9.5e-34
UNIPROTKB|D6RFF0	299	LARP7 "La-related protein 7" [	0.608	0.608	0.417	1.2e-33
UNIPROTKB|F1MR14	578	F1MR14 "Uncharacterized protei	0.605	0.313	0.414	1.8e-33
RGD|1592474	571	Larp7 "La ribonucleoprotein do	0.605	0.316	0.4	2.7e-33
UNIPROTKB|Q5XI01	571	Larp7 "La-related protein 7" [	0.605	0.316	0.4	2.7e-33
UNIPROTKB|E1BQG3	602	LARP7 "Uncharacterized protein	0.608	0.302	0.420	3e-33
UNIPROTKB|Q4G0J3	582	LARP7 "La-related protein 7" [	0.608	0.312	0.417	3.1e-33
UNIPROTKB|E2QW27	582	LARP7 "Uncharacterized protein	0.605	0.310	0.412	3.1e-33
ZFIN|ZDB-GENE-030131-6896	555	larp7 "La ribonucleoprotein do	0.612	0.329	0.406	3.6e-33

FB|FBgn0260771 Larp7 "La related protein 7" [Drosophila melanogaster (taxid:7227)]

 Score = 375 (137.1 bits), Expect = 3.5e-34, P = 3.5e-34
 Identities = 75/176 (42%), Positives = 108/176 (61%)

Query:    81 ETEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESP 140
             E  + +   +D S   +KDGG R RK+ L+  I   MEFY  D+NL KDRF  + +++ P
Sbjct:    33 EENSKEPAPEDASP-DKKDGG-RKRKRHLFNSIRGQMEFYFGDANLSKDRFLRRYVEQDP 90

Query:   141 EIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIY 200
              + + +FL  NK+  LT D   + KAL  S+LLE+ E   KV+R   + D+ DV++ T+Y
Sbjct:    91 YVPLEIFLTFNKIKTLTQDVQQIAKALSNSQLLELDETELKVKRRTKLPDQRDVNDKTLY 150

Query:   201 VEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             VE LP  A HD+++ VFS+YG V YVSLP +  T K+K FAF+EF       KA++
Sbjct:   151 VEALPANATHDWLKEVFSRYGPVAYVSLPHYPGTKKIKEFAFIEFEKSGSLEKAVK 206

GO:0005634 "nucleus" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0097322 "7SK snRNA binding" evidence=IDA

UNIPROTKB|F1NJ86 LARP7 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 367 (134.2 bits), Expect = 9.5e-34, P = 9.5e-34
 Identities = 79/188 (42%), Positives = 120/188 (63%)

Query:    80 METEAS-DNVDKDLSDLQRKDGGG--RHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLL 136
             METEA+ D   ++ S  Q+K+     R R KQ+   I   ++F+  D NL KDRF  + +
Sbjct:     4 METEAARDKAMEEESTEQKKEREKKKRSRVKQVLADIAKQVDFWFGDVNLHKDRFLREQI 63

Query:   137 QESPE--IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP-D 193
             ++S +  +++S+ +  NK+ +LT D   + +A++ S ++E+  +GT++RR   + ++P D
Sbjct:    64 EKSRDGYVDISLLVSFNKMKKLTTDGKLIARAVKSSSVVELDLEGTRIRRRRPLGERPKD 123

Query:   194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
             VD  T+YVE LP    H +IE VF K G V YVS+P++KSTG  KGFAFVEF TKE+A K
Sbjct:   124 VDSRTVYVELLPKNVNHSWIERVFGKCGNVVYVSIPRYKSTGDPKGFAFVEFETKEQAEK 183

Query:   254 ALELGLNP 261
             A+E   NP
Sbjct:   184 AIEFLNNP 191

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|D6RFF0 LARP7 "La-related protein 7" [Homo sapiens (taxid:9606)]

 Score = 366 (133.9 bits), Expect = 1.2e-33, P = 1.2e-33
 Identities = 79/189 (41%), Positives = 121/189 (64%)

Query:    80 METEAS--DNVDKDLSDLQRKD--GGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQL 135
             METE+   + V ++ S  ++K+     R R KQ+   I   ++F+  D+NL KDRF  + 
Sbjct:     1 METESGNQEKVMEEESTEKKKEVEKKKRSRVKQVLADIAKQVDFWFGDANLHKDRFLREQ 60

Query:   136 LQESPE--IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP- 192
             +++S +  +++S+ +  NK+ +LT D   + +ALR S ++E+  +GT++RR   + ++P 
Sbjct:    61 IEKSRDGYVDISLLVSFNKMKKLTTDGKLIARALRSSAVVELDLEGTRIRRKKPLGERPK 120

Query:   193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
             D DE T+YVE LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+AA
Sbjct:   121 DEDERTVYVELLPKNVNHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAA 180

Query:   253 KALELGLNP 261
             KA+E   NP
Sbjct:   181 KAIEFLNNP 189

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F1MR14 F1MR14 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 368 (134.6 bits), Expect = 1.8e-33, P = 1.8e-33
 Identities = 78/188 (41%), Positives = 122/188 (64%)

Query:    80 METEASDNVDKDLSD-LQRK--DGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLL 136
             ME E S N +K + + +++K  +   R R KQ+   I+  ++F+  D+NL KDRF  + +
Sbjct:     1 MEAE-SGNKEKAMEESIEKKKEEKKKRSRVKQVLADIVKQVDFWFGDANLHKDRFLREQI 59

Query:   137 QESPE--IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP-D 193
             ++S +  +++S+ +  NK+ +LT D   + +AL+ S ++E+  +GT++RR   + ++P D
Sbjct:    60 EKSRDGYVDISLLVSFNKMKKLTTDGKLIARALKSSAVVELDLEGTRIRRKKPLGERPKD 119

Query:   194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
              DE T+YVE LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+AAK
Sbjct:   120 EDERTVYVELLPKNVNHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAK 179

Query:   254 ALELGLNP 261
             A+E   NP
Sbjct:   180 AIEFLNNP 187

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

RGD|1592474 Larp7 "La ribonucleoprotein domain family, member 7" [Rattus norvegicus (taxid:10116)]

 Score = 366 (133.9 bits), Expect = 2.7e-33, P = 2.7e-33
 Identities = 74/185 (40%), Positives = 120/185 (64%)

Query:    80 METEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQES 139
             METE    +++  ++ ++++   R R KQ+   I   ++F+  D+NL KDRF  + +++S
Sbjct:     1 METENQKTMEES-TEKRKEEKKKRSRVKQVLADIAKQVDFWFGDANLHKDRFLREQIEKS 59

Query:   140 PE--IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP-DVDE 196
              +  +++S+ +  NK+ +LT D   + +AL+ S ++E+  +GT++RR   + ++P D +E
Sbjct:    60 RDGYVDISLLVSFNKMKKLTTDGKLIARALKSSSVVELDLEGTRIRRKKPLGERPKDEEE 119

Query:   197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
              T+YVE LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+AAKA+E
Sbjct:   120 RTVYVELLPKNVTHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIE 179

Query:   257 LGLNP 261
                NP
Sbjct:   180 FLNNP 184

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0035562 "negative regulation of chromatin binding" evidence=ISO

GO:0036093 "germ cell proliferation" evidence=ISO

GO:1900087 "positive regulation of G1/S transition of mitotic cell cycle" evidence=ISO

UNIPROTKB|Q5XI01 Larp7 "La-related protein 7" [Rattus norvegicus (taxid:10116)]

 Score = 366 (133.9 bits), Expect = 2.7e-33, P = 2.7e-33
 Identities = 74/185 (40%), Positives = 120/185 (64%)

Query:    80 METEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQES 139
             METE    +++  ++ ++++   R R KQ+   I   ++F+  D+NL KDRF  + +++S
Sbjct:     1 METENQKTMEES-TEKRKEEKKKRSRVKQVLADIAKQVDFWFGDANLHKDRFLREQIEKS 59

Query:   140 PE--IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP-DVDE 196
              +  +++S+ +  NK+ +LT D   + +AL+ S ++E+  +GT++RR   + ++P D +E
Sbjct:    60 RDGYVDISLLVSFNKMKKLTTDGKLIARALKSSSVVELDLEGTRIRRKKPLGERPKDEEE 119

Query:   197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
              T+YVE LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+AAKA+E
Sbjct:   120 RTVYVELLPKNVTHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAAKAIE 179

Query:   257 LGLNP 261
                NP
Sbjct:   180 FLNNP 184

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E1BQG3 LARP7 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 367 (134.2 bits), Expect = 3.0e-33, P = 3.0e-33
 Identities = 79/188 (42%), Positives = 120/188 (63%)

Query:    80 METEAS-DNVDKDLSDLQRKDGGG--RHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLL 136
             METEA+ D   ++ S  Q+K+     R R KQ+   I   ++F+  D NL KDRF  + +
Sbjct:     4 METEAARDKAMEEESTEQKKEREKKKRSRVKQVLADIAKQVDFWFGDVNLHKDRFLREQI 63

Query:   137 QESPE--IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP-D 193
             ++S +  +++S+ +  NK+ +LT D   + +A++ S ++E+  +GT++RR   + ++P D
Sbjct:    64 EKSRDGYVDISLLVSFNKMKKLTTDGKLIARAVKSSSVVELDLEGTRIRRRRPLGERPKD 123

Query:   194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
             VD  T+YVE LP    H +IE VF K G V YVS+P++KSTG  KGFAFVEF TKE+A K
Sbjct:   124 VDSRTVYVELLPKNVNHSWIERVFGKCGNVVYVSIPRYKSTGDPKGFAFVEFETKEQAEK 183

Query:   254 ALELGLNP 261
             A+E   NP
Sbjct:   184 AIEFLNNP 191

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|Q4G0J3 LARP7 "La-related protein 7" [Homo sapiens (taxid:9606)]

 Score = 366 (133.9 bits), Expect = 3.1e-33, P = 3.1e-33
 Identities = 79/189 (41%), Positives = 121/189 (64%)

Query:    80 METEAS--DNVDKDLSDLQRKD--GGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQL 135
             METE+   + V ++ S  ++K+     R R KQ+   I   ++F+  D+NL KDRF  + 
Sbjct:     1 METESGNQEKVMEEESTEKKKEVEKKKRSRVKQVLADIAKQVDFWFGDANLHKDRFLREQ 60

Query:   136 LQESPE--IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP- 192
             +++S +  +++S+ +  NK+ +LT D   + +ALR S ++E+  +GT++RR   + ++P 
Sbjct:    61 IEKSRDGYVDISLLVSFNKMKKLTTDGKLIARALRSSAVVELDLEGTRIRRKKPLGERPK 120

Query:   193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
             D DE T+YVE LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+AA
Sbjct:   121 DEDERTVYVELLPKNVNHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAA 180

Query:   253 KALELGLNP 261
             KA+E   NP
Sbjct:   181 KAIEFLNNP 189

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|E2QW27 LARP7 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 366 (133.9 bits), Expect = 3.1e-33, P = 3.1e-33
 Identities = 78/189 (41%), Positives = 118/189 (62%)

Query:    80 METEASDNVDKDLSDLQRK----DGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQL 135
             METE   N +K + +   K    +   R R KQ+   I   ++F+  D+NL KDRF  + 
Sbjct:     1 METEGG-NQEKAMEECTEKKKEVEKKKRSRVKQVLADIAKQVDFWFGDANLHKDRFLREQ 59

Query:   136 LQESPE--IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP- 192
             +++S +  +++S+ +  NK+ +LT D   + +AL+ S ++E+  +GT++RR   + ++P 
Sbjct:    60 IEKSRDGYVDISLLVSFNKMKKLTTDGKLIARALKSSSVVELDLEGTRIRRKKPLGERPK 119

Query:   193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
             D DE T+YVE LP    H +IE VF K G V Y+S+P +KSTG  KGFAFVEF TKE+AA
Sbjct:   120 DEDERTVYVELLPKNVNHSWIERVFGKCGNVVYISIPHYKSTGDPKGFAFVEFETKEQAA 179

Query:   253 KALELGLNP 261
             KA+E   NP
Sbjct:   180 KAIEFLNNP 188

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

ZFIN|ZDB-GENE-030131-6896 larp7 "La ribonucleoprotein domain family, member 7" [Danio rerio (taxid:7955)]

 Score = 364 (133.2 bits), Expect = 3.6e-33, P = 3.6e-33
 Identities = 76/187 (40%), Positives = 115/187 (61%)

Query:    82 TEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPE 141
             +   D    DLS+ +  +   R R KQL   +   +EF+  D NL KDRF   ++++S +
Sbjct:    15 SSVGDTACADLSEKKDNEKKKRSRVKQLLSDVKKQVEFWFGDVNLHKDRFMKSIIEQSRD 74

Query:   142 --IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP-DVDECT 198
               I+++V    N++  LT D   + +AL+ S ++EV ++GT++RR   + + P DVD  T
Sbjct:    75 GYIDIAVLTTFNRMKNLTADVKLIARALKNSTIVEVNDEGTRIRRKEPLGETPKDVDSRT 134

Query:   199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
             +YVE LP    H ++E VFSK G V Y+S+P++KST   KGFAFVEF T+E+A KA+E+ 
Sbjct:   135 VYVELLPKTVTHIWLERVFSKCGHVVYISIPRYKSTRHSKGFAFVEFETQEQAQKAVEML 194

Query:   259 LNPCPPD 265
              NP P D
Sbjct:   195 NNP-PED 200

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006396 "RNA processing" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by 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	299
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-28
cd07323	75	cd07323, LAM, LA motif RNA-binding domain	9e-22
cd07323	75	cd07323, LAM, LA motif RNA-binding domain	3e-19
smart00360	73	smart00360, RRM, RNA recognition motif	4e-16
smart00715	80	smart00715, LA, Domain in the RNA-binding Lupus La	2e-14
cd08028	82	cd08028, LARP_3, La RNA-binding domain of La-relat	2e-14
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	5e-14
cd08029	76	cd08029, LA_like_fungal, La-motif domain of fungal	2e-13
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	4e-13
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-13
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-12
smart00715	80	smart00715, LA, Domain in the RNA-binding Lupus La	2e-12
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-12
cd08033	77	cd08033, LARP_6, La RNA-binding domain of La-relat	4e-12
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	9e-12
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	9e-12
cd08029	76	cd08029, LA_like_fungal, La-motif domain of fungal	1e-11
cd08032	82	cd08032, LARP_7, La RNA-binding domain of La-relat	1e-11
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-11
cd08028	82	cd08028, LARP_3, La RNA-binding domain of La-relat	4e-11
cd08030	90	cd08030, LA_like_plant, La-motif domain of plant p	7e-11
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	7e-11
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-10
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-10
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	3e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	5e-10
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	7e-10
cd08033	77	cd08033, LARP_6, La RNA-binding domain of La-relat	8e-10
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	8e-10
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-09
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-09
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	1e-09
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-09
pfam05383	59	pfam05383, La, La domain	3e-09
pfam05383	59	pfam05383, La, La domain	3e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-09
cd08030	90	cd08030, LA_like_plant, La-motif domain of plant p	4e-09
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-09
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	4e-09
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	5e-09
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	5e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	8e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	8e-09
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	1e-08
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-08
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-08
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-08
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-08
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	3e-08
cd08031	75	cd08031, LARP_4_5_like, La RNA-binding domain of p	3e-08
cd08032	82	cd08032, LARP_7, La RNA-binding domain of La-relat	4e-08
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-08
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	4e-08
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-08
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	5e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	5e-08
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	5e-08
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	6e-08
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	6e-08
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	6e-08
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	7e-08
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	7e-08
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	9e-08
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-07
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	1e-07
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	2e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-07
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-07
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-07
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-07
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	4e-07
cd08031	75	cd08031, LARP_4_5_like, La RNA-binding domain of p	5e-07
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	6e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	7e-07
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	8e-07
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	9e-07
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	1e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	2e-06
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	2e-06
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-06
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-06
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	2e-06
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-06
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-06
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	3e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	3e-06
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-06
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	4e-06
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	4e-06
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	4e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	6e-06
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	8e-06
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	8e-06
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	8e-06
cd12611	81	cd12611, RRM1_NGR1_NAM8_like, RNA recognition moti	8e-06
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	9e-06
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	9e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-05
cd12426	79	cd12426, RRM4_PTBPH3, RNA recognition motif 4 in p	1e-05
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	1e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	1e-05
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	1e-05
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	2e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	2e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	2e-05
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	2e-05
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	3e-05
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	3e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	4e-05
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	4e-05
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	4e-05
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	4e-05
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-05
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	4e-05
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	4e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	4e-05
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	4e-05
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	5e-05
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	6e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	6e-05
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	6e-05
cd12405	72	cd12405, RRM3_NCL, RNA recognition motif 3 in vert	6e-05
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	7e-05
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	7e-05
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	7e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	8e-05
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	8e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	9e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	1e-04
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	1e-04
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	1e-04
cd12753	85	cd12753, RRM1_RBM10, RNA recognition motif 1 in ve	1e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	1e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	1e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	2e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	2e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-04
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-04
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	3e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	3e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	3e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	3e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	3e-04
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	3e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	3e-04
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	3e-04
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	4e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	4e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	4e-04
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	4e-04
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	4e-04
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	5e-04
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	5e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	5e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-04
cd12466	70	cd12466, RRM2_AtRSp31_like, RNA recognition motif	6e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	6e-04
cd08035	75	cd08035, LARP_4, La RNA-binding domain of La-relat	6e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	6e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	7e-04
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	8e-04
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	8e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	9e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.001
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	0.001
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.001
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	0.001
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.001
cd12562	86	cd12562, RRM2_RBM5_like, RNA recognition motif 2 i	0.001
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	0.001
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	0.001
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	0.001
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	0.001
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	0.001
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.001
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	0.001
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	0.001
cd08035	75	cd08035, LARP_4, La RNA-binding domain of La-relat	0.002
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	0.002
cd08034	73	cd08034, LARP_1_2, La RNA-binding domain proteins	0.002
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	0.002
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	0.002
cd08036	75	cd08036, LARP_5, La RNA-binding domain of La-relat	0.002
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	0.002
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	0.002
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	0.002
cd08037	73	cd08037, LARP_1, La RNA-binding domain of La-relat	0.002
cd12452	88	cd12452, RRM_ARP_like, RNA recognition motif in ye	0.002
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	0.003
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	0.003
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	0.003
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.004
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	0.004
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	0.004
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	0.004
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	0.004
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.004
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	0.004
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	0.004
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	0.004

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

 Score =  104 bits (261), Expect = 2e-28
 Identities = 36/59 (61%), Positives = 47/59 (79%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           T+YVE LP  A H+++++VFSKYG V YVSLP++K TG +KGFAF+EF T EEA KA +
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACK 59

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|153396 cd07323, LAM, LA motif RNA-binding domain

 Score = 86.4 bits (215), Expect = 9e-22
 Identities = 31/75 (41%), Positives = 50/75 (66%)

Query: 110 YQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRK 169
            ++I   +E+Y SD NL KDRF   L+ +   + +S+    N++ +LT D + +++ALR 
Sbjct: 1   LEKIKKQVEYYFSDENLCKDRFLRSLMDDDGWVPLSLLASFNRVKKLTTDVELILEALRD 60

Query: 170 SKLLEVTEDGTKVRR 184
           S ++EV+EDGTKVRR
Sbjct: 61  SSVVEVSEDGTKVRR 75

This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). 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. Length = 75

>gnl|CDD|153396 cd07323, LAM, LA motif RNA-binding domain

 Score = 79.9 bits (198), Expect = 3e-19
 Identities = 28/67 (41%), Positives = 46/67 (68%)

Query: 1  MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVT 60
          +E+Y SD NL KDRF   L+ +   + +S+    N++ +LT D + +++ALR S ++EV+
Sbjct: 8  VEYYFSDENLCKDRFLRSLMDDDGWVPLSLLASFNRVKKLTTDVELILEALRDSSVVEVS 67

Query: 61 EDGTKVK 67
          EDGTKV+
Sbjct: 68 EDGTKVR 74

This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). 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. Length = 75

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

 Score = 71.1 bits (175), Expect = 4e-16
 Identities = 31/60 (51%), Positives = 42/60 (70%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           T++V  LPP+   + +  +FSK+GKV  V L + K TGK KGFAFVEF ++E+A KALE 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Length = 73

>gnl|CDD|128955 smart00715, LA, Domain in the RNA-binding Lupus La protein; unknown function

 Score = 66.9 bits (164), Expect = 2e-14
 Identities = 30/78 (38%), Positives = 46/78 (58%), Gaps = 1/78 (1%)

Query: 109 LYQQIMNLMEFYLSDSNLRKDRFF-SQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKAL 167
           L Q+I   +E+Y SD NL +D+F   ++ +    + +S      ++  LT D + +V+AL
Sbjct: 3   LKQKIKKQVEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEAL 62

Query: 168 RKSKLLEVTEDGTKVRRT 185
           R S  LEV+EDG KVRR 
Sbjct: 63  RSSPKLEVSEDGLKVRRR 80

Length = 80

>gnl|CDD|153397 cd08028, LARP_3, La RNA-binding domain of La-related protein 3

 Score = 66.6 bits (163), Expect = 2e-14
 Identities = 33/80 (41%), Positives = 53/80 (66%), Gaps = 3/80 (3%)

Query: 108 QLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPE-IEVSVFLKCNKLARLTHDPDDVVKA 166
            L ++I+  +E+Y  D NL +D+F  + ++E    + + V LK N+L  L+ DP+ + KA
Sbjct: 3   DLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKA 62

Query: 167 LRKSK--LLEVTEDGTKVRR 184
           L+KSK  L+EV+ED TK+RR
Sbjct: 63  LKKSKSGLIEVSEDKTKIRR 82

This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B). Length = 82

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

 Score = 65.7 bits (161), Expect = 5e-14
 Identities = 27/71 (38%), Positives = 40/71 (56%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            T+++  LP +A  + ++ +FS++G+V Y  + K K TG  KG AFV+F TKE A K LE
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 257 LGLNPCPPDYQ 267
              N       
Sbjct: 61  AADNAEDSGLS 71

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|153398 cd08029, LA_like_fungal, La-motif domain of fungal proteins similar to the La autoantigen

 Score = 63.9 bits (156), Expect = 2e-13
 Identities = 32/74 (43%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 112 QIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCN-KLARLTHDPDDVVKALRKS 170
           +I   +EFY SDSNL  D+F   L   S    V +    + K  R     + VV+ALR+S
Sbjct: 3   EIRKQVEFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRFQPLEAVVEALRES 62

Query: 171 KLLEVTEDGTKVRR 184
           +LLEV+EDG  VRR
Sbjct: 63  ELLEVSEDGENVRR 76

This domain is found in fungal 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. Length = 76

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

 Score = 63.1 bits (154), Expect = 4e-13
 Identities = 25/58 (43%), Positives = 38/58 (65%), Gaps = 1/58 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           ++V  LPP+   + +  +FSK+G++  V + +    GK KGFAFVEF + E+A KALE
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVR-DKDGKSKGFAFVEFESPEDAEKALE 57

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

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

 Score = 62.6 bits (153), Expect = 5e-13
 Identities = 24/58 (41%), Positives = 39/58 (67%), Gaps = 1/58 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           ++V  LPP+   + ++ +FSK+G +  + + +   TG+ KGFAFVEF  +E+A KALE
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVR-DETGRSKGFAFVEFEDEEDAEKALE 57

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

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

 Score = 62.2 bits (152), Expect = 1e-12
 Identities = 25/59 (42%), Positives = 38/59 (64%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           TI V  L  +A+ D +  +F  +G ++ V L K K TG+ +GFAFV F T+E+A +A+E
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE 59

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|128955 smart00715, LA, Domain in the RNA-binding Lupus La protein; unknown function

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 25/68 (36%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 1  MEFYLSDSNLRKDRFF-SQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEV 59
          +E+Y SD NL +D+F   ++ +    + +S      ++  LT D + +V+ALR S  LEV
Sbjct: 11 VEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSPKLEV 70

Query: 60 TEDGTKVK 67
          +EDG KV+
Sbjct: 71 SEDGLKVR 78

Length = 80

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

 Score = 61.5 bits (150), Expect = 2e-12
 Identities = 25/59 (42%), Positives = 38/59 (64%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           T+++  L P  +  YI S F++ G+VT V + + K TGK  G+ FVEF+T E A +AL+
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQ 59

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|153402 cd08033, LARP_6, La RNA-binding domain of La-related protein 6

 Score = 60.4 bits (147), Expect = 4e-12
 Identities = 32/76 (42%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 111 QQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCN--KLARLTHDPDDVVKALR 168
           Q+I+  +E+Y SD NL KD F  + ++ + E  V + L  +  K+  LT D   V  ALR
Sbjct: 2   QKIVKQVEYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALR 61

Query: 169 KSKLLEVTEDGTKVRR 184
           +S  L V+EDG KVRR
Sbjct: 62  RSSKLVVSEDGKKVRR 77

This domain is found in animal and plant 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. Length = 77

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

 Score = 59.5 bits (145), Expect = 9e-12
 Identities = 21/58 (36%), Positives = 35/58 (60%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           ++V KL      D+++ +FS YG V  V LP  +     +G+A+VEF + E+A KA++
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIK 58

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

 Score = 59.3 bits (144), Expect = 9e-12
 Identities = 23/60 (38%), Positives = 37/60 (61%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           ++V  L  +A+ D I   F +YG+++ V LP    +G+ KGF +VEFS++E A  AL+  
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

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|153398 cd08029, LA_like_fungal, La-motif domain of fungal proteins similar to the La autoantigen

 Score = 58.9 bits (143), Expect = 1e-11
 Identities = 29/67 (43%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 2  EFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCN-KLARLTHDPDDVVKALRKSKLLEVT 60
          EFY SDSNL  D+F   L   S    V +    + K  R     + VV+ALR+S+LLEV+
Sbjct: 9  EFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRFQPLEAVVEALRESELLEVS 68

Query: 61 EDGTKVK 67
          EDG  V+
Sbjct: 69 EDGENVR 75

This domain is found in fungal 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. Length = 76

>gnl|CDD|153401 cd08032, LARP_7, La RNA-binding domain of La-related protein 7

 Score = 59.2 bits (143), Expect = 1e-11
 Identities = 29/82 (35%), Positives = 52/82 (63%), Gaps = 2/82 (2%)

Query: 105 RKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPE--IEVSVFLKCNKLARLTHDPDD 162
           R KQL   I   ++F+  D NL KDRF  + +++S +  I++S+ +  NK+ +LT D   
Sbjct: 1   RVKQLLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKL 60

Query: 163 VVKALRKSKLLEVTEDGTKVRR 184
           + +AL+ S ++E+  +GT++RR
Sbjct: 61  IARALKNSSVVELNLEGTRIRR 82

LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation. Length = 82

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

 Score = 58.8 bits (143), Expect = 1e-11
 Identities = 25/62 (40%), Positives = 41/62 (66%), Gaps = 2/62 (3%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           + V  LP +     ++ +FS +G V  V++P+ K  GK KGFAFV+F++K +A KA++ G
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPR-KPDGKKKGFAFVQFTSKADAEKAIK-G 59

Query: 259 LN 260
           +N
Sbjct: 60  VN 61

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|153397 cd08028, LARP_3, La RNA-binding domain of La-related protein 3

 Score = 57.7 bits (140), Expect = 4e-11
 Identities = 29/69 (42%), Positives = 46/69 (66%), Gaps = 3/69 (4%)

Query: 2  EFYLSDSNLRKDRFFSQLLQESPE-IEVSVFLKCNKLARLTHDPDDVVKALRKSK--LLE 58
          E+Y  D NL +D+F  + ++E    + + V LK N+L  L+ DP+ + KAL+KSK  L+E
Sbjct: 13 EYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKSGLIE 72

Query: 59 VTEDGTKVK 67
          V+ED TK++
Sbjct: 73 VSEDKTKIR 81

This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B). Length = 82

>gnl|CDD|153399 cd08030, LA_like_plant, La-motif domain of plant proteins similar to the La autoantigen

 Score = 57.4 bits (139), Expect = 7e-11
 Identities = 32/88 (36%), Positives = 49/88 (55%), Gaps = 14/88 (15%)

Query: 111 QQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKC------NKLARLTHDPDD-- 162
           ++++  +EFY SDSNL +D F  + ++E P+  VS+ L C      + L      P+D  
Sbjct: 3   EKVLRQVEFYFSDSNLPRDDFLLEEVEEDPDGMVSLALICSFSRMRSLLGLGGGKPEDVP 62

Query: 163 ------VVKALRKSKLLEVTEDGTKVRR 184
                 V +ALR S LL+V+EDG +V R
Sbjct: 63  EDTLKAVAEALRTSTLLKVSEDGKRVGR 90

This domain is found in plant 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. Length = 90

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

 Score = 56.8 bits (138), Expect = 7e-11
 Identities = 20/58 (34%), Positives = 32/58 (55%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +YV  L  E +   + + F  +G +  + +P    T K +GFAFVEF   E+AA A++
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAID 58

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

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 21/59 (35%), Positives = 34/59 (57%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            +YV  LP     + ++ +F ++G+VT   +   + TG+ +GF FVE  T EEA  A+E
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIE 59

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|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 = 55.7 bits (135), Expect = 2e-10
 Identities = 27/60 (45%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             + V  +P EA    +  +FS +G+V  V LPK K  G  +GFAFVEF TK+EA  A+E
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAME 59

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

 Score = 55.3 bits (134), Expect = 3e-10
 Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 5/63 (7%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLP--KFKSTGKLKGFAFVEFSTKEEAAKA 254
            T++V   PP  +   I  +F +YG++  +  P  +F  T   + F +V+F++ E AA A
Sbjct: 1   STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKT---RRFCYVQFTSPESAAAA 57

Query: 255 LEL 257
           + L
Sbjct: 58  VAL 60

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 54.5 bits (132), Expect = 5e-10
 Identities = 24/58 (41%), Positives = 35/58 (60%), Gaps = 2/58 (3%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +YV  LPP    + +   FS YGKV  V L +  +  + +GFAFVEF++ E+A  AL+
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVR--NKDRPRGFAFVEFASPEDAEAALK 56

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

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

 Score = 54.2 bits (131), Expect = 7e-10
 Identities = 22/58 (37%), Positives = 32/58 (55%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           IYV  + P+   D I+SVF  +GK+   SL     TGK KG+ F+E+   + A  A+ 
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

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|153402 cd08033, LARP_6, La RNA-binding domain of La-related protein 6

 Score = 54.2 bits (131), Expect = 8e-10
 Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 2/68 (2%)

Query: 2  EFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCN--KLARLTHDPDDVVKALRKSKLLEV 59
          E+Y SD NL KD F  + ++ + E  V + L  +  K+  LT D   V  ALR+S  L V
Sbjct: 9  EYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSSKLVV 68

Query: 60 TEDGTKVK 67
          +EDG KV+
Sbjct: 69 SEDGKKVR 76

This domain is found in animal and plant 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. Length = 77

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

 Score = 54.1 bits (131), Expect = 8e-10
 Identities = 20/60 (33%), Positives = 33/60 (55%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           T++V +L  +     +   FSK GKV  V + + +++ + KG A+VEF  +E    AL L
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGL 60

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

 Score = 53.4 bits (129), Expect = 1e-09
 Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             I+V  LP     D +   FS++G++    +   + TGK +G+ FV F  KE A +A +
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 257 LGLNPCP 263
              +P P
Sbjct: 61  ---DPNP 64

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

 Score = 53.5 bits (129), Expect = 1e-09
 Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           T++V  L   AE D +E  F + G+V  V + +    G+ KGF  VEF+T+E A KALE 
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEK 59

Query: 258 G 258
            
Sbjct: 60  S 60

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|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 53.0 bits (128), Expect = 1e-09
 Identities = 25/60 (41%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           T+YV+  P +A  D I+  F K+GKV  + + +     K KG  FVEF T+E+A K LE 
Sbjct: 1   TVYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDL-DKKFKGSVFVEFKTEEDAKKFLEK 59

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|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 = 52.6 bits (127), Expect = 2e-09
 Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 6/58 (10%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
            T+YV  LP     + ++  FS +G +  V +  FK     KG+AFV F T E AA A
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRV--FKD----KGYAFVRFDTHEAAATA 52

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|203243 pfam05383, La, La domain

 Score = 52.2 bits (126), Expect = 3e-09
 Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 113 IMNLMEFYLSDSNLRKDRFF-SQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKS 170
           I   +E+Y SD NL +D+F   Q+ ++   + +S      ++ +LT D + +V+ALR S
Sbjct: 1   IKKQVEYYFSDENLPRDKFLRKQMDKDPGYVPISTIASFKRIKKLTTDVNLIVEALRSS 59

This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain. Length = 59

>gnl|CDD|203243 pfam05383, La, La domain

 Score = 51.8 bits (125), Expect = 3e-09
 Identities = 18/55 (32%), Positives = 33/55 (60%), Gaps = 1/55 (1%)

Query: 1  MEFYLSDSNLRKDRFF-SQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKS 54
          +E+Y SD NL +D+F   Q+ ++   + +S      ++ +LT D + +V+ALR S
Sbjct: 5  VEYYFSDENLPRDKFLRKQMDKDPGYVPISTIASFKRIKKLTTDVNLIVEALRSS 59

This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain. Length = 59

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

 Score = 52.3 bits (126), Expect = 3e-09
 Identities = 20/58 (34%), Positives = 34/58 (58%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +YV  L      D +  +F  +G++ +V L +   TG+ KG+ F++F+  E+A KALE
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALE 58

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

 Score = 56.5 bits (135), Expect = 3e-09
 Identities = 26/68 (38%), Positives = 41/68 (60%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           + K   +  T++V  LP +   + +  +F K+G V  V L + + TGK +GFAFVEF ++
Sbjct: 108 RQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESE 167

Query: 249 EEAAKALE 256
           E A KA+E
Sbjct: 168 ESAEKAIE 175

Length = 306

>gnl|CDD|153399 cd08030, LA_like_plant, La-motif domain of plant proteins similar to the La autoantigen

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 31/81 (38%), Positives = 44/81 (54%), Gaps = 14/81 (17%)

Query: 1  MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKC------NKLARLTHDPDD-------- 46
          +EFY SDSNL +D F  + ++E P+  VS+ L C      + L      P+D        
Sbjct: 9  VEFYFSDSNLPRDDFLLEEVEEDPDGMVSLALICSFSRMRSLLGLGGGKPEDVPEDTLKA 68

Query: 47 VVKALRKSKLLEVTEDGTKVK 67
          V +ALR S LL+V+EDG +V 
Sbjct: 69 VAEALRTSTLLKVSEDGKRVG 89

This domain is found in plant 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. Length = 90

>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 = 52.2 bits (126), Expect = 4e-09
 Identities = 23/63 (36%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
            ++V  L        +E++FSK+G+V  V L K   TG+ +GF FV F + E+A  A+  
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR- 61

Query: 258 GLN 260
            LN
Sbjct: 62  DLN 64

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

 Score = 52.6 bits (127), Expect = 4e-09
 Identities = 19/61 (31%), Positives = 34/61 (55%)

Query: 196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
             T++V +L  +   + +  VFS+YG +  + L +   TG  KG+AFVE+  + +A +A 
Sbjct: 3   YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAY 62

Query: 256 E 256
            
Sbjct: 63  R 63

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

 Score = 52.0 bits (125), Expect = 5e-09
 Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLP-KFKSTGKLKGFAFVEFSTKEEAAKAL 255
             I V  +P EA    +  +FS +G++  V LP K   TG  +GF FV+F TK++A +A 
Sbjct: 1   SKILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRAF 60

Query: 256 E 256
           +
Sbjct: 61  K 61

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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 51.8 bits (125), Expect = 5e-09
 Identities = 25/61 (40%), Positives = 31/61 (50%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            T++V  +P     D+I  +  K GKV      K  STGKLK F F EF   E A +AL 
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 257 L 257
           L
Sbjct: 61  L 61

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

 Score = 51.4 bits (124), Expect = 8e-09
 Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +YV+ L  + + + ++ +F KYGK+T   + K    GK KGF FV F   E A KA+E
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMK-DDEGKSKGFGFVNFENHEAAQKAVE 60

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

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

 Score = 51.1 bits (123), Expect = 8e-09
 Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 3/62 (4%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLK---GFAFVEFSTKEEAAKAL 255
           IYV  L  + + D +  +FSK+G+V  + +PK +   + +   GFAFV F     A  AL
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 256 EL 257
           +L
Sbjct: 63  QL 64

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

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 51.2 bits (123), Expect = 1e-08
 Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 4/64 (6%)

Query: 198 TIYVE----KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           TI+V+     L  +     +   FS  G++T VS+P  + TG  KGFA++EF + +   K
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 254 ALEL 257
           ALEL
Sbjct: 61  ALEL 64

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|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 = 50.8 bits (122), Expect = 1e-08
 Identities = 21/58 (36%), Positives = 31/58 (53%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           ++V  LP     + +  +F  +G+++ V LP  K T + KGFAFV F   E A KA  
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYS 59

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

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 25/60 (41%), Positives = 37/60 (61%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            T+YV  LP    ++ +  +FSKYGKV  V++ K K T K KG AF+ F  +E+A K ++
Sbjct: 2   STVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVK 61

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|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 = 50.2 bits (121), Expect = 2e-08
 Identities = 24/57 (42%), Positives = 40/57 (70%)

Query: 200 YVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +V +LP  A  + + ++F +YG +  V++ + K TG+ KG AFV+FS++EEA KA+E
Sbjct: 3   FVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIE 59

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

 Score = 54.4 bits (131), Expect = 2e-08
 Identities = 24/58 (41%), Positives = 38/58 (65%), Gaps = 1/58 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +YV+ L P    D +  +F+K+G++T  ++ K  S G+ +GFAFV F   E+AAKA+E
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGS-GRSRGFAFVNFEKHEDAAKAVE 237

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

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

 Score = 49.9 bits (119), Expect = 2e-08
 Identities = 23/66 (34%), Positives = 34/66 (51%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           +YV  LP +   D +  +F  YG +   +L + KSTG  +G AFV +  +EEA  A+   
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 259 LNPCPP 264
               PP
Sbjct: 63  NGTIPP 68

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

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 22/54 (40%), Positives = 31/54 (57%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
            +Y+  LP       +   FS++G VT + L + K TGK KG+AFVEF + E A
Sbjct: 1   VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVA 54

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

 Score = 49.9 bits (120), Expect = 3e-08
 Identities = 19/58 (32%), Positives = 37/58 (63%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           I+V  +  EA+ + +   F+++G++  + L   + TG +KG+A +E+ TK+EA  A+E
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIE 66

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|153400 cd08031, LARP_4_5_like, La RNA-binding domain of proteins similar to La-related proteins 4 and 5

 Score = 49.4 bits (118), Expect = 3e-08
 Identities = 23/73 (31%), Positives = 38/73 (52%)

Query: 111 QQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKS 170
           + +   +E+Y S  NL  D +    +     + +      NK+ +LT D D +V+ALR+S
Sbjct: 2   ELLKRQLEYYFSRENLANDAYLLSQMDSDQYVPIWTIANFNKIKKLTTDIDLIVEALRES 61

Query: 171 KLLEVTEDGTKVR 183
             ++V E G KVR
Sbjct: 62  PNVQVDEKGEKVR 74

This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). 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. Length = 75

>gnl|CDD|153401 cd08032, LARP_7, La RNA-binding domain of La-related protein 7

 Score = 49.6 bits (118), Expect = 4e-08
 Identities = 22/69 (31%), Positives = 46/69 (66%), Gaps = 2/69 (2%)

Query: 1  MEFYLSDSNLRKDRFFSQLLQESPE--IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLE 58
          ++F+  D NL KDRF  + +++S +  I++S+ +  NK+ +LT D   + +AL+ S ++E
Sbjct: 13 VDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVE 72

Query: 59 VTEDGTKVK 67
          +  +GT+++
Sbjct: 73 LNLEGTRIR 81

LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation. Length = 82

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 49.3 bits (118), Expect = 4e-08
 Identities = 23/57 (40%), Positives = 36/57 (63%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           ++V  LP   + D +E +FSK+G+++ V +   K +GK KGFA+V F   E+A KA 
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAY 61

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|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 49.3 bits (118), Expect = 4e-08
 Identities = 23/57 (40%), Positives = 32/57 (56%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           +++  L      + +E +FSKYG ++ V LP  K T K KGFAFV +   E A KA 
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAF 61

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

 Score = 49.2 bits (118), Expect = 4e-08
 Identities = 20/57 (35%), Positives = 30/57 (52%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
            + V  LP E   +    + S +G V    L   +STG+ KG+ FVE+++K  A KA
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA 57

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|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 48.9 bits (117), Expect = 5e-08
 Identities = 23/59 (38%), Positives = 34/59 (57%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           +YV  +P  +  D I S FS  G++  + L  F  TG+ +G AF+ F T+E A +AL L
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALAL 59

This subfamily corresponds to the RRM1 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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 49.2 bits (118), Expect = 5e-08
 Identities = 20/59 (33%), Positives = 35/59 (59%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           T++V  LP +   + +E  FS+ G +    + K K + K +GF +V F+ +E+A +ALE
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALE 59

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

 Score = 53.1 bits (127), Expect = 5e-08
 Identities = 36/112 (32%), Positives = 57/112 (50%), Gaps = 10/112 (8%)

Query: 166 ALRKSKLLEVTEDGTKVR--RTVVVQDKP---DVDECTIYVEKLPPEAEHDYIESVFSKY 220
           + R  K L    +G  VR  R  V   +P    + +  +YV  LP     D ++++F KY
Sbjct: 162 SQRAIKNL----NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKY 217

Query: 221 GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT 272
           G++   ++ + K TG  +G AFV F+ +EEA +A+   LN   P+  S  LT
Sbjct: 218 GQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAIS-ALNNVIPEGGSQPLT 268

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

 Score = 48.7 bits (117), Expect = 6e-08
 Identities = 21/61 (34%), Positives = 33/61 (54%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           +++V  LP + E + +   F   G V  V + + + TG  KGF +V F TK+  A AL+L
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL 60

Query: 258 G 258
            
Sbjct: 61  N 61

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

 Score = 49.0 bits (117), Expect = 6e-08
 Identities = 23/60 (38%), Positives = 30/60 (50%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           C +YV  +  E   D I   FS +G +  + +     T K KGFAFVE+   E A  ALE
Sbjct: 1   CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALE 60

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

 Score = 48.8 bits (117), Expect = 6e-08
 Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           + V+ LP   + D +  +F  +G +T V L K+   GK + F FV + T+EEA KAL
Sbjct: 3   LIVKNLPKGIKEDKLRKLFEAFGTITDVQL-KYTKDGKFRKFGFVGYKTEEEAQKAL 58

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|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate RNA-binding protein 26 (RBM26) and similar proteins

 Score = 48.7 bits (117), Expect = 7e-08
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 11/63 (17%)

Query: 196 ECTIYVEKLPPEAEHDYIESV---FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
             T+ V  +PPE   + I  +   FSK+G +  + +     +      A V+FST EEA 
Sbjct: 1   NTTLEVRNIPPE--LNNITKLNEHFSKFGTIVNIQVNYNPES------ALVQFSTSEEAK 52

Query: 253 KAL 255
           KA 
Sbjct: 53  KAY 55

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

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

 Score = 48.7 bits (116), Expect = 7e-08
 Identities = 26/58 (44%), Positives = 36/58 (62%), Gaps = 1/58 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           I V+ LP EA    + ++FS YG++  V +PK K     +GFAFVEFST +EA  A+ 
Sbjct: 3   ILVKNLPFEATKKDVRTLFSSYGQLKSVRVPK-KFDQSARGFAFVEFSTAKEALNAMN 59

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

 Score = 48.4 bits (116), Expect = 9e-08
 Identities = 21/59 (35%), Positives = 35/59 (59%)

Query: 196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           E  ++V KL P    + +E +FS++GK+    + + K TG    +AF+EF TKE+  +A
Sbjct: 3   ENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEA 61

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

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 23/60 (38%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           T++V  L      D +  +FSK G++T V L      GK KG+A+VEF  +E   +AL+L
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLV-KNYKGKSKGYAYVEFENEESVQEALKL 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|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 20/63 (31%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           +D+ +I+V +L P+   + +   FS++GK+  V+L   K       FAF++F  ++ AA+
Sbjct: 1   IDKYSIFVGQLSPDVTKEELNERFSRHGKILEVNL--IKRANHTNAFAFIKFEREQAAAR 58

Query: 254 ALE 256
           A+E
Sbjct: 59  AVE 61

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

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

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 22/58 (37%), Positives = 34/58 (58%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
            I+V  LPP+A+   +  +FS +G VT V + +  +T K KG+ FV  +  EEA  A+
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60

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

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 21/58 (36%), Positives = 34/58 (58%), Gaps = 2/58 (3%)

Query: 198 TIYVEKLPPEAEHDYIES-VFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
            ++V++LP       I   +FS+ GK T+  L      G+ +GFAFVE++T E+A +A
Sbjct: 4   CLFVDRLPKTFRDVSILRKLFSQVGKPTFCQL-AIAPNGQPRGFAFVEYATAEDAEEA 60

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

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 18/58 (31%), Positives = 30/58 (51%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           ++YV  +      D +  +F KYG +  V +P    T + +GFA+V+F    +A  AL
Sbjct: 2   SLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDAL 59

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

 Score = 47.5 bits (114), Expect = 2e-07
 Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 3/69 (4%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTY--VSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           T+ +  L      + I    S    V    V L + K TG  +GFAFVEF + E+A + +
Sbjct: 4   TLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWM 63

Query: 256 ELGLNPCPP 264
           +  LN   P
Sbjct: 64  D-ALNNLDP 71

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

 Score = 47.2 bits (112), Expect = 2e-07
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           +YV  LP       +E +FS+YG++    + + + TG  +G  F+ F  + EA +A++ G
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK-G 61

Query: 259 LNPCPPDYQSSILT 272
           LN   P+  S  +T
Sbjct: 62  LNGQKPEGASEPIT 75

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

 Score = 46.6 bits (111), Expect = 4e-07
 Identities = 20/57 (35%), Positives = 34/57 (59%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           I+V  L PE + + + + F+ +G+++   + K   TGK KG+ FV F  KE+A  A+
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAI 58

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

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 20/58 (34%), Positives = 32/58 (55%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
            ++V  LP       ++  FS++GKV   ++P  K TG  KG+ FV FS+++    AL
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENAL 58

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|153400 cd08031, LARP_4_5_like, La RNA-binding domain of proteins similar to La-related proteins 4 and 5

 Score = 46.3 bits (110), Expect = 5e-07
 Identities = 22/67 (32%), Positives = 36/67 (53%)

Query: 1  MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVT 60
          +E+Y S  NL  D +    +     + +      NK+ +LT D D +V+ALR+S  ++V 
Sbjct: 8  LEYYFSRENLANDAYLLSQMDSDQYVPIWTIANFNKIKKLTTDIDLIVEALRESPNVQVD 67

Query: 61 EDGTKVK 67
          E G KV+
Sbjct: 68 EKGEKVR 74

This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). 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. Length = 75

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

 Score = 45.7 bits (109), Expect = 6e-07
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 8/58 (13%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +YV  LP     + +  +FS+YG+V  V         K+K +AFV F  +++A KA+E
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVK--------KIKDYAFVHFEERDDAVKAME 53

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

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

 Score = 45.9 bits (109), Expect = 7e-07
 Identities = 19/59 (32%), Positives = 30/59 (50%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            IY+  LP       ++  FS++G V  V + + K TG  K + F++F   E AA A +
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAK 59

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

 Score = 45.5 bits (108), Expect = 8e-07
 Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 3/58 (5%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
            IYV  LP +     IE +F KYG +  + L   K+  +   FAFVEF    +A  A+
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDPRDAEDAV 55

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

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

 Score = 45.3 bits (108), Expect = 9e-07
 Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 5/56 (8%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           +YV  L P A    +E  F KYG +  V + +        GFAFVEF    +A  A
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDA 52

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

 Score = 45.1 bits (107), Expect = 1e-06
 Identities = 21/60 (35%), Positives = 33/60 (55%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           ++V  L  E   D + + F + G++  V +  F+ +GK KGFAFV+F   E A  AL+  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 17/44 (38%), Positives = 26/44 (59%), Gaps = 8/44 (18%)

Query: 213 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +E +FSKYGK+  +SL         KG+ FV+F  +E+A  A+ 
Sbjct: 18  LEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVA 53

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

>gnl|CDD|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 30/74 (40%), Positives = 40/74 (54%), Gaps = 10/74 (13%)

Query: 185 TVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSL--PKFKSTGKLKGFAF 242
            VVV   P V E     EKL    +   +  +FSK+G    V +  P    TGK KG+AF
Sbjct: 3   VVVVDGLPVVGE-----EKLEKLKK--VLRKIFSKFGVGKIVGIYMP-VDETGKTKGYAF 54

Query: 243 VEFSTKEEAAKALE 256
           VEF+T EEA +A++
Sbjct: 55  VEFATPEEAKEAVK 68

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|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 22/51 (43%), Positives = 31/51 (60%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEF 245
           D   IY+  LP E     I  VFS+YG++  ++L + K TGK KGFAF+ +
Sbjct: 8   DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAY 58

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

 Score = 44.7 bits (105), Expect = 2e-06
 Identities = 21/57 (36%), Positives = 34/57 (59%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           ++V  L PE   + I+S F+ +GK++   + K  +TGK KG+ FV F  K +A  A+
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 60

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|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 44.6 bits (105), Expect = 2e-06
 Identities = 18/57 (31%), Positives = 34/57 (59%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           ++V  +P       +  +F ++G V  V++ K K TG  +G  FV++ST++EA +A+
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 4/66 (6%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKV---TYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
            +++  L       ++  +FSKYGK+    ++        G+ +G+ FV F TKEEA KA
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 255 LELGLN 260
           L+  LN
Sbjct: 61  LK-SLN 65

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 20/52 (38%), Positives = 31/52 (59%)

Query: 205 PPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           P     + +   F ++G + YVS+ K K+TG+ KGF +V+F    +AA ALE
Sbjct: 9   PKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 44.7 bits (105), Expect = 3e-06
 Identities = 22/57 (38%), Positives = 33/57 (57%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           I+V  L PEA+   +  +F  +G VT V + +  +T K KGF FV  +  +EAA A+
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAI 60

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

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 21/56 (37%), Positives = 32/56 (57%)

Query: 201 VEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           V+ L      D +  VF KYG+V  V +P+ + T + +GFAFV F  K +A  A++
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMD 58

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|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 = 43.4 bits (103), Expect = 4e-06
 Identities = 20/57 (35%), Positives = 31/57 (54%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           ++V  +P +A  + +  +FS+ G V    L   + TGK KG+ F EF   E AA A+
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAI 57

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

 Score = 43.9 bits (103), Expect = 4e-06
 Identities = 20/58 (34%), Positives = 35/58 (60%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           ++V  L PE   D I++ F+ +G+++   + K  +TGK KG+ FV F  K +A  A++
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61

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

 Score = 43.5 bits (103), Expect = 4e-06
 Identities = 22/58 (37%), Positives = 31/58 (53%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           I+V  L PE   + I   F K+G +  + LP  K T K +GF F+ F ++E   K LE
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILE 59

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 43.5 bits (103), Expect = 4e-06
 Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 3/62 (4%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTY--VSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           TI +  LP     + I +    +G V    V L + K+TG  +GFAFVEF + EEA + +
Sbjct: 4   TIMLRGLPLSVTEEDIRNALVSHG-VEPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWM 62

Query: 256 EL 257
           EL
Sbjct: 63  EL 64

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

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

 Score = 43.6 bits (103), Expect = 6e-06
 Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
            ++V  LP     + +E +F K+G V  V L   +S GK KG A+VE+  +  A++A+
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRS-GKPKGLAYVEYENESSASQAV 60

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

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

 Score = 42.6 bits (101), Expect = 8e-06
 Identities = 19/57 (33%), Positives = 29/57 (50%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           ++V  L  +   + +   FS+YG V  V +   K TGK +GFAFV F   +   K +
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIV 58

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|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 43.2 bits (101), Expect = 8e-06
 Identities = 21/57 (36%), Positives = 33/57 (57%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           I+V  L P+A+   +  +F  +G VT V + +  +T K KGF FV  +  +EAA A+
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

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

 Score = 42.7 bits (101), Expect = 8e-06
 Identities = 17/59 (28%), Positives = 29/59 (49%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           I+V  +      + ++  F   G +  +++   K TG+ KGFA++EF  K     AL L
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLL 60

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

>gnl|CDD|241055 cd12611, RRM1_NGR1_NAM8_like, RNA recognition motif 1 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 42.8 bits (101), Expect = 8e-06
 Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 1/80 (1%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           T+++  L P  + ++I+ V++  G     V + + +++G   G+ FVEF +   A  AL 
Sbjct: 1   TLWMGDLEPWMDENFIKQVWASLGLEPVNVKVIRSRNSGLNAGYCFVEFPSPHAAQNALS 60

Query: 257 LGLNPCPPDYQSSILTTTSR 276
           L   P P   ++  L   S 
Sbjct: 61  LNGTPIPNSNRTFKLNWASG 80

This subgroup corresponds to the RRM1 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), 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 carboxyl terminus which also harbors a methionine-rich region. The subgroup also includes NAM8, 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 = 81

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

 Score = 42.6 bits (101), Expect = 9e-06
 Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           +YV+ L    + + +   FS +G +T   +      G+ KGF FV FS+ EEA KA
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMT-DEKGRSKGFGFVCFSSPEEATKA 58

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

 Score = 42.5 bits (100), Expect = 9e-06
 Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 4/57 (7%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           IYV  LPP+     IE +F KYG +  + L   +       FAFVEF    +A  A+
Sbjct: 2   IYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKNRRG----PPFAFVEFEDPRDAEDAV 54

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

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

 Score = 46.0 bits (109), Expect = 1e-05
 Identities = 26/87 (29%), Positives = 40/87 (45%), Gaps = 2/87 (2%)

Query: 173 LEVTEDGTK--VRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPK 230
                   +   R T     + + D+ T++V +L  +A    +   FSK GKV  V   K
Sbjct: 64  DRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIK 123

Query: 231 FKSTGKLKGFAFVEFSTKEEAAKALEL 257
            +++ + KG A+VEF   E   KAL L
Sbjct: 124 DRNSRRSKGVAYVEFYDVESVIKALAL 150

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

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 26/82 (31%), Positives = 46/82 (56%), Gaps = 11/82 (13%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
            I+V  LP +   + + +  +++G +  V +  F+S GK +  A VEF+T+E+A +AL  
Sbjct: 9   MIHVSNLPSDVTEEDVINHLAEHGVIVNVKV--FESNGKKQ--ALVEFATEEQATEAL-- 62

Query: 258 GLNPCPPDYQSSILTTTSRLSF 279
               C   + SS+  +T RL+F
Sbjct: 63  ---AC--KHASSLNGSTIRLAF 79

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

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

 Score = 42.0 bits (99), Expect = 1e-05
 Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 8/58 (13%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +YV   PP+     I  +FS YG V  V +        +  FAFVEF + E A +A +
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKM--------ISNFAFVEFESLESAIRAKD 51

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

 Score = 42.0 bits (99), Expect = 1e-05
 Identities = 20/55 (36%), Positives = 29/55 (52%)

Query: 201 VEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           V  LP     D I S+FS  G++    L + K TG+  G+ FV +   E+A KA+
Sbjct: 6   VNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

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|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 42.2 bits (99), Expect = 1e-05
 Identities = 20/61 (32%), Positives = 37/61 (60%), Gaps = 1/61 (1%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           C ++V K+P +   D +  +F + GK+    L   + +G+ +G+AFV ++TKEEA  A+ 
Sbjct: 2   CEVFVGKIPRDMYEDELVPLFERAGKIYEFRL-MMEFSGENRGYAFVMYTTKEEAQLAIR 60

Query: 257 L 257
           +
Sbjct: 61  I 61

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 4/65 (6%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFK----STGKLKGFAFVEFSTKEEAA 252
             +YV+ L      + +  +F ++   +      F     + G++KG AFV F ++E A 
Sbjct: 2   KRLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMTEGRMKGQAFVTFPSEEIAT 61

Query: 253 KALEL 257
           KAL L
Sbjct: 62  KALNL 66

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|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           T+Y+  L  +   D +   F K  ++T V L   K TG+ KGF  V+F+ +E    AL+L
Sbjct: 1   TVYIGNLAWDITEDDVREFF-KGCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKL 59

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 41.0 bits (97), Expect = 2e-05
 Identities = 22/51 (43%), Positives = 28/51 (54%), Gaps = 6/51 (11%)

Query: 217 FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQ 267
           FS +G V  + L K K      GFAFVEFST+E A KA++  LN      +
Sbjct: 5   FSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQY-LNGVLFGGR 49

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

 Score = 45.4 bits (107), Expect = 2e-05
 Identities = 15/57 (26%), Positives = 31/57 (54%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           IYV  + P+     I+SVF  +G++    L +  +    KG+ F+E++  +  ++A+
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAI 263

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|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 5/69 (7%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE-- 256
           I+V  L P+   + I   F  +G+V  + LP    T K +GF F+ F  +E   K +E  
Sbjct: 2   IFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 257 ---LGLNPC 262
              +GL+ C
Sbjct: 62  YHNVGLSKC 70

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 75

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

 Score = 41.0 bits (97), Expect = 3e-05
 Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 10/61 (16%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG--KLKGFAFVEFSTKEEAAKAL 255
            ++++ LP E   + +E +F+++        P FK       +G AFVEF T+E+A  AL
Sbjct: 4   ILFLQNLPEETTKEMLEMLFNQF--------PGFKEVRLVPRRGIAFVEFETEEQATVAL 55

Query: 256 E 256
           +
Sbjct: 56  Q 56

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

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

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 7/60 (11%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           T+ V  LPPE   D  E +   +G   V           GKLK  AF  F  ++ A++AL
Sbjct: 1   TLLVRHLPPELSEDDKEDLLKHFGASSVRV-----MSRRGKLKNTAFATFDNEQAASQAL 55

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

 Score = 41.0 bits (97), Expect = 4e-05
 Identities = 20/64 (31%), Positives = 32/64 (50%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           ++V  L P      +E  FS++G V+ V + K K  G  +GFA+++  T E   K  +  
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 259 LNPC 262
           LN  
Sbjct: 62  LNGT 65

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 21/58 (36%), Positives = 29/58 (50%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           T++V  LP +A  + +   FSK+G V Y      KSTG+ KG  FV F  +      L
Sbjct: 3   TLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 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|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 = 40.7 bits (96), Expect = 4e-05
 Identities = 19/47 (40%), Positives = 28/47 (59%), Gaps = 4/47 (8%)

Query: 213 IESVFSKYGKVTYVSLPKF---KSTGKLKGFAFVEFSTKEEAAKALE 256
           +E   ++ G V   S+ KF   K+ GK KGFA+VEF+++  AA   E
Sbjct: 15  LEGALAEAGVVDVKSI-KFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

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

 Score = 41.0 bits (96), Expect = 4e-05
 Identities = 19/44 (43%), Positives = 28/44 (63%), Gaps = 1/44 (2%)

Query: 213 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           ++ +F +YGKV   ++P+ K  GKL GFAFV    ++ A  ALE
Sbjct: 18  LKKIFGRYGKVREATIPR-KRGGKLCGFAFVTMKKRKNAEIALE 60

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|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 = 41.0 bits (96), Expect = 4e-05
 Identities = 18/57 (31%), Positives = 33/57 (57%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           +++  L  +     +E VFSKYG+++ V + K + T + +GF FV F   ++A  A+
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAM 59

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

 Score = 40.6 bits (96), Expect = 4e-05
 Identities = 17/58 (29%), Positives = 28/58 (48%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +++  L  +   + +   FSKYG+V    + K   TG+ +GF FV F+      K L 
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLA 58

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|240875 cd12429, RRM_DNAJC17, RNA recognition motif in the DnaJ homolog subfamily C member 17

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 23/56 (41%), Positives = 30/56 (53%), Gaps = 7/56 (12%)

Query: 210 HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE--EAAKALELGLNPCP 263
            D +  +FSKYG V+ V +   K     KG A VEF++K+  EAA   E GL   P
Sbjct: 18  EDELRKIFSKYGDVSDVVVSSKK-----KGSAIVEFASKKAAEAAVENECGLPSNP 68

The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. . Length = 74

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

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           +Y+  LPP    + +E +   +GK+        K T K KG+ FV+F + E A KA+E G
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE-G 61

Query: 259 LN 260
           LN
Sbjct: 62  LN 63

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

 Score = 40.5 bits (95), Expect = 4e-05
 Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           T+YV  LP +     +E +F KYG +  + L   K   +  G+AF+EF    +A  A+ 
Sbjct: 1   TVYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIR 56

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

>gnl|CDD|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 40.4 bits (95), Expect = 5e-05
 Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           T +V  LP       ++++F     V  V L + K T K KGF +VEF   E   +ALE 
Sbjct: 3   TAFVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEY 61

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

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

 Score = 40.4 bits (95), Expect = 6e-05
 Identities = 18/59 (30%), Positives = 36/59 (61%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           T++V  L    + +++++ F K+G V    +   + TG+ +GF +V+F + E+A KA+E
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIE 59

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

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 17/41 (41%), Positives = 26/41 (63%)

Query: 216 VFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           VFS+YG +  V +   + TG+ +GF FV F + E+A +A E
Sbjct: 19  VFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKE 59

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 = 40.4 bits (95), Expect = 6e-05
 Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 5/65 (7%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE-----AAK 253
           I+V  LPP+   +  +  FS++GKV    L +   TG+ +GF FV F ++       +A 
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG 61

Query: 254 ALELG 258
            LELG
Sbjct: 62  MLELG 66

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

 Score = 40.3 bits (94), Expect = 6e-05
 Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 5/59 (8%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            + V  L   A  D ++ VF K    T + +P+  + G+ KG+AFVEF + E+A +AL 
Sbjct: 3   VLVVNNLSYSASEDSLQEVFEK---ATSIRIPQ--NNGRPKGYAFVEFESAEDAKEALN 56

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

 Score = 40.4 bits (94), Expect = 7e-05
 Identities = 20/58 (34%), Positives = 31/58 (53%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           I+V  L PEA  + I   F ++G++  + LP    T K +GF F+ F  ++   K LE
Sbjct: 7   IFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLE 64

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

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 40.1 bits (94), Expect = 7e-05
 Identities = 18/62 (29%), Positives = 27/62 (43%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           D   ++V  LP +   D ++  F ++G V  V +      G+L  F FV F   E   K 
Sbjct: 2   DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61

Query: 255 LE 256
           L 
Sbjct: 62  LA 63

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

 Score = 40.0 bits (94), Expect = 7e-05
 Identities = 24/60 (40%), Positives = 31/60 (51%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
            ++V  LP +   + + + F   G    V L   K TGK KG AFVEF T E   KAL+L
Sbjct: 2   ILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKL 61

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

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

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 5/65 (7%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLK-----GFAFVEFSTKEEA 251
            T++V+ L  +   + ++  F K G V  V++ K K           G+ FVEF +KE A
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 252 AKALE 256
            KAL+
Sbjct: 61  QKALK 65

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

 Score = 40.2 bits (94), Expect = 8e-05
 Identities = 15/58 (25%), Positives = 28/58 (48%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           T++V  L      + +   FS    + +  +     TG+ +G+ FV F+  E+A +AL
Sbjct: 1   TLFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEAL 58

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

 Score = 43.6 bits (103), Expect = 9e-05
 Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           +YV+ L      + +  +FS+ G++T   +      G  +GF FV FS  EEA +A+
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKV-MLDEKGVSRGFGFVCFSNPEEANRAV 343

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

 Score = 43.0 bits (101), Expect = 1e-04
 Identities = 20/58 (34%), Positives = 30/58 (51%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +YV  L        +  +F  +G +  V L +   TG+ KGF F++F   EEA +ALE
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALE 246

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

 Score = 43.5 bits (102), Expect = 1e-04
 Identities = 23/60 (38%), Positives = 32/60 (53%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           C +YV  +  E   D I   F  +G +  +++    +TGK KGFAFVE+   E A  ALE
Sbjct: 108 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALE 167

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

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 19/57 (33%), Positives = 32/57 (56%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           I+V  L P+++   +  +F  +G V  V + +  +T K KGF FV  +  +EAA A+
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAI 62

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

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 18/59 (30%), Positives = 34/59 (57%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           +YV  L  +   + +  +F + G V  V +PK + T   +G+ FVEF ++E+A  A+++
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKI 59

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

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 6/58 (10%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           C ++V  LP +   +  + +FSKYG+V+ V L       K KGF F+   T+  A KA
Sbjct: 2   CRLFVGNLPNDITEEEFKELFSKYGEVSEVFLN------KEKGFGFIRLDTRTNAEKA 53

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

 Score = 39.1 bits (91), Expect = 1e-04
 Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 8/58 (13%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           ++V  LPPEA    I S+F +YGKV    +        +K + FV    K  A +A+ 
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDI--------IKNYGFVHMDDKTAADEAIR 52

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|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate RNA-binding protein 10 (RBM10)

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           I +  LP  A    I     ++G +   V L + KS+G+ +GFAFVEF+  ++A + +E
Sbjct: 5   IMLRMLPQNATETDIRGQLQEHGIQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWME 63

This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). 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. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains 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 = 85

>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 = 39.2 bits (92), Expect = 1e-04
 Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 13/83 (15%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           T++V  L P    D + S+F  +G++ YV +P  K  G      FV+F  +  A  A++ 
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCG------FVQFVHRAAAEAAIQ- 55

Query: 258 GLNPCPPDYQSSILTTTSRLSFG 280
            L        + I  +  RLS+G
Sbjct: 56  QLQ------GTIIGGSRIRLSWG 72

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

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

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 20/57 (35%), Positives = 32/57 (56%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           I++  L  +A+   +  +F  +G VT V + +  +T K KGF FV  +  EEAA A+
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAI 60

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

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 1/60 (1%)

Query: 201 VEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLN 260
           V  LP +   + + S+F   G +    + + + TG+  G+ FV++  + +A KA+   LN
Sbjct: 5   VNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN-TLN 63

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

 Score = 42.2 bits (99), Expect = 2e-04
 Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           I+V  L P+ +   +  +F  +G V  V + +  +T + KG+ FV  +  +EAA A+ L 
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAI-LS 330

Query: 259 LN 260
           LN
Sbjct: 331 LN 332

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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 17/58 (29%), Positives = 31/58 (53%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           ++V  L P+   + I+  F  +G++  + LP    T + +GF FV ++ +E   K LE
Sbjct: 2   VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLE 59

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 16/53 (30%), Positives = 30/53 (56%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
           T++V +L  +     +   F +YG +  + L + K TGK +G+AF+EF  + +
Sbjct: 3   TLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERD 55

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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           C ++V K+P +   D +  +F K G +  + L     +G  +G+AFV ++ KE A +A++
Sbjct: 2   CEVFVGKIPRDLFEDELVPLFEKAGPIYELRL-MMDFSGLNRGYAFVTYTNKEAAQRAVK 60

Query: 257 LGLN 260
              N
Sbjct: 61  QLHN 64

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

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 7/63 (11%)

Query: 198 TIYV----EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           T+Y+    EK+  +     + ++FS++G V  +   K   T K++G AFV F   E A  
Sbjct: 1   TLYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASK---TLKMRGQAFVVFKDVESATN 57

Query: 254 ALE 256
           AL 
Sbjct: 58  ALR 60

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
            I+V  +PP+   + +   FS++G V  V +      G  KG+ FV F T+E+A K L +
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKI-ITDRAGVSKGYGFVTFETQEDAEKILAM 62

Query: 258 G 258
           G
Sbjct: 63  G 63

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|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 = 38.6 bits (90), Expect = 2e-04
 Identities = 19/57 (33%), Positives = 32/57 (56%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           ++V  +P EA  + ++ +FS+ G V    L   + TGK KG+ F E+  +E A  A+
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAM 57

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

 Score = 41.7 bits (98), Expect = 3e-04
 Identities = 25/102 (24%), Positives = 43/102 (42%), Gaps = 7/102 (6%)

Query: 158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDEC---TIYVEKLPPEAEHDYIE 214
            +P D  +AL     +     G K  R +  Q  P +       I+V+ L    ++  + 
Sbjct: 50  QNPADAERALET---MNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALF 106

Query: 215 SVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             FSK+G +    +      GK +G+ FV F  +E A  A++
Sbjct: 107 DTFSKFGNILSCKVAT-DENGKSRGYGFVHFEKEESAKAAIQ 147

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

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           C I++ KLP +   D +  +  K GK+  + +      G  +G+AFV FS K+EA  A++
Sbjct: 2   CEIFIGKLPRDLFEDELIPLCEKIGKIYEMRM-MMDFNGNNRGYAFVTFSNKQEAKNAIK 60

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

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 9/62 (14%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           ++V  LP     + + ++F KYG VT            +K + FV    +E+A  A++  
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVT--------ECDVVKNYGFVHMEEEEDAEDAIK-A 52

Query: 259 LN 260
           LN
Sbjct: 53  LN 54

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

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           I V+ LP     D +   F   G+VT V + +    GK + F FV F ++E+A +A++
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMR-TRDGKSRRFGFVGFKSEEDAQQAVK 59

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

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

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           +  +YV  LP       +E +FS+YG++    +   + TG  +G  F+ F  + EA +A+
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60

Query: 256 ELGLNPCPP 264
           + GLN   P
Sbjct: 61  K-GLNGQKP 68

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|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 = 38.5 bits (90), Expect = 3e-04
 Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 2/61 (3%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           TI+V  +      D ++  FS  G+VT   +           FAFVEF+  E A  AL L
Sbjct: 2   TIHVGGIDGSLSEDDLKEFFSNCGEVT--RVRLCGDRQHSARFAFVEFADAESALSALNL 59

Query: 258 G 258
            
Sbjct: 60  S 60

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

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           +  +YV  LP       +E +FS+YG++    +   + TG  +G  F+ F  + EA +A+
Sbjct: 2   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61

Query: 256 ELGLNPCPPDYQSSILT 272
           + GLN   P   +  +T
Sbjct: 62  K-GLNGQKPSGAAEPIT 77

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|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 = 38.4 bits (90), Expect = 3e-04
 Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 2/59 (3%)

Query: 199 IYVEKLPPEAEHDYIESVFSK-YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           + V+ LP       ++  FSK  G++T V L      GK +  AF+ + T+EEA KA +
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKL-LRTEDGKSRRIAFIGYKTEEEAQKAKD 60

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

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 8/55 (14%)

Query: 213 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL--GLNPCPPD 265
           +  VF KYG V  + +P  K       + FV +S+ E+AA A +   G     P 
Sbjct: 20  LLRVFEKYGTVEDLVMPPGKP------YCFVSYSSIEDAAAAYDALNGKELELPQ 68

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

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

 Score = 38.6 bits (89), Expect = 4e-04
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           + +  +YV  LP       +E +FS+YG++    +   + TG  +G  F+ F  + EA +
Sbjct: 3   IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEE 62

Query: 254 ALELGLNPCPP 264
           A++ GLN   P
Sbjct: 63  AIK-GLNGQKP 72

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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 15/49 (30%), Positives = 28/49 (57%)

Query: 208 AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
              D +   F+ +G++  + + K K T + KG A+V+F+    AA+A+E
Sbjct: 14  VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAME 62

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|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 38.2 bits (89), Expect = 4e-04
 Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 199 IYVEKLPPEAEHDYIESVF-SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           +++  +P + +   ++ +F  K G+VTYV L K    GK +G   VEF  KE   KALE 
Sbjct: 2   VFISNIPYDLKWQDLKDLFREKVGEVTYVELFK-DEEGKSRGCGVVEFKDKESVQKALET 60

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|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 38.0 bits (88), Expect = 4e-04
 Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           C ++V K+P +   D +  VF   G++  + L      GK +G+AFV ++ K EA +A+
Sbjct: 2   CEVFVGKIPRDVYEDELVPVFESVGRIYEMRL-MMDFDGKNRGYAFVMYTQKHEAKRAV 59

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 5/60 (8%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             ++V +L  +   + +   FS++G+VT V +PK       + FAFV F+  E A     
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPK-----PFRAFAFVTFADPEVAQSLCG 55

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

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 37.9 bits (88), Expect = 5e-04
 Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 6/64 (9%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKV--TYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           ++V  L  +A    +E VFS YG+V   Y+   + K +   +G AFV++S+KE A  A++
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQS---RGCAFVKYSSKEMAQAAIK 58

Query: 257 LGLN 260
             LN
Sbjct: 59  -ALN 61

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

 Score = 37.9 bits (89), Expect = 5e-04
 Identities = 16/57 (28%), Positives = 28/57 (49%)

Query: 200 YVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           YV  L P+     +  +FS  G V  + + +   T +  G+A+V F    +A +AL+
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALD 59

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

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           +YV  LP       +E++FS YG++    +     TG  +G  F+ F  + EA +A++  
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIK-A 61

Query: 259 LN 260
           LN
Sbjct: 62  LN 63

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

 Score = 40.7 bits (95), Expect = 6e-04
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           +YV  LP       +ES+FS +G++    +     TG  KG  F+ F  ++EA +A++  
Sbjct: 92  LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIK-T 150

Query: 259 LNPCPP 264
           LN   P
Sbjct: 151 LNGTTP 156

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|240912 cd12466, RRM2_AtRSp31_like, RNA recognition motif 2 in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 37.5 bits (87), Expect = 6e-04
 Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 9/48 (18%)

Query: 209 EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             D +E  F  YGK+  V + +         FAFV++ T+E+A KALE
Sbjct: 14  TRD-LERHFEPYGKLVNVRIRR--------NFAFVQYETQEDATKALE 52

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

 Score = 40.8 bits (95), Expect = 6e-04
 Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           C ++V K+P +   D +  +F K G +  + L     +G+ +G+AFV F  KEEA +A++
Sbjct: 59  CEVFVGKIPRDLYEDELVPLFEKAGPIYELRL-MMDFSGQNRGYAFVTFCGKEEAKEAVK 117

Query: 257 L 257
           L
Sbjct: 118 L 118

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|153404 cd08035, LARP_4, La RNA-binding domain of La-related protein 4

 Score = 37.3 bits (86), Expect = 6e-04
 Identities = 20/67 (29%), Positives = 32/67 (47%)

Query: 117 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVT 176
           +EF  S  NL KD +    +     + +        + +LT D D ++  LR S +++V 
Sbjct: 8   LEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSPMVQVD 67

Query: 177 EDGTKVR 183
           E G KVR
Sbjct: 68  ETGEKVR 74

This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). 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. Length = 75

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

 Score = 37.5 bits (87), Expect = 6e-04
 Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 3/57 (5%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           IYV  LP +     +E +F KYG++  + L   K+   L  FAFV F    +A  A+
Sbjct: 2   IYVGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFEDPRDAEDAV 55

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 37.8 bits (88), Expect = 7e-04
 Identities = 20/62 (32%), Positives = 35/62 (56%)

Query: 193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
           D D   ++V ++P   E   +  +F ++GK+  +++ K K TG  KG AF+ +  +E A 
Sbjct: 2   DDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESAL 61

Query: 253 KA 254
           KA
Sbjct: 62  KA 63

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

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

 Score = 37.2 bits (86), Expect = 8e-04
 Identities = 16/44 (36%), Positives = 29/44 (65%)

Query: 213 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +  VFS+YG +  V++   + TG+ +GFAFV F   +++ +A+E
Sbjct: 16  LREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAME 59

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|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 37.0 bits (86), Expect = 8e-04
 Identities = 18/52 (34%), Positives = 28/52 (53%)

Query: 204 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           LP +     ++  FS +G++  V + K   TG+ KGF FV F+  E+  K L
Sbjct: 7   LPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58

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

 Score = 36.9 bits (86), Expect = 9e-04
 Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           + T++V  L      + +  +F + G +  V +PK    GK K FAFV F  +     A+
Sbjct: 1   DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPK-DPNGKPKSFAFVTFKHEVSVPYAI 59

Query: 256 EL 257
           +L
Sbjct: 60  QL 61

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 8/56 (14%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           +Y+ +LP  A    +E  F  YG++  ++L          GF FVEF    +A  A
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINLK--------NGFGFVEFEDPRDADDA 49

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

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 16/55 (29%), Positives = 29/55 (52%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           I+V  +  + E  ++   F +YGK+  + +   + +GK +GFAFV F   +   K
Sbjct: 3   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 57

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|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 22/59 (37%), Positives = 34/59 (57%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           I+V K+P +   D +  +F K G +  + L     TG  +G+AFV F TKE A +A++L
Sbjct: 4   IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAVKL 62

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|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 36.8 bits (85), Expect = 0.001
 Identities = 17/60 (28%), Positives = 35/60 (58%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           ++YV  +   +  + +E+ FS  G +  V++   K +G  KG+A++EF+T++    A+ L
Sbjct: 1   SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVAL 60

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 19/59 (32%), Positives = 30/59 (50%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           I+V  L      D ++  FS++GKV    L   K T + +GF FV F +++   K  E+
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

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|241006 cd12562, RRM2_RBM5_like, RNA recognition motif 2 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 4/68 (5%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGK--VTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           TI +  + P    D I S  + Y    V+ + L K K T + +GFAFV+ S+  EA++ L
Sbjct: 4   TIILRNIAPHTVVDSILSALAPYASLSVSNIRLIKDKQTQQNRGFAFVQLSSALEASQLL 63

Query: 256 EL--GLNP 261
           ++   L+P
Sbjct: 64  QILQALHP 71

This subgroup corresponds to the RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 86

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 17/55 (30%), Positives = 30/55 (54%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           I+V  +  + E  ++   F KYGK+  + + + + +GK +GFAFV F   +   K
Sbjct: 3   IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDK 57

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|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 6/60 (10%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             I V+ LP     + +  +F K+G +  + LP  ++       A VEF    +A KA +
Sbjct: 1   TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRT------IALVEFLEPSDARKAFK 54

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVT--YVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           I+++ L    ++  +   FS +G +    V+       G  KG+ FV F T+E A +A+E
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVAT---DENGGSKGYGFVHFETEEAAVRAIE 61

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|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 = 36.3 bits (84), Expect = 0.001
 Identities = 22/61 (36%), Positives = 29/61 (47%), Gaps = 11/61 (18%)

Query: 198 TIYVEKLPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           T++V    P    E D IE +F  +G +    + K         FAFVEF   E+A KAL
Sbjct: 1   TLFVVGFDPGTTREED-IEKLFEPFGPLVRCDIRK--------TFAFVEFEDSEDATKAL 51

Query: 256 E 256
           E
Sbjct: 52  E 52

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|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 1/68 (1%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           T+YV     E     +   F +YG++    +P  + T + + FAFVE+ +  +A  A E 
Sbjct: 1   TLYVTGFGAETRARDLAYEFERYGRLVRCDIPPPR-TFQSRPFAFVEYESHRDAEDAYEE 59

Query: 258 GLNPCPPD 265
                 PD
Sbjct: 60  MHGRRFPD 67

This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain. Length = 78

>gnl|CDD|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 = 36.4 bits (85), Expect = 0.001
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           I++  LP     D ++ +   +GK+   +L K  +TG  KG+AF E+       +A+  G
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA-G 61

Query: 259 LN 260
           LN
Sbjct: 62  LN 63

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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 36.7 bits (84), Expect = 0.001
 Identities = 18/62 (29%), Positives = 30/62 (48%)

Query: 194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           + +  +Y+  LPP      +  +   YGK+        K+T K KG+ FV+F +   A K
Sbjct: 5   LSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQK 64

Query: 254 AL 255
           A+
Sbjct: 65  AV 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|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKS-TGKLKGFAFVEFSTKEEAAKALE 256
           T Y+  LP +   + I+  F +   V+ V LP+     G+L+GF + EF  ++   +AL 
Sbjct: 3   TAYLGNLPYDVTEEDIKEFF-RGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALS 61

Query: 257 L 257
           L
Sbjct: 62  L 62

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

>gnl|CDD|153404 cd08035, LARP_4, La RNA-binding domain of La-related protein 4

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 19/67 (28%), Positives = 32/67 (47%)

Query: 1  MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVT 60
          +EF  S  NL KD +    +     + +        + +LT D D ++  LR S +++V 
Sbjct: 8  LEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSPMVQVD 67

Query: 61 EDGTKVK 67
          E G KV+
Sbjct: 68 ETGEKVR 74

This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). 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. Length = 75

>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 8/43 (18%)

Query: 213 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           +E++FSKYGK+   S+         KGFAFV++  +  A  A+
Sbjct: 19  VEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAV 53

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

>gnl|CDD|153403 cd08034, LARP_1_2, La RNA-binding domain proteins similar to La-related proteins 1 and 2

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 113 IMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKL 172
           I   +E+Y S  NL KD F  + +     + +++    +++  LT D + +++AL+ S +
Sbjct: 4   IKKQIEYYFSVDNLEKDFFLRRKMDPEGYLPIALIASFHRVQALTTDVNLILEALKDSTV 63

Query: 173 LEVTEDGTKVRR 184
           +E+     KVR 
Sbjct: 64  VELV--DEKVRC 73

This domain is found in proteins similar to vertebrate La-related proteins 1 and 2 (LARP1, LARP2). 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. Length = 73

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 2/60 (3%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           TIYV  L P    D +   FS+ G+V YV +       +   +AFVEF+ +     AL+L
Sbjct: 6   TIYVGNLDPTTTADQLLEFFSQAGEVKYVRMA--GDETQPTRYAFVEFAEQTSVINALKL 63

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

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

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 20/58 (34%), Positives = 29/58 (50%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           I+V  L  E   + +   FSKY       + + K TGK KG+ FV FS   +  KA++
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMK 66

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|153405 cd08036, LARP_5, La RNA-binding domain of La-related protein 5

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 20/73 (27%), Positives = 34/73 (46%)

Query: 111 QQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKS 170
           + +   +EF LS  NL  D +    +     + +      + + +L+ D D +V  LR  
Sbjct: 2   ELLKKTLEFCLSRENLASDMYLISQMDSDQYVPIMTVANLDHIKKLSTDVDLIVDVLRSL 61

Query: 171 KLLEVTEDGTKVR 183
            L++V E G KVR
Sbjct: 62  PLVQVDEKGEKVR 74

This domain is found in vertebrate La-related protein 5 (LARP5). 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. Length = 75

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 3/62 (4%)

Query: 196 ECTIYVEKLPPEAEHDY-IESVF-SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           + +I+V  L P+   DY ++  F ++Y  V    +     TG+ KG+ FV F  ++E  +
Sbjct: 1   DHSIFVGDLAPDV-TDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDR 59

Query: 254 AL 255
           AL
Sbjct: 60  AL 61

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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 18/59 (30%), Positives = 34/59 (57%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           ++V K+P +   D +  +F K G +  + L     +G+ +G+AF+ F  KE A +A++L
Sbjct: 4   VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKL 62

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|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 1/60 (1%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           T++V  L P+   + I  +F + G V  V +PK K  GK K FAFV F  +     A+ L
Sbjct: 3   TLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKD-GKPKQFAFVNFKHEVSVPYAMNL 61

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|153406 cd08037, LARP_1, La RNA-binding domain of La-related protein 1

 Score = 35.6 bits (82), Expect = 0.002
 Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 113 IMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKL 172
           I   +E+Y S  NL +D F  + + E   + V++    +++  LT D   ++KAL+ SK+
Sbjct: 4   IKRQIEYYFSVDNLERDFFLRRKMDEDGFLPVTLIASFHRVQALTTDISLIIKALKDSKV 63

Query: 173 LEVTEDGTKVRR 184
           +E+ +   K+RR
Sbjct: 64  VEIIDM--KIRR 73

This domain is found in vertebrate La-related protein 1 (LARP1). 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. Length = 73

>gnl|CDD|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast asparagine-rich protein (ARP) and similar proteins

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 6/65 (9%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYG--KVTYVSL----PKFKSTGKLKGFAFVEFSTKEEAA 252
           +Y+  LPP+     +ES F++YG   V + +L         + K     F  F + EEA 
Sbjct: 3   LYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDSISGFAVFQSHEEAM 62

Query: 253 KALEL 257
           +AL L
Sbjct: 63  EALAL 67

This subfamily corresponds to the RRM of ARP, also termed NRP1, encoded by Saccharomyces cerevisiae YDL167C. Although its exact biological function remains unclear, ARP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), two Ran-binding protein zinc fingers (zf-RanBP), and an asparagine-rich region. It may possess RNA-binding and zinc ion binding activities. Additional research had indicated that ARP may function as a factor involved in the stress response. . Length = 88

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 35.5 bits (82), Expect = 0.003
 Identities = 22/60 (36%), Positives = 33/60 (55%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           ++YV  +   A  + +E+ F   G V  V++   K +G  KGFA++EFS KE    AL L
Sbjct: 1   SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALAL 60

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

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

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 22/62 (35%), Positives = 31/62 (50%), Gaps = 4/62 (6%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           D  T++V+ LP     D ++ VF     +   S       G  KG A++EF T+ EA KA
Sbjct: 2   DARTLFVKNLPYNITVDELKEVFEDAVDIRLPS----GKDGSSKGIAYIEFKTEAEAEKA 57

Query: 255 LE 256
           LE
Sbjct: 58  LE 59

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|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 = 35.3 bits (82), Expect = 0.003
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKF--KSTGKLKGFAFVEFSTKEEAAKALE 256
           +++  LP E     +  +F+ +G V  +S   F  K+TG+ K F FV +   E A  A++
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNV--ISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIK 58

Query: 257 LGLN 260
             +N
Sbjct: 59  -AMN 61

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

 Score = 38.0 bits (88), Expect = 0.004
 Identities = 18/55 (32%), Positives = 29/55 (52%)

Query: 201 VEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           V  LP     + I S+F+  G++    L + K TG+  G+ FV +   E+A KA+
Sbjct: 8   VNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAV 62

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

 Score = 35.8 bits (82), Expect = 0.004
 Identities = 17/44 (38%), Positives = 27/44 (61%)

Query: 213 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +  VFSKYG +  VS+   + + + +GFAFV F   ++A +A E
Sbjct: 26  LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

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

 Score = 35.2 bits (81), Expect = 0.004
 Identities = 18/61 (29%), Positives = 34/61 (55%)

Query: 196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
            C ++V  L  +     +   F++YGK+T   +    +T + +GF F+ FS+ +EA +A+
Sbjct: 2   LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

Query: 256 E 256
           E
Sbjct: 62  E 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|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 35.2 bits (81), Expect = 0.004
 Identities = 14/57 (24%), Positives = 29/57 (50%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           I+V  L PE     + + FS +   +   +     +G+ +G+ FV F ++++A  A+
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAI 58

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|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 35.2 bits (81), Expect = 0.004
 Identities = 22/66 (33%), Positives = 32/66 (48%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           ++V  L  E   + +  VF K G + YV + +   T   KGFA+V+F  +    KAL L 
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLN 61

Query: 259 LNPCPP 264
               PP
Sbjct: 62  EKKFPP 67

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 35.3 bits (81), Expect = 0.004
 Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 208 AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNP 261
            E D  E  FS++G V    +   K TGK +GF FV F   + A KA  +  +P
Sbjct: 12  GEGDLTEH-FSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVKFHP 64

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

 Score = 35.0 bits (81), Expect = 0.004
 Identities = 16/57 (28%), Positives = 33/57 (57%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           +++  L  E   D +++ FS++G++T   + K  +T + +GF FV F++  E   A+
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAM 58

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|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 3/60 (5%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           IYV K+P +     +   F  +G++  ++L  F+  G    + FV +    +A +A+E G
Sbjct: 5   IYVGKIPIDTTRSELRQRFQPFGEIEEITL-HFRDDG--DNYGFVTYRYACDAFRAIEHG 61

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

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

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 16/83 (19%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL-EL 257
           +Y+  LP     + +     K+G +  + +       K K  AFV F +   A K +  L
Sbjct: 6   VYIGNLPESYSEEELREDLEKFGPIDQIKIV------KEKNIAFVHFLSIANAIKVVTTL 59

Query: 258 GLNPCPPDYQSSILTTTSRLSFG 280
              PC PDY S       R+ +G
Sbjct: 60  ---PCEPDYAS------RRIFYG 73

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	299
cd08036	75	LARP_5 La RNA-binding domain of La-related protein	99.97
cd08035	75	LARP_4 La RNA-binding domain of La-related protein	99.97
cd08033	77	LARP_6 La RNA-binding domain of La-related protein	99.96
cd08032	82	LARP_7 La RNA-binding domain of La-related protein	99.96
cd08031	75	LARP_4_5_like La RNA-binding domain of proteins si	99.96
cd08037	73	LARP_1 La RNA-binding domain of La-related protein	99.95
cd08038	73	LARP_2 La RNA-binding domain of La-related protein	99.95
smart00715	80	LA Domain in the RNA-binding Lupus La protein; unk	99.95
cd08029	76	LA_like_fungal La-motif domain of fungal proteins	99.95
cd08028	82	LARP_3 La RNA-binding domain of La-related protein	99.95
cd08034	73	LARP_1_2 La RNA-binding domain proteins similar to	99.95
cd08030	90	LA_like_plant La-motif domain of plant proteins si	99.94
cd07323	75	LAM LA motif RNA-binding domain. This domain is fo	99.94
KOG1855|consensus	484		99.93
PF05383	61	La: La domain; InterPro: IPR006630 Human Ro ribonu	99.87
KOG4213|consensus	205		99.83
KOG2591|consensus	684		99.81
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.8
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.74
cd08032	82	LARP_7 La RNA-binding domain of La-related protein	99.72
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.72
KOG0148|consensus	321		99.72
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.7
KOG0145|consensus	360		99.69
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.68
cd08036	75	LARP_5 La RNA-binding domain of La-related protein	99.67
cd08035	75	LARP_4 La RNA-binding domain of La-related protein	99.66
cd08033	77	LARP_6 La RNA-binding domain of La-related protein	99.66
cd08031	75	LARP_4_5_like La RNA-binding domain of proteins si	99.65
cd08028	82	LARP_3 La RNA-binding domain of La-related protein	99.65
smart00715	80	LA Domain in the RNA-binding Lupus La protein; unk	99.65
cd08037	73	LARP_1 La RNA-binding domain of La-related protein	99.64
cd08038	73	LARP_2 La RNA-binding domain of La-related protein	99.64
cd08029	76	LA_like_fungal La-motif domain of fungal proteins	99.61
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.61
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.6
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.6
cd08034	73	LARP_1_2 La RNA-binding domain proteins similar to	99.6
cd07323	75	LAM LA motif RNA-binding domain. This domain is fo	99.56
cd08030	90	LA_like_plant La-motif domain of plant proteins si	99.56
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.56
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.55
COG5193	438	LHP1 La protein, small RNA-binding pol III transcr	99.54
KOG0121|consensus	153		99.51
KOG0122|consensus	270		99.5
KOG0109|consensus	346		99.5
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.48
KOG0144|consensus	510		99.48
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.47
KOG0124|consensus	544		99.45
KOG0127|consensus	678		99.45
KOG0113|consensus	335		99.45
KOG0149|consensus	247		99.45
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.45
PLN03120	260	nucleic acid binding protein; Provisional	99.45
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.44
KOG0126|consensus	219		99.42
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.4
KOG0148|consensus	321		99.4
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.39
KOG0107|consensus	195		99.39
PF05383	61	La: La domain; InterPro: IPR006630 Human Ro ribonu	99.38
PLN03121	243	nucleic acid binding protein; Provisional	99.37
KOG0131|consensus	203		99.37
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.37
KOG4213|consensus	205		99.36
KOG4207|consensus	256		99.36
KOG0117|consensus	506		99.35
KOG0117|consensus	506		99.35
KOG0123|consensus	369		99.34
KOG0130|consensus	170		99.33
KOG0127|consensus	678		99.33
smart00362	72	RRM_2 RNA recognition motif.	99.32
KOG0147|consensus	549		99.32
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.3
KOG0144|consensus	510		99.28
PLN03213	759	repressor of silencing 3; Provisional	99.28
smart00360	71	RRM RNA recognition motif.	99.27
KOG0105|consensus	241		99.24
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.23
KOG0114|consensus	124		99.23
KOG0125|consensus	376		99.22
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.21
KOG0111|consensus	298		99.19
KOG0131|consensus	203		99.19
KOG0108|consensus	435		99.19
KOG1855|consensus	484		99.18
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.18
KOG0145|consensus	360		99.17
KOG0110|consensus	725		99.16
KOG0146|consensus	371		99.15
smart00361	70	RRM_1 RNA recognition motif.	99.08
KOG0123|consensus	369		99.08
KOG0124|consensus	544		99.03
KOG4212|consensus	608		99.0
KOG4205|consensus	311		98.92
KOG0109|consensus	346		98.89
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.87
KOG4208|consensus	214		98.86
KOG0153|consensus	377		98.83
COG5193	438	LHP1 La protein, small RNA-binding pol III transcr	98.81
KOG0116|consensus	419		98.79
KOG2590|consensus	448		98.74
KOG0415|consensus	479		98.73
KOG4205|consensus	311		98.7
KOG4206|consensus	221		98.67
KOG0132|consensus	894		98.61
KOG0146|consensus	371		98.6
KOG0533|consensus	243		98.58
KOG4212|consensus	608		98.55
KOG0110|consensus	725		98.51
KOG4209|consensus	231		98.46
KOG2591|consensus	684		98.46
KOG4661|consensus	940		98.46
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.44
KOG4206|consensus	221		98.42
KOG0105|consensus	241		98.41
KOG1457|consensus	284		98.38
KOG4211|consensus	510		98.36
KOG4660|consensus	549		98.34
KOG1548|consensus	382		98.32
KOG4454|consensus	267		98.32
KOG0151|consensus	877		98.21
KOG0226|consensus	290		98.21
KOG0106|consensus	216		98.2
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.14
KOG0106|consensus	216		98.06
KOG4211|consensus	510		97.88
KOG0120|consensus	500		97.8
KOG1190|consensus	492		97.71
KOG0120|consensus	500		97.55
KOG0147|consensus	549		97.55
KOG1457|consensus	284		97.54
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.45
KOG1995|consensus	351		97.42
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.41
KOG1190|consensus	492		97.36
KOG2314|consensus	698		97.33
KOG4210|consensus	285		97.31
KOG0112|consensus	975		97.24
KOG0129|consensus	520		97.19
KOG1548|consensus	382		97.18
KOG2590|consensus	448		97.04
KOG3152|consensus	278		97.04
KOG0128|consensus	881		97.0
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.78
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.74
KOG0115|consensus	275		96.7
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.45
KOG1365|consensus	508		96.39
KOG1456|consensus	494		96.3
KOG4307|consensus	944		96.3
KOG0129|consensus	520		96.15
KOG1456|consensus	494		96.02
KOG4849|consensus	498		95.86
PF09421	989	FRQ: Frequency clock protein; InterPro: IPR018554	95.8
KOG0128|consensus	881		95.72
KOG1365|consensus	508		95.37
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.32
KOG4454|consensus	267		95.28
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.72
COG0724	306	RNA-binding proteins (RRM domain) [General functio	94.58
KOG2202|consensus	260		94.24
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	93.64
KOG4676|consensus	479		93.47
KOG0112|consensus	975		93.03
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	92.52
KOG0111|consensus	298		92.28
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	92.2
KOG2416|consensus	718		91.86
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	91.48
KOG4307|consensus	944		91.31
KOG2193|consensus	584		91.09
KOG1996|consensus	378		90.92
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	90.87
KOG2278|consensus	207		90.05
KOG2068|consensus	327		88.38
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	87.81
PF01885	186	PTS_2-RNA: RNA 2'-phosphotransferase, Tpt1 / KptA	87.41
KOG0130|consensus	170		85.35
KOG4210|consensus	285		84.56
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	84.4
KOG4285|consensus	350		83.75
PLN03213	759	repressor of silencing 3; Provisional	83.54
KOG4574|consensus	1007		81.18
PRK00819	179	RNA 2'-phosphotransferase; Reviewed	80.84

>cd08036 LARP_5 La RNA-binding domain of La-related protein 5

Probab=99.97  E-value=3.4e-32  Score=187.79  Aligned_cols=68  Identities=28%  Similarity=0.473  Sum_probs=66.7

Q ss_pred             CeeecCCCCcCcChHHHHhhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeec
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKG   68 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr   68 (299)
                      |||||||+||++|.||+++|+.+|||||++|++||||++||+|.+.|++||+.|++||||+||++||.
T Consensus         8 vEyYFS~~NL~~D~fLr~~md~~g~Vpi~~ia~F~rik~Lt~D~~lI~~aL~~S~~vevse~g~kVRp   75 (75)
T cd08036           8 LEFCLSRENLASDMYLISQMDSDQYVPIMTVANLDHIKKLSTDVDLIVDVLRSLPLVQVDEKGEKVRP   75 (75)
T ss_pred             eeeeechhhccccHHHHHHhccCCCEehHHHhccHHHHHhcCCHHHHHHHHhhCCeEEECCCCCccCc
Confidence            79999999999999999999999999999999999999999999999999999999999999999983

This domain is found in vertebrate La-related protein 5 (LARP5). 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.

>cd08035 LARP_4 La RNA-binding domain of La-related protein 4

Probab=99.97  E-value=1.3e-31  Score=186.61  Aligned_cols=68  Identities=28%  Similarity=0.458  Sum_probs=66.7

Q ss_pred             CeeecCCCCcCcChHHHHhhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeec
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKG   68 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr   68 (299)
                      |||||||+||++|.||+++|+.+|||||++|++||||++||+|++.|++||+.|+.||||+||++||.
T Consensus         8 vEyYFSd~NL~~D~fL~~~md~~G~Vpi~~iasF~rik~lt~d~~~I~~AL~~S~~levsedg~kVRp   75 (75)
T cd08035           8 LEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSPMVQVDETGEKVRP   75 (75)
T ss_pred             HHhhcCHhhcccCHHHHHhhCcCCCEehHHHhccHHHHHhcCCHHHHHHHHHcCCeEEEcCCCCccCc
Confidence            79999999999999999999999999999999999999999999999999999999999999999983

This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). 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.

>cd08033 LARP_6 La RNA-binding domain of La-related protein 6

Probab=99.96  E-value=2.1e-30  Score=183.23  Aligned_cols=68  Identities=37%  Similarity=0.534  Sum_probs=66.2

Q ss_pred             CeeecCCCCcCcChHHHHhh--ccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeec
Q psy3930           1 MEFYLSDSNLRKDRFFSQLL--QESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKG   68 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~--~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr   68 (299)
                      |||||||+||++|.||+++|  +.+|||||++|++||||++|+.|.+.|++||+.|+.|||++|+++|||
T Consensus         8 vEfYFSd~NL~~D~fL~~~~~~~~dG~Vpl~~i~~F~rmk~l~~d~~~I~~Al~~S~~lev~~d~~~VRR   77 (77)
T cd08033           8 VEYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSSKLVVSEDGKKVRR   77 (77)
T ss_pred             HHhhcCHhhhccCHHHHHHhccCCCCcEehHHHhcchHHHHHcCCHHHHHHHHHhCCeEEEcCCCCccCC
Confidence            79999999999999999999  568999999999999999999999999999999999999999999997

This domain is found in animal and plant 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.

>cd08032 LARP_7 La RNA-binding domain of La-related protein 7

Probab=99.96  E-value=3.6e-30  Score=183.79  Aligned_cols=68  Identities=31%  Similarity=0.644  Sum_probs=66.3

Q ss_pred             CeeecCCCCcCcChHHHHhhc--cCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeec
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQ--ESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKG   68 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~--~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr   68 (299)
                      |||||||+||++|.||+++|+  .+|||||++|++||||++||.|.+.|++||+.|+.|||++|+++|||
T Consensus        13 vEfYFSd~NL~~D~fL~~~~~~~~dG~Vpl~~i~~F~rmk~lt~d~~~i~~Al~~S~~lev~ed~~~VRR   82 (82)
T cd08032          13 VDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVELNLEGTRIRR   82 (82)
T ss_pred             HHhhcchhhcccCHHHHHHhcCCCCCCEeHHHHhcchHHHHHcCCHHHHHHHHhcCCEEEEcCCCCccCC
Confidence            799999999999999999998  57999999999999999999999999999999999999999999997

LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.

>cd08031 LARP_4_5_like La RNA-binding domain of proteins similar to La-related proteins 4 and 5

Probab=99.96  E-value=3.6e-30  Score=181.10  Aligned_cols=68  Identities=32%  Similarity=0.529  Sum_probs=66.6

Q ss_pred             CeeecCCCCcCcChHHHHhhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeec
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKG   68 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr   68 (299)
                      |||||||+||++|.||+++|+.+|||||++|++||||++|+.|.+.|++||+.|+.|||++|+++||.
T Consensus         8 vEfYFSd~NL~~D~fL~~~m~~dG~Vpl~~i~~F~rmk~lt~d~~~i~~Al~~S~~lev~ed~~~VR~   75 (75)
T cd08031           8 LEYYFSRENLANDAYLLSQMDSDQYVPIWTIANFNKIKKLTTDIDLIVEALRESPNVQVDEKGEKVRP   75 (75)
T ss_pred             HHHHcCHhhhccCHHHHHHhCCCCCEEHHHHhCchhHHHHcCCHHHHHHHHHhCCeEEEcCCCCccCc
Confidence            69999999999999999999999999999999999999999999999999999999999999999984

This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). 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.

>cd08037 LARP_1 La RNA-binding domain of La-related protein 1

Probab=99.95  E-value=1.9e-29  Score=175.42  Aligned_cols=66  Identities=29%  Similarity=0.522  Sum_probs=63.5

Q ss_pred             CeeecCCCCcCcChHHHHhhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeec
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKG   68 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr   68 (299)
                      |||||||+||++|.||+++|+.+|||||++|++||||++||.|.+.|++||+.|+.|||+++  +|||
T Consensus         8 vEyYFSd~NL~~D~fLr~~md~dG~Vpi~~ia~F~rmk~Lt~d~~~I~~Al~~S~~vev~~~--~~r~   73 (73)
T cd08037           8 IEYYFSVDNLERDFFLRRKMDEDGFLPVTLIASFHRVQALTTDISLIIKALKDSKVVEIIDM--KIRR   73 (73)
T ss_pred             HHHhccHhhhccCHHHHHHhccCCCEeHHHHhcchHHHHhcCCHHHHHHHHHcCCeEEEecc--hhcC
Confidence            79999999999999999999999999999999999999999999999999999999999998  5664

This domain is found in vertebrate La-related protein 1 (LARP1). 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.

>cd08038 LARP_2 La RNA-binding domain of La-related protein 2

Probab=99.95  E-value=2.4e-29  Score=174.83  Aligned_cols=66  Identities=23%  Similarity=0.443  Sum_probs=63.3

Q ss_pred             CeeecCCCCcCcChHHHHhhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeec
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKG   68 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr   68 (299)
                      |||||||+||++|.||+++|+.+|||||++|++||||++|+.|.+.|++||+.|+.||+++|+  |||
T Consensus         8 vEfYFSd~NL~~D~fLr~~m~~~G~Vpl~~ia~F~rmk~lt~d~~~I~~Al~~S~~ve~~~~~--~r~   73 (73)
T cd08038           8 IEYYFSTENLERDFFLRRKMDLQGFLPISLIAGFYRVQALTTNVDLILEALKDSTEVEIVDQK--IRR   73 (73)
T ss_pred             HHhhcchhhhccCHHHHHHhCCCCCEeHHHHhcchHHHHhcCCHHHHHHHHHcCCeEEEeCCc--ccC
Confidence            799999999999999999999999999999999999999999999999999999999999994  554

This domain is found in vertebrate La-related protein 2 (LARP2). 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.

>smart00715 LA Domain in the RNA-binding Lupus La protein; unknown function

Probab=99.95  E-value=2.4e-29  Score=180.02  Aligned_cols=69  Identities=36%  Similarity=0.607  Sum_probs=67.6

Q ss_pred             CeeecCCCCcCcChHHHHhhcc-CCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeecc
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQE-SPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGN   69 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~-~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr~   69 (299)
                      |||||||+||++|.||+++|+. +|||||++|++||||++|+.|.+.|++||+.|+.|||++|+++|||+
T Consensus        11 vEfYFSd~NL~~D~fLr~~~~~~~g~Vpl~~i~~F~r~k~l~~d~~~i~~Al~~S~~lel~~d~~~VRR~   80 (80)
T smart00715       11 VEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSPKLEVSEDGLKVRRR   80 (80)
T ss_pred             HHHHcCHhhhhhCHHHHHHhccCCCCEEhHHHhCchhHHHHcCCHHHHHHHHHhCCeEEEcCCCCeeCcC
Confidence            6999999999999999999999 89999999999999999999999999999999999999999999984

>cd08029 LA_like_fungal La-motif domain of fungal proteins similar to the La autoantigen

Probab=99.95  E-value=4e-29  Score=176.71  Aligned_cols=67  Identities=39%  Similarity=0.625  Sum_probs=64.3

Q ss_pred             CeeecCCCCcCcChHHHHhh--ccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeec
Q psy3930           1 MEFYLSDSNLRKDRFFSQLL--QESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKG   68 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~--~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr   68 (299)
                      |||||||+||++|.||+++|  +.+|||||++|++||||++|+.+ +.|++||+.|+.|||++||++|||
T Consensus         8 vEfYFSd~NL~~D~fLr~~~~~~~~G~Vpl~~i~~F~rmk~l~~~-~~i~~Al~~S~~lev~~d~~~VRR   76 (76)
T cd08029           8 VEFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRFQPL-EAVVEALRESELLEVSEDGENVRR   76 (76)
T ss_pred             HHhhcCHhhhccCHHHHHHhccCCCCcEehHHHhCchHHHHcCCH-HHHHHHHHhCCeEEEeCCCCcccC
Confidence            79999999999999999999  57899999999999999999866 999999999999999999999997

This domain is found in fungal 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.

>cd08028 LARP_3 La RNA-binding domain of La-related protein 3

Probab=99.95  E-value=5.7e-29  Score=178.07  Aligned_cols=68  Identities=43%  Similarity=0.746  Sum_probs=66.1

Q ss_pred             CeeecCCCCcCcChHHHHhhcc-CCCEEeeeeecchhhhhccCCHHHHHHHHhcCc--ceeeccCcceeec
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQE-SPEIEVSVFLKCNKLARLTHDPDDVVKALRKSK--LLEVTEDGTKVKG   68 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~-~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~--~~~v~~~~~~vrr   68 (299)
                      |||||||+||++|.||+++|+. +|||||++|++||||++|+.|.+.|++||+.|+  .|||++|+++|||
T Consensus        12 vEfYFSd~NL~~D~fLr~~m~~~~G~Vpl~~i~~F~rmk~l~~d~~~i~~Al~~S~~~~lev~~d~~~VRR   82 (82)
T cd08028          12 IEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKSGLIEVSEDKTKIRR   82 (82)
T ss_pred             HHhhcCHhhhccCHHHHHHHhccCCCEEhHHHhCChhHHHhcCCHHHHHHHHHhCCCCEEEEcCCCCccCC
Confidence            7999999999999999999984 899999999999999999999999999999999  9999999999997

This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).

>cd08034 LARP_1_2 La RNA-binding domain proteins similar to La-related proteins 1 and 2

Probab=99.95  E-value=8.6e-29  Score=173.00  Aligned_cols=66  Identities=26%  Similarity=0.493  Sum_probs=63.7

Q ss_pred             CeeecCCCCcCcChHHHHhhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeec
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKG   68 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr   68 (299)
                      |||||||+||++|.||+++|+.+|||||++|++||||++|++|.+.|++||+.|+.|||++  ++||+
T Consensus         8 vEfYFSd~NL~~D~fLr~~m~~~G~Vpl~~i~~F~rmk~l~~d~~~i~~Al~~S~~lev~e--~kvR~   73 (73)
T cd08034           8 IEYYFSVDNLEKDFFLRRKMDPEGYLPIALIASFHRVQALTTDVNLILEALKDSTVVELVD--EKVRC   73 (73)
T ss_pred             HHhhcCHhhhccCHHHHHHcCCCCCEeHHHHhccHHHHHHcCCHHHHHHHHHcCCeEEEec--CeecC
Confidence            7999999999999999999999999999999999999999999999999999999999999  47875

This domain is found in proteins similar to vertebrate La-related proteins 1 and 2 (LARP1, LARP2). 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.

>cd08030 LA_like_plant La-motif domain of plant proteins similar to the La autoantigen

Probab=99.94  E-value=2.5e-28  Score=176.94  Aligned_cols=68  Identities=34%  Similarity=0.535  Sum_probs=64.3

Q ss_pred             CeeecCCCCcCcChHHHHhh--ccCCCEEeeeeecchhhhhccCC------------HHHHHHHHhcCcceeeccCccee
Q psy3930           1 MEFYLSDSNLRKDRFFSQLL--QESPEIEVSVFLKCNKLARLTHD------------PDDVVKALRKSKLLEVTEDGTKV   66 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~--~~~~~v~~~~~~~f~~~~~~~~~------------~~~i~~a~~~s~~~~v~~~~~~v   66 (299)
                      |||||||+||++|+||+++|  +.+|||||++|++||||++|+.+            .+.|++||+.|+.|||++|+++|
T Consensus         9 vEfYFSd~NL~~D~fL~~~~~~~~dG~V~i~~i~~F~rmk~l~~~~~~~~~~~~~~~~~~I~~ALk~S~~levseD~~~V   88 (90)
T cd08030           9 VEFYFSDSNLPRDDFLLEEVEEDPDGMVSLALICSFSRMRSLLGLGGGKPEDVPEDTLKAVAEALRTSTLLKVSEDGKRV   88 (90)
T ss_pred             HHcccchhhcccCHHHHHHhccCCCCCEehHHHhcChHHHHHhhcccccccccchhHHHHHHHHHccCCEEEEcCCCCcc
Confidence            79999999999999999999  56899999999999999999853            68999999999999999999999


Q ss_pred             ec
Q psy3930          67 KG   68 (299)
Q Consensus        67 rr   68 (299)
                      ||
T Consensus        89 RR   90 (90)
T cd08030          89 GR   90 (90)
T ss_pred             CC
Confidence            98

This domain is found in plant 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.

>cd07323 LAM LA motif RNA-binding domain

Probab=99.94  E-value=4.4e-28  Score=171.85  Aligned_cols=68  Identities=41%  Similarity=0.707  Sum_probs=66.8

Q ss_pred             CeeecCCCCcCcChHHHHhhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeec
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKG   68 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr   68 (299)
                      |||||||+||++|.||+++|+.+|||||++|++||||++|+.|.+.|++||+.|+.|||++|+++|||
T Consensus         8 vEfYFSd~NL~~D~fL~~~~~~~g~Vpl~~i~~F~r~k~l~~~~~~i~~Al~~s~~lel~~~~~~Vrr   75 (75)
T cd07323           8 VEYYFSDENLCKDRFLRSLMDDDGWVPLSLLASFNRVKKLTTDVELILEALRDSSVVEVSEDGTKVRR   75 (75)
T ss_pred             hHhccCHhhhCcCHHHHHhcCCCCCEEHHHHhCchHHHHHcCCHHHHHHHHHhCCeEEEeCCCCccCC
Confidence            79999999999999999999999999999999999999999999999999999999999999999997

This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). 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.

>KOG1855|consensus

Probab=99.93  E-value=1.8e-26  Score=206.04  Aligned_cols=164  Identities=32%  Similarity=0.395  Sum_probs=132.3

Q ss_pred             CeeecCCCCcCcChHHHHhhccC--CCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeeccccccccccc
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQES--PEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGNIIRHFLVPI   78 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~~--~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr~~~~~~~~p~   78 (299)
                      |||||||+||.+|.||.++|..+  |||||.+|++|+|||+||.|+.+|+.||+.|..|+||+|+++|||..      |+
T Consensus       148 VEyyFSDenL~~d~fLlkhvrrnkeGyVpv~~vaSFKKvK~LTrd~~~va~ALr~S~kL~vseDgkKVrRis------Pl  221 (484)
T KOG1855|consen  148 VEYYFSDENLLKDAFLLKHVRRNKEGYVPVKLVASFKKVKALTRDWKLVADALRKSSKLEVSEDGKKVRRIS------PL  221 (484)
T ss_pred             hheeeccccccchHHHHHHHhcCCCCceeeehhhhHHHHHHHhhhhHHHHHHHhhcceEEEccCCceeeecC------CC
Confidence            79999999999999999999876  99999999999999999999999999999999999999999999963      33


Q ss_pred             cccccccccccCccccccccCCCCcCchHHHHHHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCCC
Q psy3930          79 SMETEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTH  158 (299)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~k~r~r~~~~~~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~~  158 (299)
                      ++-.++                                        +                                 
T Consensus       222 p~~~~e----------------------------------------e---------------------------------  228 (484)
T KOG1855|consen  222 PEFDEE----------------------------------------E---------------------------------  228 (484)
T ss_pred             CCcccc----------------------------------------c---------------------------------
Confidence            322211                                        0                                 


Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeecc---CC--
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKF---KS--  233 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~---~~--  233 (299)
                                                         ...++|.+.|||.+-.-+-|.++|+.+|.|..|+|...   ..  
T Consensus       229 -----------------------------------l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~  273 (484)
T KOG1855|consen  229 -----------------------------------LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDV  273 (484)
T ss_pred             -----------------------------------cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCccc
Confidence                                               11367888899999888999999999999999998764   21  


Q ss_pred             CCC--------cceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeeccc
Q psy3930         234 TGK--------LKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSF  279 (299)
Q Consensus       234 ~g~--------~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~~  279 (299)
                      .|.        .+-+|+|+|...+.|.+|.+. +|....+-.|.+.+...+.+.
T Consensus       274 r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~-~~~e~~wr~glkvkLl~k~a~  326 (484)
T KOG1855|consen  274 RGFPKKYFELQTKECALVEYEEVEAARKAREL-LNPEQNWRMGLKVKLLGKKAP  326 (484)
T ss_pred             ccCCccchhhhhhhhhhhhhhhhHHHHHHHHh-hchhhhhhhcchhhhhhccCc
Confidence            222        245799999999999999998 654444445555555555444

>PF05383 La: La domain; InterPro: IPR006630 Human Ro ribonucleoproteins (RNPs) are composed of one of the four small Y RNAs and at least two proteins, Ro60 and La

Probab=99.87  E-value=4.8e-24  Score=144.89  Aligned_cols=54  Identities=37%  Similarity=0.620  Sum_probs=49.5

Q ss_pred             CeeecCCCCcCcChHHHHhhcc--CCCEEeeeeecchhhhhcc-CCHHHHHHHHhcC
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQE--SPEIEVSVFLKCNKLARLT-HDPDDVVKALRKS   54 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~--~~~v~~~~~~~f~~~~~~~-~~~~~i~~a~~~s   54 (299)
                      |||||||+||++|.||+++|++  +|||||++|++|+||++|+ .|.+.|++||+.|
T Consensus         5 vEfYFSd~NL~~D~fL~~~~~~~~~g~Vpi~~i~~F~r~k~l~~~~~~~I~~al~~S   61 (61)
T PF05383_consen    5 VEFYFSDENLPRDKFLRSQMDSNPDGWVPISTILSFNRMKALTNTDIELIVDALRDS   61 (61)
T ss_dssp             HHHHTSHHHHCC-HHHHHHHCTTTTTBEEHHHHTTSHHHHHH--S-HHHHHHHHHTS
T ss_pred             HHHhcCHHHhCcCHHHHHHHHhcCCCcEeHHHHHchHHHHHHhcCCHHHHHHHHHcC
Confidence            6999999999999999999999  7999999999999999999 8999999999987

The La protein is a 47 kDa polypeptide that frequently acts as an autoantigen in systemic lupus erythematosus and Sjogren's syndrome []. In the nucleus, La acts as a RNA polymerase III (RNAP III) transcription factor, while in the cytoplasm, La acts as a translation factor []. In the nucleus, La binds to the 3'UTR of nascent RNAP III transcripts to assist in folding and maturation []. In the cytoplasm, La recognises specific classes of mRNAs that contain a 5'-terminal oligopyrimidine (5'TOP) motif known to control protein synthesis []. The specific recognition is mediated by the N-terminal domain of La, which comprises a La motif and a RNA recognition motif (RRM). The La motif adopts an alpha/beta fold that comprises a winged-helix motif []. Homologous La domain-containing proteins have been identified in a wide range of organisms except Archaea, bacteria and viruses [].; PDB: 1S29_A 1YTY_B 2VOO_B 1S7A_A 2VOP_A 2VON_B 1ZH5_B 2VOD_A 2CQK_A.

>KOG4213|consensus

Probab=99.83  E-value=5.1e-22  Score=158.47  Aligned_cols=134  Identities=24%  Similarity=0.384  Sum_probs=100.6

Q ss_pred             CeeecCCCCcCcChHHHHhh-c-cCCCEEeeeeecchhhhhccCCHHHHHHHHhcCc--ceeeccCcceeeccccccccc
Q psy3930           1 MEFYLSDSNLRKDRFFSQLL-Q-ESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSK--LLEVTEDGTKVKGNIIRHFLV   76 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~-~-~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~--~~~v~~~~~~vrr~~~~~~~~   76 (299)
                      |||||+|.||+||+||++++ . .+|||||.+++.|||+.+|++|.+.|++||+.|.  ++++|+|++++||.+    ..
T Consensus        21 leyy~Gd~nl~rdkfl~eqi~k~~~gwvpi~i~i~FnRla~lttD~~~Iv~al~ksk~~l~eisedk~k~rr~~----sk   96 (205)
T KOG4213|consen   21 LEYYFGDLNLPRDKFLREQIHKLDDGWVPIEIMIKFNRLASLTTDFNVIVEALSKSKAELMEISEDKTKIRRSP----SK   96 (205)
T ss_pred             hhhhhcccCchHHHHHHHHhhhhccCCccchhhhhhhhhhhccccHHHHHHHHhhCHHhhhhhhhchhhhhcCc----CC
Confidence            69999999999999999998 3 4699999999999999999999999999999776  899999999999976    88


Q ss_pred             cccccccccccccCccccccccCCCCcCchHHHHHHHHHHhhhhcCCCCcchhHHHHHhhhcCC----Ceeeeeeecccc
Q psy3930          77 PISMETEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESP----EIEVSVFLKCNK  152 (299)
Q Consensus        77 p~~~~~~~~~~~~~~~~~~~~~~~k~r~r~~~~~~~i~~q~efyfsd~nL~~d~fl~~~~~~~~----~~~l~~f~~F~~  152 (299)
                      |+|+.+.+..   +++.+.+++.+   ....++ ..+..+..          ++..+-.|+..+    .+.+++|++|.+
T Consensus        97 plpEvt~e~~---~~~~~r~v~~K---~td~ql-~~l~qw~~----------~k~~nv~mr~~~~k~~~fkGsvkv~f~t  159 (205)
T KOG4213|consen   97 PLPEVTDEYK---EGIKERTVYKK---ITDDQL-DDLNQWAS----------GKGHNVKMRRHGNKAHPFKGSVKVTFQT  159 (205)
T ss_pred             CCccccHHHH---HHHHHhhhhcc---CCHHHH-HHHHHHhc----------ccceEeeccccCCCCCCCCCceEEEeec
Confidence            9998887765   33444456642   222333 33332221          222233343322    488899999998


Q ss_pred             ccc
Q psy3930         153 LAR  155 (299)
Q Consensus       153 i~~  155 (299)
                      .++
T Consensus       160 k~q  162 (205)
T KOG4213|consen  160 KEQ  162 (205)
T ss_pred             HHH
Confidence            544

>KOG2591|consensus

Probab=99.81  E-value=3.4e-20  Score=170.53  Aligned_cols=145  Identities=22%  Similarity=0.416  Sum_probs=124.6

Q ss_pred             CeeecCCCCcCcChHHHHhhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeeccccccccccccc
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGNIIRHFLVPISM   80 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr~~~~~~~~p~~~   80 (299)
                      +|||||.+||..|.||..+|++|.||||.+++.|+.|++||+|+++|+++|+.|+.|+|++++.+||.+.+|        
T Consensus       104 lEy~fSreNlssD~YL~sQMDSDqyVPI~tva~~~~i~klttDvdLI~Evlresp~VqvDekgekVrp~~kR--------  175 (684)
T KOG2591|consen  104 LEYYFSRENLSSDRYLISQMDSDQYVPINTVANFPEIMKLTTDVDLIVEVLRESPNVQVDEKGEKVRPNHKR--------  175 (684)
T ss_pred             HHHhhccccccchhhhhhhcccccccchhhhccchhhhhhccchHHHHHHHhcCCCceeccCccccccCcce--------
Confidence            699999999999999999999999999999999999999999999999999999999999999999975321        


Q ss_pred             cccccccccCccccccccCCCCcCchHHHHHHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCCCCH
Q psy3930          81 ETEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDP  160 (299)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~k~r~r~~~~~~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~~~~  160 (299)
                                                                                                      
T Consensus       176 --------------------------------------------------------------------------------  175 (684)
T KOG2591|consen  176 --------------------------------------------------------------------------------  175 (684)
T ss_pred             --------------------------------------------------------------------------------
Confidence                                                                                            


Q ss_pred             HHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhc--CCceEEEEeeccCCCCCcc
Q psy3930         161 DDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSK--YGKVTYVSLPKFKSTGKLK  238 (299)
Q Consensus       161 ~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~--~G~i~~v~i~~~~~~g~~k  238 (299)
                                                          |.|.+.-||..+..|+++.+|+.  +..+..|.+..+.      
T Consensus       176 ------------------------------------cIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~------  213 (684)
T KOG2591|consen  176 ------------------------------------CIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND------  213 (684)
T ss_pred             ------------------------------------eEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC------
Confidence                                                44556667777777778888864  6677788876553      


Q ss_pred             eEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeec
Q psy3930         239 GFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRL  277 (299)
Q Consensus       239 g~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~  277 (299)
                       -+||+|++..+|+.|.+. +......|.|.+|..++|.
T Consensus       214 -nWyITfesd~DAQqAyky-lreevk~fqgKpImARIKa  250 (684)
T KOG2591|consen  214 -NWYITFESDTDAQQAYKY-LREEVKTFQGKPIMARIKA  250 (684)
T ss_pred             -ceEEEeecchhHHHHHHH-HHHHHHhhcCcchhhhhhh
Confidence             289999999999999998 6656678889998888874

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.80  E-value=1.7e-19  Score=164.90  Aligned_cols=118  Identities=27%  Similarity=0.419  Sum_probs=102.2

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL  237 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~  237 (299)
                      .+.++|.+|+..+++..+.++.++|..+.+...  ....++|||+|||..+++++|+++|++||.|..|.+++++.+|.+
T Consensus       157 ~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p~~~--~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~  234 (346)
T TIGR01659       157 GSEADSQRAIKNLNGITVRNKRLKVSYARPGGE--SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTP  234 (346)
T ss_pred             ccHHHHHHHHHHcCCCccCCceeeeeccccccc--ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCcc
Confidence            348999999999999999999999987664332  344678999999999999999999999999999999999889999


Q ss_pred             ceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeecc
Q psy3930         238 KGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLS  278 (299)
Q Consensus       238 kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~  278 (299)
                      +|||||+|.+.++|++|++. +|+..+....++|.|++...
T Consensus       235 kG~aFV~F~~~e~A~~Ai~~-lng~~~~g~~~~l~V~~a~~  274 (346)
T TIGR01659       235 RGVAFVRFNKREEAQEAISA-LNNVIPEGGSQPLTVRLAEE  274 (346)
T ss_pred             ceEEEEEECCHHHHHHHHHH-hCCCccCCCceeEEEEECCc
Confidence            99999999999999999999 89855555567888876544

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=99.74  E-value=6.7e-18  Score=162.60  Aligned_cols=117  Identities=21%  Similarity=0.305  Sum_probs=101.9

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccCC---------CCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEe
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDK---------PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSL  228 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~---------~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i  228 (299)
                      .+.++|..|+..+|+..+.++.++|.+.......         .....++|||+|||+++++++|+++|+.||.|..|++
T Consensus       157 ~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl  236 (612)
T TIGR01645       157 EVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQL  236 (612)
T ss_pred             CcHHHHHHHHHhcCCeEEecceeeecccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEE
Confidence            4589999999999999999999999865432211         1233578999999999999999999999999999999


Q ss_pred             eccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeec
Q psy3930         229 PKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRL  277 (299)
Q Consensus       229 ~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~  277 (299)
                      +++..+|.++|||||+|.+.++|.+|++. +||  ..++|+.|+|....
T Consensus       237 ~~D~~tgksKGfGFVeFe~~e~A~kAI~a-mNg--~elgGr~LrV~kAi  282 (612)
T TIGR01645       237 ARAPTGRGHKGYGFIEYNNLQSQSEAIAS-MNL--FDLGGQYLRVGKCV  282 (612)
T ss_pred             EecCCCCCcCCeEEEEECCHHHHHHHHHH-hCC--CeeCCeEEEEEecC
Confidence            99988899999999999999999999999 998  89999999986543

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.

>cd08032 LARP_7 La RNA-binding domain of La-related protein 7

Probab=99.72  E-value=2.8e-18  Score=122.64  Aligned_cols=80  Identities=35%  Similarity=0.647  Sum_probs=75.1

Q ss_pred             chHHHHHHHHHHhhhhcCCCCcchhHHHHHhhh--cCCCeeeeeeecccccccCCCCHHHHHHHHHhcCcccccccccee
Q psy3930         105 RKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQ--ESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKV  182 (299)
Q Consensus       105 r~~~~~~~i~~q~efyfsd~nL~~d~fl~~~~~--~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v  182 (299)
                      |.+++...|++|+||||||+||++|.||+.+|.  ..||++++++++|++|+.++.+.+.+.+|++.+..+++++++.+|
T Consensus         1 ~~~~l~~~I~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~Vpl~~i~~F~rmk~lt~d~~~i~~Al~~S~~lev~ed~~~V   80 (82)
T cd08032           1 RVKQLLADIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLIARALKNSSVVELNLEGTRI   80 (82)
T ss_pred             CHHHHHHHHHHHHHhhcchhhcccCHHHHHHhcCCCCCCEeHHHHhcchHHHHHcCCHHHHHHHHhcCCEEEEcCCCCcc
Confidence            347889999999999999999999999999997  478999999999999999999999999999999999999999988


Q ss_pred             ee
Q psy3930         183 RR  184 (299)
Q Consensus       183 ~r  184 (299)
                      +|
T Consensus        81 RR   82 (82)
T cd08032          81 RR   82 (82)
T ss_pred             CC
Confidence            75

LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.72  E-value=1.5e-17  Score=153.43  Aligned_cols=81  Identities=25%  Similarity=0.402  Sum_probs=76.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      ++|||+|||+++++++|+++|++||.|.+|+++++..+|.++|||||+|.+.++|.+|+.+ |||  ..+.|++|.|..+
T Consensus       270 ~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~-lnG--~~~~gr~i~V~~~  346 (352)
T TIGR01661       270 YCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILS-LNG--YTLGNRVLQVSFK  346 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHH-hCC--CEECCeEEEEEEc
Confidence            3699999999999999999999999999999999988999999999999999999999999 999  8889999999887


Q ss_pred             cccC
Q psy3930         277 LSFG  280 (299)
Q Consensus       277 ~~~~  280 (299)
                      ....
T Consensus       347 ~~~~  350 (352)
T TIGR01661       347 TNKA  350 (352)
T ss_pred             cCCC
Confidence            7654

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

>KOG0148|consensus

Probab=99.72  E-value=1.5e-17  Score=141.27  Aligned_cols=113  Identities=23%  Similarity=0.375  Sum_probs=97.4

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccC--------------CCCCCCcEEEEecCCCCCCHHHHHHHhhcCCce
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD--------------KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKV  223 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~--------------~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i  223 (299)
                      ...++|++||..||+--|+.+.++-.++...+.              +..+++|+|||||++...++++|+..|+.||+|
T Consensus       112 ~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I  191 (321)
T KOG0148|consen  112 PNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPI  191 (321)
T ss_pred             cchHHHHHHHHHhCCeeeccceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcc
Confidence            457899999999999999999998877654332              125789999999999999999999999999999


Q ss_pred             EEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeecccCCCC
Q psy3930         224 TYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSFGITP  283 (299)
Q Consensus       224 ~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~~~~~~  283 (299)
                      ..||+-.+      +||+||.|++.|+|..||.. +||  .++.|..+    ||+|++..
T Consensus       192 ~EVRvFk~------qGYaFVrF~tkEaAahAIv~-mNn--tei~G~~V----kCsWGKe~  238 (321)
T KOG0148|consen  192 QEVRVFKD------QGYAFVRFETKEAAAHAIVQ-MNN--TEIGGQLV----RCSWGKEG  238 (321)
T ss_pred             eEEEEecc------cceEEEEecchhhHHHHHHH-hcC--ceeCceEE----EEeccccC
Confidence            99999876      47999999999999999999 888  77778776    77885543

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

Probab=99.70  E-value=1.6e-16  Score=127.84  Aligned_cols=84  Identities=15%  Similarity=0.320  Sum_probs=77.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||+++++++|+++|++||.|..|.++.+..+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.|
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~-lng--~~i~Gr~l~V  108 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE-MDG--KELNGRHIRV  108 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHH-cCC--CEECCEEEEE
Confidence            3467899999999999999999999999999999999998999999999999999999999999 898  7889999999


Q ss_pred             EeecccC
Q psy3930         274 TSRLSFG  280 (299)
Q Consensus       274 ~~k~~~~  280 (299)
                      .......
T Consensus       109 ~~a~~~~  115 (144)
T PLN03134        109 NPANDRP  115 (144)
T ss_pred             EeCCcCC
Confidence            8765443

>KOG0145|consensus

Probab=99.69  E-value=5.9e-17  Score=136.98  Aligned_cols=117  Identities=24%  Similarity=0.357  Sum_probs=107.8

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL  237 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~  237 (299)
                      -++++|.+|+..+|++.+..+.++|..+.|..+  ...+..+||+|||..+|..+|+.+|++||.|..-+|..|..+|.+
T Consensus        91 v~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~--~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~s  168 (360)
T KOG0145|consen   91 VRPKDAEKAINTLNGLRLQNKTIKVSYARPSSD--SIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLS  168 (360)
T ss_pred             cChHHHHHHHhhhcceeeccceEEEEeccCChh--hhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhccccee
Confidence            358999999999999999999999998876654  566789999999999999999999999999999999999999999


Q ss_pred             ceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeec
Q psy3930         238 KGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRL  277 (299)
Q Consensus       238 kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~  277 (299)
                      +|.|||+|....+|+.||+. +||.+......+|.|+...
T Consensus       169 rGVgFiRFDKr~EAe~AIk~-lNG~~P~g~tepItVKFan  207 (360)
T KOG0145|consen  169 RGVGFIRFDKRIEAEEAIKG-LNGQKPSGCTEPITVKFAN  207 (360)
T ss_pred             cceeEEEecchhHHHHHHHh-ccCCCCCCCCCCeEEEecC
Confidence            99999999999999999999 9999888888999998753

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.68  E-value=1.1e-16  Score=147.73  Aligned_cols=115  Identities=26%  Similarity=0.410  Sum_probs=98.2

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL  237 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~  237 (299)
                      .+.++|.+||..+++..+.++.++|..+.+...  ....++|||+|||..+++++|+.+|++||.|..+.++.+..+|.+
T Consensus        53 ~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~~~--~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~  130 (352)
T TIGR01661        53 VRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSD--SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLS  130 (352)
T ss_pred             CcHHHHHHHHhhcccEEECCeeEEEEeeccccc--ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCc
Confidence            448999999999999999999999988765433  345678999999999999999999999999999999998878899


Q ss_pred             ceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         238 KGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       238 kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      +|||||+|.+.++|+.|++. +||..+...+.++.+..
T Consensus       131 ~g~~fv~f~~~~~A~~ai~~-l~g~~~~g~~~~i~v~~  167 (352)
T TIGR01661       131 KGVGFIRFDKRDEADRAIKT-LNGTTPSGCTEPITVKF  167 (352)
T ss_pred             CcEEEEEECCHHHHHHHHHH-hCCCccCCCceeEEEEE
Confidence            99999999999999999999 89844443445555544

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

>cd08036 LARP_5 La RNA-binding domain of La-related protein 5

Probab=99.67  E-value=1.4e-17  Score=115.34  Aligned_cols=73  Identities=27%  Similarity=0.462  Sum_probs=69.5

Q ss_pred             HHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceee
Q psy3930         111 QQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVR  183 (299)
Q Consensus       111 ~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~  183 (299)
                      +.|++|+|||||++||++|.||+.+|...||++++++++|++|+.++.|.+.+.+|++.+..+++++.+.+|+
T Consensus         2 e~i~kQvEyYFS~~NL~~D~fLr~~md~~g~Vpi~~ia~F~rik~Lt~D~~lI~~aL~~S~~vevse~g~kVR   74 (75)
T cd08036           2 ELLKKTLEFCLSRENLASDMYLISQMDSDQYVPIMTVANLDHIKKLSTDVDLIVDVLRSLPLVQVDEKGEKVR   74 (75)
T ss_pred             hhhhcceeeeechhhccccHHHHHHhccCCCEehHHHhccHHHHHhcCCHHHHHHHHhhCCeEEECCCCCccC
Confidence            4578899999999999999999999999999999999999999999999999999999999999999888875

This domain is found in vertebrate La-related protein 5 (LARP5). 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.

>cd08035 LARP_4 La RNA-binding domain of La-related protein 4

Probab=99.66  E-value=2.9e-17  Score=114.74  Aligned_cols=73  Identities=27%  Similarity=0.443  Sum_probs=69.6

Q ss_pred             HHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceee
Q psy3930         111 QQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVR  183 (299)
Q Consensus       111 ~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~  183 (299)
                      +.|++|+||||||+||++|.||+..|...||++++++++|++|++++.|.+.+.+|++.+..+++++++.+|+
T Consensus         2 e~i~~QvEyYFSd~NL~~D~fL~~~md~~G~Vpi~~iasF~rik~lt~d~~~I~~AL~~S~~levsedg~kVR   74 (75)
T cd08035           2 ECLKKQLEFCFSRENLSKDLYLISQMDSDQFVPIWTVANMEGIKKLTTDMDLILDVLRSSPMVQVDETGEKVR   74 (75)
T ss_pred             hHHHhhHHhhcCHhhcccCHHHHHhhCcCCCEehHHHhccHHHHHhcCCHHHHHHHHHcCCeEEEcCCCCccC
Confidence            4688999999999999999999999999999999999999999999999999999999999999999888875

This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). 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.

>cd08033 LARP_6 La RNA-binding domain of La-related protein 6

Probab=99.66  E-value=4.1e-17  Score=115.50  Aligned_cols=74  Identities=39%  Similarity=0.569  Sum_probs=69.3

Q ss_pred             HHHHHHhhhhcCCCCcchhHHHHHhhh--cCCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeee
Q psy3930         111 QQIMNLMEFYLSDSNLRKDRFFSQLLQ--ESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       111 ~~i~~q~efyfsd~nL~~d~fl~~~~~--~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      ++|++|+||||||+||++|.||+.+|.  ..||++++++++|++|++++.+.+.+.+|++.+..+++++++.+|+|
T Consensus         2 ~~i~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~Vpl~~i~~F~rmk~l~~d~~~I~~Al~~S~~lev~~d~~~VRR   77 (77)
T cd08033           2 QKIVKQVEYYFSDENLLKDAFLLKHVRRNKEGYVPIKLIASFKKVKALTRDWRVVAAALRRSSKLVVSEDGKKVRR   77 (77)
T ss_pred             hHHHhHHHhhcCHhhhccCHHHHHHhccCCCCcEehHHHhcchHHHHHcCCHHHHHHHHHhCCeEEEcCCCCccCC
Confidence            468899999999999999999999995  46899999999999999999999999999999999999999988875

This domain is found in animal and plant 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.

>cd08031 LARP_4_5_like La RNA-binding domain of proteins similar to La-related proteins 4 and 5

Probab=99.65  E-value=4.8e-17  Score=114.60  Aligned_cols=73  Identities=32%  Similarity=0.510  Sum_probs=69.6

Q ss_pred             HHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceee
Q psy3930         111 QQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVR  183 (299)
Q Consensus       111 ~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~  183 (299)
                      ++|++|+||||||+||++|.||+..|...||++++++++|++|++++.+.+.+.+|++.+..+++++++.+|+
T Consensus         2 ~~i~~QvEfYFSd~NL~~D~fL~~~m~~dG~Vpl~~i~~F~rmk~lt~d~~~i~~Al~~S~~lev~ed~~~VR   74 (75)
T cd08031           2 ELLKRQLEYYFSRENLANDAYLLSQMDSDQYVPIWTIANFNKIKKLTTDIDLIVEALRESPNVQVDEKGEKVR   74 (75)
T ss_pred             hHHHHHHHHHcCHhhhccCHHHHHHhCCCCCEEHHHHhCchhHHHHcCCHHHHHHHHHhCCeEEEcCCCCccC
Confidence            5688999999999999999999999999999999999999999999999999999999999999999988875

This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). 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.

>cd08028 LARP_3 La RNA-binding domain of La-related protein 3

Probab=99.65  E-value=8.3e-17  Score=115.36  Aligned_cols=77  Identities=42%  Similarity=0.733  Sum_probs=72.3

Q ss_pred             HHHHHHHHHhhhhcCCCCcchhHHHHHhhh-cCCCeeeeeeecccccccCCCCHHHHHHHHHhcC--ccccccccceeee
Q psy3930         108 QLYQQIMNLMEFYLSDSNLRKDRFFSQLLQ-ESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSK--LLEVTEDGTKVRR  184 (299)
Q Consensus       108 ~~~~~i~~q~efyfsd~nL~~d~fl~~~~~-~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~--~~~~~~~~~~v~r  184 (299)
                      ++..+|++|+||||||+||++|.||+.+|. ..||++++++++|++|++++.+.+.+.+|++.+.  .+++++++.+|+|
T Consensus         3 ~l~~~I~~QvEfYFSd~NL~~D~fLr~~m~~~~G~Vpl~~i~~F~rmk~l~~d~~~i~~Al~~S~~~~lev~~d~~~VRR   82 (82)
T cd08028           3 DLEKKIIRQIEYYFGDFNLPRDKFLKEQIKEDDGWVPMEVMLKFNRLKSLSSDPEVIAKALKKSKSGLIEVSEDKTKIRR   82 (82)
T ss_pred             HHHHHHHHHHHhhcCHhhhccCHHHHHHHhccCCCEEhHHHhCChhHHHhcCCHHHHHHHHHhCCCCEEEEcCCCCccCC
Confidence            567889999999999999999999999997 4799999999999999999999999999999998  8999999998875

This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B).

>smart00715 LA Domain in the RNA-binding Lupus La protein; unknown function

Probab=99.65  E-value=6.6e-17  Score=115.79  Aligned_cols=77  Identities=39%  Similarity=0.618  Sum_probs=73.2

Q ss_pred             HHHHHHHHHhhhhcCCCCcchhHHHHHhhhc-CCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeee
Q psy3930         108 QLYQQIMNLMEFYLSDSNLRKDRFFSQLLQE-SPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       108 ~~~~~i~~q~efyfsd~nL~~d~fl~~~~~~-~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      ++.+.|++|+||||||+||++|.||+.+|.. .||++++++.+|++|++++.+.+.+.+|++.+..+++++++.+|+|
T Consensus         2 ~~~~~i~~QvEfYFSd~NL~~D~fLr~~~~~~~g~Vpl~~i~~F~r~k~l~~d~~~i~~Al~~S~~lel~~d~~~VRR   79 (80)
T smart00715        2 ELKQKIKKQVEYYFSDENLPRDKFLRKKMDKNDGYVPISTIASFKRVKSLTTDVNLIVEALRSSPKLEVSEDGLKVRR   79 (80)
T ss_pred             hHHHHHHHHHHHHcCHhhhhhCHHHHHHhccCCCCEEhHHHhCchhHHHHcCCHHHHHHHHHhCCeEEEcCCCCeeCc
Confidence            4567899999999999999999999999998 8999999999999999999999999999999999999999999986

>cd08037 LARP_1 La RNA-binding domain of La-related protein 1

Probab=99.64  E-value=8.3e-17  Score=112.13  Aligned_cols=71  Identities=27%  Similarity=0.455  Sum_probs=67.4

Q ss_pred             HHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccce
Q psy3930         111 QQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTK  181 (299)
Q Consensus       111 ~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~  181 (299)
                      +.|++|+||||||+||++|.||+..|...||++++++++|++|++++.+.+.+.+|++.+..+++++..++
T Consensus         2 ~~I~~QvEyYFSd~NL~~D~fLr~~md~dG~Vpi~~ia~F~rmk~Lt~d~~~I~~Al~~S~~vev~~~~~r   72 (73)
T cd08037           2 DYIKRQIEYYFSVDNLERDFFLRRKMDEDGFLPVTLIASFHRVQALTTDISLIIKALKDSKVVEIIDMKIR   72 (73)
T ss_pred             hHHHHHHHHhccHhhhccCHHHHHHhccCCCEeHHHHhcchHHHHhcCCHHHHHHHHHcCCeEEEecchhc
Confidence            56889999999999999999999999999999999999999999999999999999999999999988754

This domain is found in vertebrate La-related protein 1 (LARP1). 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.

>cd08038 LARP_2 La RNA-binding domain of La-related protein 2

Probab=99.64  E-value=9.2e-17  Score=111.88  Aligned_cols=71  Identities=23%  Similarity=0.405  Sum_probs=67.3

Q ss_pred             HHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccce
Q psy3930         111 QQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTK  181 (299)
Q Consensus       111 ~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~  181 (299)
                      +.|++|+||||||+||++|.||+..|...||++++++++|++|++++.+.+.+.+|++.+..+++.++.++
T Consensus         2 e~I~~QvEfYFSd~NL~~D~fLr~~m~~~G~Vpl~~ia~F~rmk~lt~d~~~I~~Al~~S~~ve~~~~~~r   72 (73)
T cd08038           2 EYIKRQIEYYFSTENLERDFFLRRKMDLQGFLPISLIAGFYRVQALTTNVDLILEALKDSTEVEIVDQKIR   72 (73)
T ss_pred             hHHHhhHHhhcchhhhccCHHHHHHhCCCCCEeHHHHhcchHHHHhcCCHHHHHHHHHcCCeEEEeCCccc
Confidence            46889999999999999999999999999999999999999999999999999999999999999988754

This domain is found in vertebrate La-related protein 2 (LARP2). 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.

>cd08029 LA_like_fungal La-motif domain of fungal proteins similar to the La autoantigen

Probab=99.61  E-value=2.3e-16  Score=111.62  Aligned_cols=73  Identities=40%  Similarity=0.626  Sum_probs=67.5

Q ss_pred             HHHHHHhhhhcCCCCcchhHHHHHhhh--cCCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeee
Q psy3930         111 QQIMNLMEFYLSDSNLRKDRFFSQLLQ--ESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       111 ~~i~~q~efyfsd~nL~~d~fl~~~~~--~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      ++|++|+||||||+||++|.||+.+|.  ..||++++++++|++|++++.+ +.+.+|++.+..+++++++.+|+|
T Consensus         2 ~~I~~QvEfYFSd~NL~~D~fLr~~~~~~~~G~Vpl~~i~~F~rmk~l~~~-~~i~~Al~~S~~lev~~d~~~VRR   76 (76)
T cd08029           2 EEIRKQVEFYFSDSNLPTDKFLWTLTGGSNNGWVPIKTIASFKRMRRFQPL-EAVVEALRESELLEVSEDGENVRR   76 (76)
T ss_pred             hHHHhhHHhhcCHhhhccCHHHHHHhccCCCCcEehHHHhCchHHHHcCCH-HHHHHHHHhCCeEEEeCCCCcccC
Confidence            468899999999999999999999995  6779999999999999999875 899999999999999999998875

This domain is found in fungal 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.

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

Probab=99.61  E-value=8.4e-16  Score=150.41  Aligned_cols=114  Identities=18%  Similarity=0.299  Sum_probs=98.0

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL  237 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~  237 (299)
                      .+.++|.+|+..+++..+.++.++|.+.............+|||+|||.++++++|+++|+.||.|..|.++.+. +|.+
T Consensus        50 ~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~s  128 (562)
T TIGR01628        50 QNPADAERALETMNFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKS  128 (562)
T ss_pred             CCHHHHHHHHHHhCCCEECCeeEEeecccccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCc
Confidence            448999999999999999999999987643332223345689999999999999999999999999999999886 8889


Q ss_pred             ceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         238 KGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       238 kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      +|||||+|.+.++|.+|++. +||  ..+.++.+.+..
T Consensus       129 kg~afV~F~~~e~A~~Ai~~-lng--~~~~~~~i~v~~  163 (562)
T TIGR01628       129 RGYGFVHFEKEESAKAAIQK-VNG--MLLNDKEVYVGR  163 (562)
T ss_pred             ccEEEEEECCHHHHHHHHHH-hcc--cEecCceEEEec
Confidence            99999999999999999999 898  777888887743

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

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

Probab=99.60  E-value=1.3e-15  Score=149.08  Aligned_cols=116  Identities=21%  Similarity=0.283  Sum_probs=100.0

Q ss_pred             CCHHHHHHHHHhcCccccc----cccceeeeeecccCC----------------CCCCCcEEEEecCCCCCCHHHHHHHh
Q psy3930         158 HDPDDVVKALRKSKLLEVT----EDGTKVRRTVVVQDK----------------PDVDECTIYVEKLPPEAEHDYIESVF  217 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~----~~~~~v~r~~~~~~~----------------~~~~~~~l~V~nLp~~~t~e~L~~~F  217 (299)
                      .+.++|.+|++.+++..+.    +..+.+.++.+..+.                ....+++|||+|||.++++++|+++|
T Consensus       227 ~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F  306 (562)
T TIGR01628       227 EKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELF  306 (562)
T ss_pred             CCHHHHHHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHH
Confidence            4589999999999999998    777888765443222                13456789999999999999999999


Q ss_pred             hcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeec
Q psy3930         218 SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRL  277 (299)
Q Consensus       218 ~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~  277 (299)
                      ++||.|..|.++.+. +|.++|||||+|.+.++|.+|+.. +||  ..++|++|.|....
T Consensus       307 ~~~G~i~~~~i~~d~-~g~~~g~gfV~f~~~~~A~~A~~~-~~g--~~~~gk~l~V~~a~  362 (562)
T TIGR01628       307 SECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTE-MHG--RMLGGKPLYVALAQ  362 (562)
T ss_pred             HhcCCeEEEEEEECC-CCCcCCeEEEEeCCHHHHHHHHHH-hcC--CeeCCceeEEEecc
Confidence            999999999999984 899999999999999999999999 998  88899999997643

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

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

Probab=99.60  E-value=2.1e-15  Score=144.07  Aligned_cols=115  Identities=23%  Similarity=0.321  Sum_probs=97.4

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccC----------CCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEE
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD----------KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVS  227 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~----------~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~  227 (299)
                      .+.++|.+|| .+++..+.+..+.|........          ...+..++|||+|||..+++++|+++|++||.|..|.
T Consensus       139 ~~~e~A~~Al-~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~  217 (457)
T TIGR01622       139 YDVESVIKAL-ALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQ  217 (457)
T ss_pred             CCHHHHHHHH-HhCCCEECCeeeEEeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEE
Confidence            3479999999 5888888888887765432111          1123358999999999999999999999999999999


Q ss_pred             eeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         228 LPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       228 i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      ++++..+|.++|||||+|.+.++|.+|++. |||  ..+.|+.|.|...
T Consensus       218 ~~~d~~~g~~~g~afV~f~~~e~A~~A~~~-l~g--~~i~g~~i~v~~a  263 (457)
T TIGR01622       218 LHRDPETGRSKGFGFIQFHDAEEAKEALEV-MNG--FELAGRPIKVGYA  263 (457)
T ss_pred             EEEcCCCCccceEEEEEECCHHHHHHHHHh-cCC--cEECCEEEEEEEc
Confidence            999988899999999999999999999999 999  8888999999874

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.

>cd08034 LARP_1_2 La RNA-binding domain proteins similar to La-related proteins 1 and 2

Probab=99.60  E-value=3.2e-16  Score=109.70  Aligned_cols=69  Identities=23%  Similarity=0.454  Sum_probs=65.5

Q ss_pred             HHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCCCCHHHHHHHHHhcCcccccccc
Q psy3930         111 QQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDG  179 (299)
Q Consensus       111 ~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~  179 (299)
                      +.|++|+||||||+||++|.||+..|...||++++++++|++|++++.+.+.+.+|+..+..+++++..
T Consensus         2 ~~i~~QvEfYFSd~NL~~D~fLr~~m~~~G~Vpl~~i~~F~rmk~l~~d~~~i~~Al~~S~~lev~e~k   70 (73)
T cd08034           2 EYIKKQIEYYFSVDNLEKDFFLRRKMDPEGYLPIALIASFHRVQALTTDVNLILEALKDSTVVELVDEK   70 (73)
T ss_pred             hHHHhhHHhhcCHhhhccCHHHHHHcCCCCCEeHHHHhccHHHHHHcCCHHHHHHHHHcCCeEEEecCe
Confidence            568899999999999999999999999999999999999999999999999999999999999999844

This domain is found in proteins similar to vertebrate La-related proteins 1 and 2 (LARP1, LARP2). 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.

>cd07323 LAM LA motif RNA-binding domain

Probab=99.56  E-value=1.1e-15  Score=108.36  Aligned_cols=74  Identities=42%  Similarity=0.706  Sum_probs=69.1

Q ss_pred             HHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeee
Q psy3930         111 QQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       111 ~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      ..|++|+||||||+||++|.||+..|...+|++++++.+|++|++++.+.+.+.+|++.+..+++++.+.+|+|
T Consensus         2 ~~i~~QvEfYFSd~NL~~D~fL~~~~~~~g~Vpl~~i~~F~r~k~l~~~~~~i~~Al~~s~~lel~~~~~~Vrr   75 (75)
T cd07323           2 EKIKKQVEYYFSDENLCKDRFLRSLMDDDGWVPLSLLASFNRVKKLTTDVELILEALRDSSVVEVSEDGTKVRR   75 (75)
T ss_pred             hHHHhhhHhccCHhhhCcCHHHHHhcCCCCCEEHHHHhCchHHHHHcCCHHHHHHHHHhCCeEEEeCCCCccCC
Confidence            46889999999999999999999999888999999999999999999999999999999999999998777764

This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). 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.

>cd08030 LA_like_plant La-motif domain of plant proteins similar to the La autoantigen

Probab=99.56  E-value=1.1e-15  Score=111.05  Aligned_cols=74  Identities=32%  Similarity=0.574  Sum_probs=67.1

Q ss_pred             HHHHHHhhhhcCCCCcchhHHHHHhhh--cCCCeeeeeeecccccccCCC------------CHHHHHHHHHhcCccccc
Q psy3930         111 QQIMNLMEFYLSDSNLRKDRFFSQLLQ--ESPEIEVSVFLKCNKLARLTH------------DPDDVVKALRKSKLLEVT  176 (299)
Q Consensus       111 ~~i~~q~efyfsd~nL~~d~fl~~~~~--~~~~~~l~~f~~F~~i~~~~~------------~~~~a~~Al~~~~~~~~~  176 (299)
                      ++|++|+||||||.||++|.||+.+|.  ..||++++++++|++|++++.            +.+.+.+||+.+..++++
T Consensus         3 ~~i~~QvEfYFSd~NL~~D~fL~~~~~~~~dG~V~i~~i~~F~rmk~l~~~~~~~~~~~~~~~~~~I~~ALk~S~~levs   82 (90)
T cd08030           3 EKVLRQVEFYFSDSNLPRDDFLLEEVEEDPDGMVSLALICSFSRMRSLLGLGGGKPEDVPEDTLKAVAEALRTSTLLKVS   82 (90)
T ss_pred             HHHHHHHHcccchhhcccCHHHHHHhccCCCCCEehHHHhcChHHHHHhhcccccccccchhHHHHHHHHHccCCEEEEc
Confidence            578899999999999999999999995  578999999999999999874            257899999999999999


Q ss_pred             cccceeee
Q psy3930         177 EDGTKVRR  184 (299)
Q Consensus       177 ~~~~~v~r  184 (299)
                      +++.+|+|
T Consensus        83 eD~~~VRR   90 (90)
T cd08030          83 EDGKRVGR   90 (90)
T ss_pred             CCCCccCC
Confidence            99999875

This domain is found in plant 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.

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

Probab=99.56  E-value=4.4e-14  Score=136.69  Aligned_cols=121  Identities=22%  Similarity=0.258  Sum_probs=101.0

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC---------------------------CCCCCCcE
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD---------------------------KPDVDECT  198 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~---------------------------~~~~~~~~  198 (299)
                      .|+.|.+       .++|..|| .++++.+.+..++|.+......                           ......++
T Consensus       226 afVeF~~-------~e~A~~Al-~l~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  297 (509)
T TIGR01642       226 AFLEFRT-------VEEATFAM-ALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDR  297 (509)
T ss_pred             EEEEeCC-------HHHHhhhh-cCCCeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCE
Confidence            3555554       79999999 6999999999988876432110                           00123478


Q ss_pred             EEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeec
Q psy3930         199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRL  277 (299)
Q Consensus       199 l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~  277 (299)
                      |||+|||..+++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|..|++. |||  ..+.|+.|.|....
T Consensus       298 l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~-l~g--~~~~~~~l~v~~a~  373 (509)
T TIGR01642       298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAA-LNG--KDTGDNKLHVQRAC  373 (509)
T ss_pred             EEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHH-cCC--CEECCeEEEEEECc
Confidence            99999999999999999999999999999999988999999999999999999999999 999  78889999887754

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.55  E-value=1.8e-14  Score=101.06  Aligned_cols=70  Identities=39%  Similarity=0.702  Sum_probs=64.9

Q ss_pred             EEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       199 l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      |||+|||+++++++|+++|++||.|..+.+..+ .++..+|+|||+|.+.++|++|++. +||  ..++|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~-l~g--~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEE-LNG--KKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHH-HTT--EEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHH-cCC--CEECccCcC
Confidence            799999999999999999999999999999987 5899999999999999999999999 888  777787764

(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 ....

>COG5193 LHP1 La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]

Probab=99.54  E-value=6.1e-15  Score=131.76  Aligned_cols=169  Identities=22%  Similarity=0.285  Sum_probs=120.9

Q ss_pred             CeeecC-----CCCcCcChHHHHhhcc----CCCEEeeeeecchhhhhccCCHHHHHHHHhcC---cceeeccCcceeec
Q psy3930           1 MEFYLS-----DSNLRKDRFFSQLLQE----SPEIEVSVFLKCNKLARLTHDPDDVVKALRKS---KLLEVTEDGTKVKG   68 (299)
Q Consensus         1 ~e~yfs-----~~nl~~d~~l~~~~~~----~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s---~~~~v~~~~~~vrr   68 (299)
                      +|||||     |.|+++|+||+.+..+    +|||||.++++|+||+..+...+.|..|+++|   ..++++.+|...+|
T Consensus        79 vE~~fS~s~~~d~n~~~dk~~ktta~Kn~~~~kwVpIkt~~tfn~~k~~gs~~~~v~~a~rks~~~rv~e~Sssgsn~~r  158 (438)
T COG5193          79 VEFYFSGSKDTDSNFPKDKFLKTTAPKNKKRDKWVPIKTIATFNRMKNSGSPVSAVSGALRKSLDARVLEVSSSGSNKNR  158 (438)
T ss_pred             eeEEeeccccccccccchhhhccccccccCCCCceeeeeeeeeccccccCCchhhhhhhhhcCcccceeeeccccccccc
Confidence            699999     9999999999977443    69999999999999999999999999999999   79999999999888


Q ss_pred             cccccccccccccccccccc--------------------------cC-------cccc-------c---cccCCCCcCc
Q psy3930          69 NIIRHFLVPISMETEASDNV--------------------------DK-------DLSD-------L---QRKDGGGRHR  105 (299)
Q Consensus        69 ~~~~~~~~p~~~~~~~~~~~--------------------------~~-------~~~~-------~---~~~~~k~r~r  105 (299)
                      .+...-..-.. ..+..+..                          +.       .+..       .   ++....+-.+
T Consensus       159 ~~k~~s~n~~s-~~~~qr~~y~n~fG~e~~~~a~~~e~~~d~~~~~p~h~h~~~~~i~~rrd~~nkn~~gSv~~efk~~~  237 (438)
T COG5193         159 TEKLISNNNKS-TSQMQRDVYQNGFGKEDVNNASRPEQQEDLEIQFPPHYHAPPSQIRNRRDWLNKNFRGSVFVEFKYFR  237 (438)
T ss_pred             cchhhhhhhhh-hhhHhhhHHhhcCCcccccccccchhhhhHHhhCCCcccCChhhccchhhhhhccccCcccccccChH
Confidence            75211000000 00000000                          00       0000       0   0011001011


Q ss_pred             hHHH-----------------------------HHHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccC
Q psy3930         106 KKQL-----------------------------YQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARL  156 (299)
Q Consensus       106 ~~~~-----------------------------~~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~  156 (299)
                      ..+.                             -..+..|+||||+..||..|.|++..+++.|++++++...|-++.++
T Consensus       238 ~~q~~nn~~~r~~~~~~~~~~~~~~~~ep~~lsI~a~k~QiEyYFseenl~~d~~lrkk~~kaGf~plsfi~kf~Rn~Sf  317 (438)
T COG5193         238 EAQRFNNGFYRNKKYPNDPETVYYYSVEPILLSIMAKKEQIEYYFSEENLKSDEFLRKKFKKAGFIPLSFIGKFYRNLSF  317 (438)
T ss_pred             HHHHHhccccCCcCCCcchhhhcccccCceeeehhhHHhhhHhhhhHHhhhhhhHHHhhhhhcccccHhhhhhhhhcccc
Confidence            1111                             13466799999999999999999999999999999999999998888


Q ss_pred             CCCHHHHHHHHHhc
Q psy3930         157 THDPDDVVKALRKS  170 (299)
Q Consensus       157 ~~~~~~a~~Al~~~  170 (299)
                      ..+...+.+|++..
T Consensus       318 ~gd~nLilaa~ke~  331 (438)
T COG5193         318 GGDKNLILAAMKEV  331 (438)
T ss_pred             CCchhhhHHHHHHH
Confidence            88887777777654

>KOG0121|consensus

Probab=99.51  E-value=5.5e-14  Score=106.97  Aligned_cols=81  Identities=22%  Similarity=0.353  Sum_probs=74.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ...+++||||||+..+++|+|-++|+++|+|..|.|-.|+.+-.+.|||||+|.+.++|..|++. +||  ..+..++|.
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alry-isg--trLddr~ir  109 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRY-ISG--TRLDDRPIR  109 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHH-hcc--Cccccccee
Confidence            45579999999999999999999999999999999999988888999999999999999999999 999  777899987


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      +-..
T Consensus       110 ~D~D  113 (153)
T KOG0121|consen  110 IDWD  113 (153)
T ss_pred             eecc
Confidence            7654

>KOG0122|consensus

Probab=99.50  E-value=7.9e-14  Score=117.26  Aligned_cols=79  Identities=38%  Similarity=0.567  Sum_probs=74.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      .+.++|-|.|||.++++++|+++|.+||.|..|.+.+|+.||.++|||||.|.+.++|++||.. |||  +.+.+.+|+|
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~-LnG--~gyd~LILrv  263 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIAD-LNG--YGYDNLILRV  263 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHH-ccC--cccceEEEEE
Confidence            3678899999999999999999999999999999999999999999999999999999999999 999  7888888866


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      +.
T Consensus       264 Ew  265 (270)
T KOG0122|consen  264 EW  265 (270)
T ss_pred             Ee
Confidence            54

>KOG0109|consensus

Probab=99.50  E-value=1.9e-14  Score=123.67  Aligned_cols=138  Identities=22%  Similarity=0.302  Sum_probs=116.9

Q ss_pred             HHHHHhhhcCCCeee-eeeecccccccCC----------CCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcE
Q psy3930         130 RFFSQLLQESPEIEV-SVFLKCNKLARLT----------HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECT  198 (299)
Q Consensus       130 ~fl~~~~~~~~~~~l-~~f~~F~~i~~~~----------~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~  198 (299)
                      .|+.++.++.+.-.| ++|..||++.+|.          ++...+..||.++++..|++..+.|+.+++.    .....+
T Consensus         5 LFIGNLp~~~~~~elr~lFe~ygkVlECDIvKNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK----sk~stk   80 (346)
T KOG0109|consen    5 LFIGNLPREATEQELRSLFEQYGKVLECDIVKNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK----SKASTK   80 (346)
T ss_pred             hhccCCCcccchHHHHHHHHhhCceEeeeeecccceEEeecccccHHHHhhcccceecceEEEEEecccc----CCCccc
Confidence            466666666666666 6677777777766          6677888999999999999999999876644    334678


Q ss_pred             EEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeecc
Q psy3930         199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLS  278 (299)
Q Consensus       199 l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~  278 (299)
                      ++|+|+.+.++.++|++.|.+||+|..|.|+++        |+||+|.-.++|..|+.. |||  ..+.|.++.|++..+
T Consensus        81 l~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~-l~~--~~~~gk~m~vq~sts  149 (346)
T KOG0109|consen   81 LHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRG-LDN--TEFQGKRMHVQLSTS  149 (346)
T ss_pred             cccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhc-ccc--cccccceeeeeeecc
Confidence            999999999999999999999999999999865        899999999999999999 888  999999999999877


Q ss_pred             cCCC
Q psy3930         279 FGIT  282 (299)
Q Consensus       279 ~~~~  282 (299)
                      .-++
T Consensus       150 rlrt  153 (346)
T KOG0109|consen  150 RLRT  153 (346)
T ss_pred             cccc
Confidence            6443

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

Probab=99.48  E-value=9.3e-14  Score=133.37  Aligned_cols=120  Identities=17%  Similarity=0.214  Sum_probs=90.4

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeeccc-----C----------C--------------------CCCCCcEEEEe
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ-----D----------K--------------------PDVDECTIYVE  202 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~-----~----------~--------------------~~~~~~~l~V~  202 (299)
                      .+.++|..|+..+++..+.++.++|..+....     +          .                    ..+...+|||+
T Consensus       321 ~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~  400 (481)
T TIGR01649       321 ADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLS  400 (481)
T ss_pred             CCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEe
Confidence            45899999999999999999999887543210     0          0                    01235689999


Q ss_pred             cCCCCCCHHHHHHHhhcCCc--eEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCce--EEEEeecc
Q psy3930         203 KLPPEAEHDYIESVFSKYGK--VTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSI--LTTTSRLS  278 (299)
Q Consensus       203 nLp~~~t~e~L~~~F~~~G~--i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~--l~v~~k~~  278 (299)
                      |||.++++++|+++|+.||.  +..|++.... ++ .+|+|||+|.+.++|..|+.. +||  ..+.++.  ....+|++
T Consensus       401 NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~-~~-~~~~gfVeF~~~e~A~~Al~~-ln~--~~l~~~~~~~~~~lkv~  475 (481)
T TIGR01649       401 NIPLSVSEEDLKELFAENGVHKVKKFKFFPKD-NE-RSKMGLLEWESVEDAVEALIA-LNH--HQLNEPNGSAPYHLKVS  475 (481)
T ss_pred             cCCCCCCHHHHHHHHHhcCCccceEEEEecCC-CC-cceeEEEEcCCHHHHHHHHHH-hcC--CccCCCCCCccceEEEE
Confidence            99999999999999999997  8888876443 33 578999999999999999999 998  4454443  22334455


Q ss_pred             cCCC
Q psy3930         279 FGIT  282 (299)
Q Consensus       279 ~~~~  282 (299)
                      ++++
T Consensus       476 fs~~  479 (481)
T TIGR01649       476 FSTS  479 (481)
T ss_pred             eccC
Confidence            5443

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).

>KOG0144|consensus

Probab=99.48  E-value=2.1e-14  Score=129.25  Aligned_cols=122  Identities=22%  Similarity=0.294  Sum_probs=91.7

Q ss_pred             eeecccccccCCCCHHHHHHHHHhc-Ccccccc--ccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCc
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKS-KLLEVTE--DGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGK  222 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~-~~~~~~~--~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~  222 (299)
                      -|++|.+       .++|.+|+..+ |...+.|  ..+.|+.++...++ ....++||||-|+..++|.+++++|++||.
T Consensus        79 CFv~~~t-------rk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er-~~~e~KLFvg~lsK~~te~evr~iFs~fG~  150 (510)
T KOG0144|consen   79 CFVKYYT-------RKEADEAINALHNQKTLPGMHHPVQVKYADGERER-IVEERKLFVGMLSKQCTENEVREIFSRFGH  150 (510)
T ss_pred             EEEEecc-------HHHHHHHHHHhhcccccCCCCcceeecccchhhhc-cccchhhhhhhccccccHHHHHHHHHhhCc
Confidence            3666665       45555555544 3333444  34566655544333 255689999999999999999999999999


Q ss_pred             eEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCC-CCCCCCceEEEEeec
Q psy3930         223 VTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPC-PPDYQSSILTTTSRL  277 (299)
Q Consensus       223 i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~-~~~~~g~~l~v~~k~  277 (299)
                      |+.|+|.+|. .|.+||||||.|.+.+-|..|+++ +||. .......+|.|+...
T Consensus       151 Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika-~ng~~tmeGcs~PLVVkFAD  204 (510)
T KOG0144|consen  151 IEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKA-LNGTQTMEGCSQPLVVKFAD  204 (510)
T ss_pred             cchhhheecc-cccccceeEEEEehHHHHHHHHHh-hccceeeccCCCceEEEecc
Confidence            9999999997 899999999999999999999999 7763 355566777776643

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.47  E-value=2.6e-13  Score=124.28  Aligned_cols=80  Identities=20%  Similarity=0.347  Sum_probs=74.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|+.||+|..|+|+++..+|+++|||||+|.++++|++|++. |||  ..+.+++|.
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~-LnG--~~l~gr~i~  180 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKN-LNG--ITVRNKRLK  180 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHH-cCC--CccCCceee
Confidence            45678999999999999999999999999999999999988999999999999999999999999 898  778899887


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |..
T Consensus       181 V~~  183 (346)
T TIGR01659       181 VSY  183 (346)
T ss_pred             eec
Confidence            764

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).

>KOG0124|consensus

Probab=99.45  E-value=2.4e-13  Score=120.14  Aligned_cols=129  Identities=19%  Similarity=0.290  Sum_probs=112.3

Q ss_pred             eeeecccccccCC------------------CCHHHHHHHHHhcCccccccccceeeeeecccCCC---------CCCCc
Q psy3930         145 SVFLKCNKLARLT------------------HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP---------DVDEC  197 (299)
Q Consensus       145 ~~f~~F~~i~~~~------------------~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~---------~~~~~  197 (299)
                      ..|..||.|+++.                  +-++.|+-|++.+|+..++|+.++|.|....+...         ...-.
T Consensus       132 ~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNmpQAQpiID~vqeeAk~fn  211 (544)
T KOG0124|consen  132 RAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFN  211 (544)
T ss_pred             hhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCCcccchHHHHHHHHHHhhh
Confidence            4599999999987                  45788999999999999999999999876443321         23456


Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      .|||..++++.+++||+..|+.||+|.+|.+.++...+.++||||++|.+..+...|+.. +|-  ++++|.-|+|-..
T Consensus       212 RiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAias-MNl--FDLGGQyLRVGk~  287 (544)
T KOG0124|consen  212 RIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS-MNL--FDLGGQYLRVGKC  287 (544)
T ss_pred             eEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhh-cch--hhcccceEecccc
Confidence            899999999999999999999999999999999987788999999999999999999999 886  8889999988443

>KOG0127|consensus

Probab=99.45  E-value=2.6e-13  Score=125.48  Aligned_cols=84  Identities=30%  Similarity=0.425  Sum_probs=74.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhc--CCCCC-CCCCCceEE
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG--LNPCP-PDYQSSILT  272 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~--lng~~-~~~~g~~l~  272 (299)
                      +.+|||.|||+++|+++|.+.|++||+|.++.++.++.||.++|+|||.|.++.+|+.||.+.  -+|.. +.+.|+.|.
T Consensus       292 ~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lk  371 (678)
T KOG0127|consen  292 GKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLK  371 (678)
T ss_pred             cceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEe
Confidence            379999999999999999999999999999999999999999999999999999999999972  22323 667899999


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |.+.+..
T Consensus       372 v~~Av~R  378 (678)
T KOG0127|consen  372 VTLAVTR  378 (678)
T ss_pred             eeeccch
Confidence            9876543

>KOG0113|consensus

Probab=99.45  E-value=3.2e-13  Score=116.54  Aligned_cols=95  Identities=23%  Similarity=0.342  Sum_probs=84.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ...-+||||+-|+.++++..|+..|+.||+|..|+|++++.||+++|||||+|+++-+...|.+. -.|  +.++|+.|-
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~-adG--~~Idgrri~  174 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKD-ADG--IKIDGRRIL  174 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHh-ccC--ceecCcEEE
Confidence            34568999999999999999999999999999999999999999999999999999999999999 788  889999998


Q ss_pred             EEe---ecccCCCCCCCCCCC
Q psy3930         273 TTS---RLSFGITPLGFESGG  290 (299)
Q Consensus       273 v~~---k~~~~~~~r~~~~g~  290 (299)
                      |-+   +..++.-||+.|+|-
T Consensus       175 VDvERgRTvkgW~PRRLGGGL  195 (335)
T KOG0113|consen  175 VDVERGRTVKGWLPRRLGGGL  195 (335)
T ss_pred             EEecccccccccccccccCCc
Confidence            854   456677777766543

>KOG0149|consensus

Probab=99.45  E-value=2e-13  Score=114.39  Aligned_cols=78  Identities=24%  Similarity=0.356  Sum_probs=70.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      .-.+||||||++.+..+.|+.+|++||+|....++.|+.+|+++|||||+|.+.++|.+|++. -|   ..++||+-.+.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~---piIdGR~aNcn   86 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PN---PIIDGRKANCN   86 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CC---Ccccccccccc
Confidence            346799999999999999999999999999999999999999999999999999999999987 55   67778877665


Q ss_pred             ee
Q psy3930         275 SR  276 (299)
Q Consensus       275 ~k  276 (299)
                      +.
T Consensus        87 lA   88 (247)
T KOG0149|consen   87 LA   88 (247)
T ss_pred             hh
Confidence            53

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

Probab=99.45  E-value=2.8e-13  Score=130.08  Aligned_cols=113  Identities=17%  Similarity=0.108  Sum_probs=86.8

Q ss_pred             CCHHHHHHHHHh--cCccccccccceeeeeeccc-CCC---------CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEE
Q psy3930         158 HDPDDVVKALRK--SKLLEVTEDGTKVRRTVVVQ-DKP---------DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY  225 (299)
Q Consensus       158 ~~~~~a~~Al~~--~~~~~~~~~~~~v~r~~~~~-~~~---------~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~  225 (299)
                      .+.++|.+|+..  .++..+.++.++|..+.... ...         .....+|||+||+..+++++|+++|+.||.|..
T Consensus        46 ~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~  125 (481)
T TIGR01649        46 EDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLR  125 (481)
T ss_pred             CchHHHHHHHHHhhcCCceEcCeEEEEEecCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEE
Confidence            458999999986  47788999999998764321 000         111237899999999999999999999999999


Q ss_pred             EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         226 VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       226 v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      |.+.++..    .|+|||+|.+.++|.+|++. |||..+.-++..|+|..
T Consensus       126 v~i~~~~~----~~~afVef~~~~~A~~A~~~-Lng~~i~~~~~~l~v~~  170 (481)
T TIGR01649       126 IVTFTKNN----VFQALVEFESVNSAQHAKAA-LNGADIYNGCCTLKIEY  170 (481)
T ss_pred             EEEEecCC----ceEEEEEECCHHHHHHHHHH-hcCCcccCCceEEEEEE
Confidence            99877542    36899999999999999999 99944433445666543

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).

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.45  E-value=6.5e-13  Score=114.77  Aligned_cols=82  Identities=23%  Similarity=0.299  Sum_probs=73.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .++|||+|||+.+++++|+++|+.||+|..|+|+++..   .+|||||+|.++++|+.|+.  +||  ..+.|+.|.|..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All--LnG--~~l~gr~V~Vt~   76 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL--LSG--ATIVDQSVTITP   76 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH--hcC--CeeCCceEEEEe
Confidence            57999999999999999999999999999999998753   46899999999999999994  788  788999999999


Q ss_pred             ecccCCCCC
Q psy3930         276 RLSFGITPL  284 (299)
Q Consensus       276 k~~~~~~~r  284 (299)
                      ...+..++.
T Consensus        77 a~~~~~p~~   85 (260)
T PLN03120         77 AEDYQLPPE   85 (260)
T ss_pred             ccCCCCCcc
Confidence            887755544

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.44  E-value=4e-13  Score=94.50  Aligned_cols=70  Identities=43%  Similarity=0.752  Sum_probs=62.4

Q ss_pred             EEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       199 l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      |||+|||+++++++|.++|+.||.|..+.+..++. |..+|+|||+|.+.++|.+|++. ++|  ..++|+.|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~-~~~--~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALEL-LNG--KEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHH-HTT--EEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHH-CCC--cEECCEEcC
Confidence            79999999999999999999999999999999875 89999999999999999999999 776  777787763

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 ....

>KOG0126|consensus

Probab=99.42  E-value=3.3e-14  Score=114.52  Aligned_cols=86  Identities=29%  Similarity=0.410  Sum_probs=79.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..++.-|||||||.+.|+.+|-.+|++||+|+.|.++||+.||+++||||..|++..+..-|+.. +||  ..+.|+.|+
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN-~NG--iki~gRtir  108 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDN-LNG--IKILGRTIR  108 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEec-cCC--ceecceeEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999 999  889999999


Q ss_pred             EEeecccCC
Q psy3930         273 TTSRLSFGI  281 (299)
Q Consensus       273 v~~k~~~~~  281 (299)
                      |-.-..|..
T Consensus       109 VDHv~~Yk~  117 (219)
T KOG0126|consen  109 VDHVSNYKK  117 (219)
T ss_pred             eeecccccC
Confidence            977655533

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

Probab=99.40  E-value=1.5e-12  Score=125.62  Aligned_cols=111  Identities=24%  Similarity=0.357  Sum_probs=84.6

Q ss_pred             HHHHHHHHHhcCccccccccceeeeeecccC---CCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCC
Q psy3930         160 PDDVVKALRKSKLLEVTEDGTKVRRTVVVQD---KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGK  236 (299)
Q Consensus       160 ~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~---~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~  236 (299)
                      .++|.+||...++..+...........|.+.   .....+++|||+|||.++++++|+++|++||.|..|+|++| .+|.
T Consensus        19 ~~~a~~a~~~~~gy~~~~~~g~r~~g~Pp~~~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~   97 (578)
T TIGR01648        19 DEAALKALLERTGYTLVQENGQRKYGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQ   97 (578)
T ss_pred             cHHHHHHHHHhhCccccccCCcccCCCCCCcccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCC
Confidence            4677888887777665443322222222211   12345689999999999999999999999999999999999 5999


Q ss_pred             cceEEEEEecCHHHHHHHHHhcCCCCCCCC-CCceEEEE
Q psy3930         237 LKGFAFVEFSTKEEAAKALELGLNPCPPDY-QSSILTTT  274 (299)
Q Consensus       237 ~kg~~fV~F~~~~~A~~Al~~~lng~~~~~-~g~~l~v~  274 (299)
                      ++|||||+|.+.++|++||+. +||  ..+ .++.+.+.
T Consensus        98 sRGfaFV~F~~~e~A~~Ai~~-lng--~~i~~Gr~l~V~  133 (578)
T TIGR01648        98 NRGYAFVTFCGKEEAKEAVKL-LNN--YEIRPGRLLGVC  133 (578)
T ss_pred             ccceEEEEeCCHHHHHHHHHH-cCC--CeecCCcccccc
Confidence            999999999999999999999 887  444 35555443

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0148|consensus

Probab=99.40  E-value=2.4e-13  Score=115.85  Aligned_cols=75  Identities=28%  Similarity=0.551  Sum_probs=70.5

Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeec
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRL  277 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~  277 (299)
                      -+||+.|.+.++-+.|++.|.+||+|..+++++|..|++++|||||.|-..++|+.||.. |||  ..+++|.|    |.
T Consensus        64 hvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~-MnG--qWlG~R~I----RT  136 (321)
T KOG0148|consen   64 HVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQ-MNG--QWLGRRTI----RT  136 (321)
T ss_pred             eEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHH-hCC--eeecccee----ec
Confidence            589999999999999999999999999999999999999999999999999999999999 999  88888877    55


Q ss_pred             cc
Q psy3930         278 SF  279 (299)
Q Consensus       278 ~~  279 (299)
                      .|
T Consensus       137 NW  138 (321)
T KOG0148|consen  137 NW  138 (321)
T ss_pred             cc
Confidence            55

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

Probab=99.39  E-value=4.4e-12  Score=122.39  Aligned_cols=115  Identities=24%  Similarity=0.320  Sum_probs=93.8

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcC--ccccccccceeeeeecccCCC---CCCCcEEEEecCCCCCCHHHHHHHhhcC
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSK--LLEVTEDGTKVRRTVVVQDKP---DVDECTIYVEKLPPEAEHDYIESVFSKY  220 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~--~~~~~~~~~~v~r~~~~~~~~---~~~~~~l~V~nLp~~~t~e~L~~~F~~~  220 (299)
                      .|+.|.+       +++|..|++.+.  .+.+.++.+.|.++.+.....   ....++|||+|||.++++++|+++|++|
T Consensus       185 AFVeF~s-------~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f  257 (578)
T TIGR01648       185 AFVEYES-------HRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEF  257 (578)
T ss_pred             EEEEcCC-------HHHHHHHHHHhhccceEecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhc
Confidence            4667755       788999988764  356788888888876543321   2345789999999999999999999999


Q ss_pred             --CceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeecc
Q psy3930         221 --GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLS  278 (299)
Q Consensus       221 --G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~  278 (299)
                        |.|..|.+++        +||||+|.+.++|++|++. +||  ..+.|+.|.|.....
T Consensus       258 ~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~-lnG--~~i~Gr~I~V~~Akp  306 (578)
T TIGR01648       258 KPGKVERVKKIR--------DYAFVHFEDREDAVKAMDE-LNG--KELEGSEIEVTLAKP  306 (578)
T ss_pred             CCCceEEEEeec--------CeEEEEeCCHHHHHHHHHH-hCC--CEECCEEEEEEEccC
Confidence              9999998753        4999999999999999999 998  788999998876543

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.

>KOG0107|consensus

Probab=99.39  E-value=1.7e-12  Score=104.21  Aligned_cols=75  Identities=31%  Similarity=0.459  Sum_probs=68.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .+.||||||+..+++.+|+..|..||++..|.|.+.+     .|||||+|+++-+|+.|+.. |+|  ..+.|..+.|++
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~-LDG--~~~cG~r~rVE~   81 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRY-LDG--KDICGSRIRVEL   81 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhh-cCC--ccccCceEEEEe
Confidence            6899999999999999999999999999999987754     68999999999999999999 999  888999999988


Q ss_pred             ecc
Q psy3930         276 RLS  278 (299)
Q Consensus       276 k~~  278 (299)
                      ..-
T Consensus        82 S~G   84 (195)
T KOG0107|consen   82 STG   84 (195)
T ss_pred             ecC
Confidence            543

>PF05383 La: La domain; InterPro: IPR006630 Human Ro ribonucleoproteins (RNPs) are composed of one of the four small Y RNAs and at least two proteins, Ro60 and La

Probab=99.38  E-value=4.2e-14  Score=96.11  Aligned_cols=58  Identities=36%  Similarity=0.587  Sum_probs=51.4

Q ss_pred             HHHHhhhhcCCCCcchhHHHHHhhhc--CCCeeeeeeecccccccCC-CCHHHHHHHHHhc
Q psy3930         113 IMNLMEFYLSDSNLRKDRFFSQLLQE--SPEIEVSVFLKCNKLARLT-HDPDDVVKALRKS  170 (299)
Q Consensus       113 i~~q~efyfsd~nL~~d~fl~~~~~~--~~~~~l~~f~~F~~i~~~~-~~~~~a~~Al~~~  170 (299)
                      |++|+||||||+||++|.||+.+|..  .||++++++.+|++|+.++ .+.+.+.+|++.+
T Consensus         1 I~~QvEfYFSd~NL~~D~fL~~~~~~~~~g~Vpi~~i~~F~r~k~l~~~~~~~I~~al~~S   61 (61)
T PF05383_consen    1 IKKQVEFYFSDENLPRDKFLRSQMDSNPDGWVPISTILSFNRMKALTNTDIELIVDALRDS   61 (61)
T ss_dssp             HHHHHHHHTSHHHHCC-HHHHHHHCTTTTTBEEHHHHTTSHHHHHH--S-HHHHHHHHHTS
T ss_pred             ChhHHHHhcCHHHhCcCHHHHHHHHhcCCCcEeHHHHHchHHHHHHhcCCHHHHHHHHHcC
Confidence            57899999999999999999999998  6899999999999999999 8999999999764

The La protein is a 47 kDa polypeptide that frequently acts as an autoantigen in systemic lupus erythematosus and Sjogren's syndrome []. In the nucleus, La acts as a RNA polymerase III (RNAP III) transcription factor, while in the cytoplasm, La acts as a translation factor []. In the nucleus, La binds to the 3'UTR of nascent RNAP III transcripts to assist in folding and maturation []. In the cytoplasm, La recognises specific classes of mRNAs that contain a 5'-terminal oligopyrimidine (5'TOP) motif known to control protein synthesis []. The specific recognition is mediated by the N-terminal domain of La, which comprises a La motif and a RNA recognition motif (RRM). The La motif adopts an alpha/beta fold that comprises a winged-helix motif []. Homologous La domain-containing proteins have been identified in a wide range of organisms except Archaea, bacteria and viruses [].; PDB: 1S29_A 1YTY_B 2VOO_B 1S7A_A 2VOP_A 2VON_B 1ZH5_B 2VOD_A 2CQK_A.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.37  E-value=4e-12  Score=108.25  Aligned_cols=81  Identities=19%  Similarity=0.178  Sum_probs=71.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ..+.+|||+||++.+|+++|+++|+.||+|..|+|+++.   ...|||||+|.++++|+.|+.  |||  ..+.+++|.|
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll--LnG--a~l~d~~I~I   75 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL--LSG--ATIVDQRVCI   75 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh--cCC--CeeCCceEEE
Confidence            456899999999999999999999999999999999874   445799999999999999995  899  7788999999


Q ss_pred             EeecccCC
Q psy3930         274 TSRLSFGI  281 (299)
Q Consensus       274 ~~k~~~~~  281 (299)
                      ..-..+..
T Consensus        76 t~~~~y~~   83 (243)
T PLN03121         76 TRWGQYED   83 (243)
T ss_pred             EeCccccc
Confidence            88666544

>KOG0131|consensus

Probab=99.37  E-value=2.3e-12  Score=104.02  Aligned_cols=120  Identities=18%  Similarity=0.296  Sum_probs=103.6

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEE
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY  225 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~  225 (299)
                      -|+.|-+       .++|.-|++-+|++.+.++.+++.++... ......+..+||+||.+.+++..|...|+.||.+..
T Consensus        54 gF~Ef~~-------eedadYAikiln~VkLYgrpIrv~kas~~-~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~  125 (203)
T KOG0131|consen   54 GFAEFRT-------EEDADYAIKILNMVKLYGRPIRVNKASAH-QKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLIS  125 (203)
T ss_pred             eEEEEec-------hhhhHHHHHHHHHHHhcCceeEEEecccc-cccccccccccccccCcchhHHHHHHHHHhcccccc
Confidence            4677755       79999999999999999999999988733 334555689999999999999999999999998765


Q ss_pred             -EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         226 -VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       226 -v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                       -.+.++..||.++|||||-|.+.+.+.+|+.. +||  .-+..+++.|...
T Consensus       126 ~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s-~ng--q~l~nr~itv~ya  174 (203)
T KOG0131|consen  126 PPKIMRDPDTGNPKGFGFINYASFEASDAAIGS-MNG--QYLCNRPITVSYA  174 (203)
T ss_pred             CCcccccccCCCCCCCeEEechhHHHHHHHHHH-hcc--chhcCCceEEEEE
Confidence             47788888999999999999999999999999 898  7778888888653

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

Probab=99.37  E-value=1.5e-12  Score=125.91  Aligned_cols=79  Identities=30%  Similarity=0.457  Sum_probs=74.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||+++++++|+++|++||+|..|++++++.+|+++|||||+|.+.++|+.|++. +||  ..+.|+.|.|
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~-lnG--~~i~GR~IkV  181 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ-MNG--QMLGGRNIKV  181 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHh-cCC--eEEecceeee
Confidence            4468999999999999999999999999999999999988999999999999999999999999 899  7888999988


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      ..
T Consensus       182 ~r  183 (612)
T TIGR01645       182 GR  183 (612)
T ss_pred             cc
Confidence            64

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.

>KOG4213|consensus

Probab=99.36  E-value=1.4e-12  Score=104.67  Aligned_cols=146  Identities=31%  Similarity=0.477  Sum_probs=115.1

Q ss_pred             HHHHHHHHHHhhhhcCCCCcchhHHHHHhhh--cCCCeeeeeeecccccccCCCCHHHHHHHHHhc--Ccccccccccee
Q psy3930         107 KQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQ--ESPEIEVSVFLKCNKLARLTHDPDDVVKALRKS--KLLEVTEDGTKV  182 (299)
Q Consensus       107 ~~~~~~i~~q~efyfsd~nL~~d~fl~~~~~--~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~--~~~~~~~~~~~v  182 (299)
                      ..+.+.|..|++|||+|.||++|+|+++.+.  ..+|+++.++..|++.-++++|...+..|+..+  ..++++++..++
T Consensus        11 a~lE~kii~qleyy~Gd~nl~rdkfl~eqi~k~~~gwvpi~i~i~FnRla~lttD~~~Iv~al~ksk~~l~eisedk~k~   90 (205)
T KOG4213|consen   11 AALEAKIIHQLEYYFGDLNLPRDKFLREQIHKLDDGWVPIEIMIKFNRLASLTTDFNVIVEALSKSKAELMEISEDKTKI   90 (205)
T ss_pred             hHHHHhhhhhhhhhhcccCchHHHHHHHHhhhhccCCccchhhhhhhhhhhccccHHHHHHHHhhCHHhhhhhhhchhhh
Confidence            6777888999999999999999999999993  457999999999999999999999999999876  457899999888


Q ss_pred             eeeecc--cCCC-----CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCC--CcceEEEEEecCHHHHHH
Q psy3930         183 RRTVVV--QDKP-----DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG--KLKGFAFVEFSTKEEAAK  253 (299)
Q Consensus       183 ~r~~~~--~~~~-----~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g--~~kg~~fV~F~~~~~A~~  253 (299)
                      +|..+.  ++..     ....+++|..  |.+...++|..+-+  |.+..|.+-+.. .+  ..+|--||.|.+.+.|.+
T Consensus        91 rr~~skplpEvt~e~~~~~~~r~v~~K--~td~ql~~l~qw~~--~k~~nv~mr~~~-~k~~~fkGsvkv~f~tk~qa~a  165 (205)
T KOG4213|consen   91 RRSPSKPLPEVTDEYKEGIKERTVYKK--ITDDQLDDLNQWAS--GKGHNVKMRRHG-NKAHPFKGSVKVTFQTKEQAFA  165 (205)
T ss_pred             hcCcCCCCccccHHHHHHHHHhhhhcc--CCHHHHHHHHHHhc--ccceEeeccccC-CCCCCCCCceEEEeecHHHHHh
Confidence            886543  3221     3445677776  44445555555555  788888876543 33  457788999999999999


Q ss_pred             HHHh
Q psy3930         254 ALEL  257 (299)
Q Consensus       254 Al~~  257 (299)
                      +++.
T Consensus       166 ~~~~  169 (205)
T KOG4213|consen  166 NDDT  169 (205)
T ss_pred             hhhh
Confidence            8876

>KOG4207|consensus

Probab=99.36  E-value=1.8e-12  Score=106.59  Aligned_cols=78  Identities=29%  Similarity=0.468  Sum_probs=74.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      ..+|-|.||...++.++|..+|++||.|..|.|++|..|++++|||||.|.+..+|+.|+++ |+|  ..++|+.|.|++
T Consensus        13 m~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~da-mDG--~~ldgRelrVq~   89 (256)
T KOG4207|consen   13 MTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDA-MDG--AVLDGRELRVQM   89 (256)
T ss_pred             ceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHh-hcc--eeeccceeeehh
Confidence            46799999999999999999999999999999999999999999999999999999999999 999  888999999987


Q ss_pred             e
Q psy3930         276 R  276 (299)
Q Consensus       276 k  276 (299)
                      .
T Consensus        90 a   90 (256)
T KOG4207|consen   90 A   90 (256)
T ss_pred             h
Confidence            3

>KOG0117|consensus

Probab=99.35  E-value=7.4e-12  Score=113.48  Aligned_cols=117  Identities=27%  Similarity=0.374  Sum_probs=87.9

Q ss_pred             HHHHHHHHHhcCc--cccccccceeeeeecccC-CCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCC
Q psy3930         160 PDDVVKALRKSKL--LEVTEDGTKVRRTVVVQD-KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGK  236 (299)
Q Consensus       160 ~~~a~~Al~~~~~--~~~~~~~~~v~r~~~~~~-~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~  236 (299)
                      .+++.+||..-.+  +++...+.+-.-..|--+ ...+.+|.||||.||.++.+++|..+|++.|+|-.+|+++|+.+|.
T Consensus        44 ~eaal~al~E~tgy~l~ve~gqrk~ggPpP~weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~  123 (506)
T KOG0117|consen   44 EEAALKALLERTGYTLVVENGQRKYGGPPPGWEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGD  123 (506)
T ss_pred             HHHHHHHHHHhcCceEEEeccccccCCCCCcccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCC
Confidence            4666677655443  333322222221111111 1246789999999999999999999999999999999999988999


Q ss_pred             cceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeecc
Q psy3930         237 LKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLS  278 (299)
Q Consensus       237 ~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~  278 (299)
                      ++|||||.|.+.++|++|++. +|++.+. .|+.|+|.+..+
T Consensus       124 nRGYAFVtf~~Ke~Aq~Aik~-lnn~Eir-~GK~igvc~Sva  163 (506)
T KOG0117|consen  124 NRGYAFVTFCTKEEAQEAIKE-LNNYEIR-PGKLLGVCVSVA  163 (506)
T ss_pred             CcceEEEEeecHHHHHHHHHH-hhCcccc-CCCEeEEEEeee
Confidence            999999999999999999999 7873322 788888877554

>KOG0117|consensus

Probab=99.35  E-value=1e-11  Score=112.53  Aligned_cols=108  Identities=22%  Similarity=0.322  Sum_probs=92.1

Q ss_pred             CCHHHHHHHHHhc--CccccccccceeeeeecccCCC---CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccC
Q psy3930         158 HDPDDVVKALRKS--KLLEVTEDGTKVRRTVVVQDKP---DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFK  232 (299)
Q Consensus       158 ~~~~~a~~Al~~~--~~~~~~~~~~~v~r~~~~~~~~---~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~  232 (299)
                      .++.+|+.|-+.+  ..+.+.++.+.|.|+.|..+..   -..-..|||.||+.++|+|.|+++|++||.|..|..++| 
T Consensus       216 e~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-  294 (506)
T KOG0117|consen  216 ESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-  294 (506)
T ss_pred             ecchhHHHHHhhccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-
Confidence            5677777776665  4478899999999998765543   233457999999999999999999999999999998866 


Q ss_pred             CCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         233 STGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       233 ~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                             ||||+|.+.++|-+|++. +||  ..+.|..|.|.+.
T Consensus       295 -------YaFVHf~eR~davkAm~~-~ng--keldG~~iEvtLA  328 (506)
T KOG0117|consen  295 -------YAFVHFAEREDAVKAMKE-TNG--KELDGSPIEVTLA  328 (506)
T ss_pred             -------eeEEeecchHHHHHHHHH-hcC--ceecCceEEEEec
Confidence                   899999999999999999 999  8999999999764

>KOG0123|consensus

Probab=99.34  E-value=1.8e-11  Score=112.89  Aligned_cols=129  Identities=18%  Similarity=0.305  Sum_probs=104.1

Q ss_pred             HHHHhhhcCCC-eeeeeeecccccccCC------CCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEec
Q psy3930         131 FFSQLLQESPE-IEVSVFLKCNKLARLT------HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEK  203 (299)
Q Consensus       131 fl~~~~~~~~~-~~l~~f~~F~~i~~~~------~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~n  203 (299)
                      -|...+...+. +.+.+-... +  ++.      .++++|.+||..+|...+.++.+++-+....+       ..+||.|
T Consensus        14 ~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~-------~~~~i~n   83 (369)
T KOG0123|consen   14 MLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP-------SLVFIKN   83 (369)
T ss_pred             HHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC-------ceeeecC
Confidence            34445555554 444444444 3  444      67999999999999999999999987654322       2399999


Q ss_pred             CCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         204 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       204 Lp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      |+++++..+|.++|+.||+|.+|.+.++. .| ++|| ||+|+++++|.+|++. +||  ..+.+..+.+-.
T Consensus        84 l~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~-~ng--~ll~~kki~vg~  149 (369)
T KOG0123|consen   84 LDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEK-LNG--MLLNGKKIYVGL  149 (369)
T ss_pred             CCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHH-hcC--cccCCCeeEEee
Confidence            99999999999999999999999999986 66 8999 9999999999999999 998  677777777744

>KOG0130|consensus

Probab=99.33  E-value=4.8e-12  Score=97.30  Aligned_cols=84  Identities=27%  Similarity=0.430  Sum_probs=77.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ...+..|||.|+++.+++++|...|..||+|..+.+..|+-||..+||+.|+|++.+.|++|+.+ +||  ..+.|..+.
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~-~Ng--~~ll~q~v~  145 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDA-LNG--AELLGQNVS  145 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHh-ccc--hhhhCCcee
Confidence            56689999999999999999999999999999999999988999999999999999999999999 999  888899888


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |-.....
T Consensus       146 VDw~Fv~  152 (170)
T KOG0130|consen  146 VDWCFVK  152 (170)
T ss_pred             EEEEEec
Confidence            8765544

>KOG0127|consensus

Probab=99.33  E-value=4.2e-12  Score=117.56  Aligned_cols=116  Identities=28%  Similarity=0.441  Sum_probs=95.3

Q ss_pred             HHHHHHHHHhcCccccccccceeeeeeccc-----------------CC-----C--CCCCcEEEEecCCCCCCHHHHHH
Q psy3930         160 PDDVVKALRKSKLLEVTEDGTKVRRTVVVQ-----------------DK-----P--DVDECTIYVEKLPPEAEHDYIES  215 (299)
Q Consensus       160 ~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~-----------------~~-----~--~~~~~~l~V~nLp~~~t~e~L~~  215 (299)
                      .+++++|+...+...+.++.+.+..+.+..                 ++     .  ......|.|.|||+.+...+|+.
T Consensus        57 ~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~  136 (678)
T KOG0127|consen   57 EEDVQRALAETEQSKFEGRILNVDPAKKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKN  136 (678)
T ss_pred             HhHHHHHHHHhhcCcccceecccccccccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHH
Confidence            688999999888888888877665433211                 00     1  22367899999999999999999


Q ss_pred             HhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeeccc
Q psy3930         216 VFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSF  279 (299)
Q Consensus       216 ~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~~  279 (299)
                      +|+.||.|..|.||+.. .|...|||||.|....+|..|++. +||  ..+.|+++.|-..++.
T Consensus       137 vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~-~N~--~~i~gR~VAVDWAV~K  196 (678)
T KOG0127|consen  137 VFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEF-FNG--NKIDGRPVAVDWAVDK  196 (678)
T ss_pred             HHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHh-ccC--ceecCceeEEeeeccc
Confidence            99999999999999765 677779999999999999999999 999  8899999988665543

>smart00362 RRM_2 RNA recognition motif

Probab=99.32  E-value=9.7e-12  Score=86.50  Aligned_cols=71  Identities=42%  Similarity=0.736  Sum_probs=64.0

Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      +|||+|||..++.++|+++|.+||++..+.+..+.  +.++|+|||+|.+.++|++|++. ++|  ..+.|+.+.+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~-~~~--~~~~~~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEA-LNG--TKLGGRPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHH-hCC--cEECCEEEee
Confidence            58999999999999999999999999999998765  77889999999999999999998 887  6667877765

>KOG0147|consensus

Probab=99.32  E-value=1.6e-12  Score=120.57  Aligned_cols=118  Identities=26%  Similarity=0.319  Sum_probs=92.6

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeeccc-------C----C-CCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEE
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ-------D----K-PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY  225 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~-------~----~-~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~  225 (299)
                      .|.+.+..|| .+.|-.+-+-.+.|.......       .    . ...+...+|||||++++++++|+.+|+.||.|..
T Consensus       229 ~D~~sVp~ai-aLsGqrllg~pv~vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~  307 (549)
T KOG0147|consen  229 CDEQSVPLAI-ALSGQRLLGVPVIVQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIEN  307 (549)
T ss_pred             ecccchhhHh-hhcCCcccCceeEecccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCccccee
Confidence            4567777777 555555555565554322110       0    0 0122334999999999999999999999999999


Q ss_pred             EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeeccc
Q psy3930         226 VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSF  279 (299)
Q Consensus       226 v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~~  279 (299)
                      |.+++|..+|.++|||||+|...++|.+|+.+ +||  +.+.|+.|+|-.....
T Consensus       308 v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~-lng--felAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  308 VQLTKDSETGRSKGFGFITFVNKEDARKALEQ-LNG--FELAGRLIKVSVVTER  358 (549)
T ss_pred             eeeccccccccccCcceEEEecHHHHHHHHHH-hcc--ceecCceEEEEEeeee
Confidence            99999988999999999999999999999999 999  9999999998765443

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

Probab=99.30  E-value=4.2e-12  Score=122.87  Aligned_cols=115  Identities=18%  Similarity=0.279  Sum_probs=90.6

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccCC--------------------------CCCCCcEEEEecCCCCC---
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDK--------------------------PDVDECTIYVEKLPPEA---  208 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~--------------------------~~~~~~~l~V~nLp~~~---  208 (299)
                      .+.++|..|+..+++..+.+..+.|.++......                          ......+|++.|+...-   
T Consensus       345 ~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~  424 (509)
T TIGR01642       345 KDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLM  424 (509)
T ss_pred             CCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhc
Confidence            3489999999999999999999888775321100                          01235678999986421   


Q ss_pred             -------CHHHHHHHhhcCCceEEEEeeccC---CCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         209 -------EHDYIESVFSKYGKVTYVSLPKFK---STGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       209 -------t~e~L~~~F~~~G~i~~v~i~~~~---~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                             ..++|++.|++||.|..|.|+++.   .++...|++||+|.+.++|++|+.. |||  ..++|+.|.+..
T Consensus       425 ~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~-lnG--r~~~gr~v~~~~  498 (509)
T TIGR01642       425 DDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEG-MNG--RKFNDRVVVAAF  498 (509)
T ss_pred             CcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHH-cCC--CEECCeEEEEEE
Confidence                   236899999999999999998753   3456789999999999999999999 999  888999998765

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

>KOG0144|consensus

Probab=99.28  E-value=7.2e-12  Score=113.09  Aligned_cols=88  Identities=30%  Similarity=0.414  Sum_probs=74.1

Q ss_pred             ccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCC
Q psy3930         188 VQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQ  267 (299)
Q Consensus       188 ~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~  267 (299)
                      ..+..+.+.-++|||.+|..++|.+|+++|++||.|..|.+++|+.+|.++|||||.|.+.++|.+|+.++.|-..+...
T Consensus        26 ~~d~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~  105 (510)
T KOG0144|consen   26 HTDNPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGM  105 (510)
T ss_pred             CCCCCCchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCC
Confidence            33444566678999999999999999999999999999999999999999999999999999999999997776444444


Q ss_pred             CceEEEEe
Q psy3930         268 SSILTTTS  275 (299)
Q Consensus       268 g~~l~v~~  275 (299)
                      .+++.|+.
T Consensus       106 ~~pvqvk~  113 (510)
T KOG0144|consen  106 HHPVQVKY  113 (510)
T ss_pred             Ccceeecc
Confidence            44444443

>PLN03213 repressor of silencing 3; Provisional

Probab=99.28  E-value=1.6e-11  Score=112.53  Aligned_cols=76  Identities=21%  Similarity=0.311  Sum_probs=68.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCH--HHHHHHHHhcCCCCCCCCCCceE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK--EEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~--~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ....+||||||++++++++|...|+.||.|..|.|++.  +|  +|||||+|...  .++.+|+.. |||  ..++|+.|
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISa-LNG--AEWKGR~L   80 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFST-YNG--CVWKGGRL   80 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHH-hcC--CeecCcee
Confidence            34578999999999999999999999999999999954  67  89999999987  789999999 999  88899999


Q ss_pred             EEEee
Q psy3930         272 TTTSR  276 (299)
Q Consensus       272 ~v~~k  276 (299)
                      +|...
T Consensus        81 KVNKA   85 (759)
T PLN03213         81 RLEKA   85 (759)
T ss_pred             EEeec
Confidence            99653

>smart00360 RRM RNA recognition motif

Probab=99.27  E-value=2.3e-11  Score=84.23  Aligned_cols=70  Identities=46%  Similarity=0.721  Sum_probs=63.5

Q ss_pred             EecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         201 VEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       201 V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      |+|||..+++++|+.+|++||.|..+.+..+..++.++|+|||+|.+.++|..|+.. ++|  ..+.|+.+.|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~-~~~--~~~~~~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEA-LNG--KELDGRPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHH-cCC--CeeCCcEEEe
Confidence            579999999999999999999999999998877789999999999999999999998 887  6667887765

>KOG0105|consensus

Probab=99.24  E-value=3.3e-11  Score=97.53  Aligned_cols=78  Identities=29%  Similarity=0.417  Sum_probs=68.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||.++-+.+|+.+|-+||.|..|.+...   -...+||||+|+++-+|+.||.. -+|  +.+.|..|+|+
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiyg-RdG--Ydydg~rLRVE   78 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYG-RDG--YDYDGCRLRVE   78 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhc-ccc--cccCcceEEEE
Confidence            4689999999999999999999999999999988532   23467999999999999999998 999  99999999998


Q ss_pred             eecc
Q psy3930         275 SRLS  278 (299)
Q Consensus       275 ~k~~  278 (299)
                      ....
T Consensus        79 fprg   82 (241)
T KOG0105|consen   79 FPRG   82 (241)
T ss_pred             eccC
Confidence            8543

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

Probab=99.23  E-value=3.7e-11  Score=114.76  Aligned_cols=80  Identities=31%  Similarity=0.365  Sum_probs=73.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||..+++++|+++|++||.|..|.++.+..+|.++|||||+|.+.++|.+|+.  ++|  ..+.|++|.
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~--l~g--~~~~g~~i~  161 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA--LTG--QMLLGRPII  161 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH--hCC--CEECCeeeE
Confidence            3456899999999999999999999999999999999998899999999999999999999997  677  778899988


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      +...
T Consensus       162 v~~~  165 (457)
T TIGR01622       162 VQSS  165 (457)
T ss_pred             Eeec
Confidence            8764

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>KOG0114|consensus

Probab=99.23  E-value=6.3e-11  Score=87.10  Aligned_cols=76  Identities=21%  Similarity=0.334  Sum_probs=67.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ..++.|||.|||..+|.++.-++|++||.|..|++-..   ...+|.|||.|++..+|.+|+.+ |+|  ..+.++.+.|
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~---k~TrGTAFVVYedi~dAk~A~dh-lsg--~n~~~ryl~v   89 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNT---KETRGTAFVVYEDIFDAKKACDH-LSG--YNVDNRYLVV   89 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCc---cCcCceEEEEehHhhhHHHHHHH-hcc--cccCCceEEE
Confidence            34678999999999999999999999999999999754   44589999999999999999999 999  8888999887


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      -.
T Consensus        90 ly   91 (124)
T KOG0114|consen   90 LY   91 (124)
T ss_pred             Ee
Confidence            43

>KOG0125|consensus

Probab=99.22  E-value=3.2e-11  Score=105.55  Aligned_cols=81  Identities=20%  Similarity=0.240  Sum_probs=72.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...+.|+|+|||+..-+.||+.+|++||.|..|.|+-+  ...+||||||+|++.++|++|-++ |+|  ..+.||+|.|
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~-LHg--t~VEGRkIEV  168 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAE-LHG--TVVEGRKIEV  168 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHH-hhc--ceeeceEEEE
Confidence            34578999999999999999999999999999999976  345799999999999999999999 999  8889999999


Q ss_pred             Eeeccc
Q psy3930         274 TSRLSF  279 (299)
Q Consensus       274 ~~k~~~  279 (299)
                      ....+.
T Consensus       169 n~ATar  174 (376)
T KOG0125|consen  169 NNATAR  174 (376)
T ss_pred             eccchh
Confidence            765544

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

Probab=99.21  E-value=6.1e-11  Score=104.03  Aligned_cols=79  Identities=35%  Similarity=0.577  Sum_probs=75.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .++|||+|||.++++++|.++|..||.+..+.++.++.+|.++|||||+|.+.++|..|+.. ++|  ..+.|+++.|..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~-~~~--~~~~~~~~~v~~  191 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEE-LNG--KELEGRPLRVQK  191 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHH-cCC--CeECCceeEeec
Confidence            58999999999999999999999999999999999988999999999999999999999999 888  889999999988


Q ss_pred             ec
Q psy3930         276 RL  277 (299)
Q Consensus       276 k~  277 (299)
                      ..
T Consensus       192 ~~  193 (306)
T COG0724         192 AQ  193 (306)
T ss_pred             cc
Confidence            54

>KOG0111|consensus

Probab=99.19  E-value=2.2e-11  Score=101.02  Aligned_cols=80  Identities=25%  Similarity=0.451  Sum_probs=73.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++||||+|..++++.-|...|-+||.|..|.+|.|..+++.+|||||+|...++|.+|+.. +|+  -.+-|+.|+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDN-Mne--sEL~Grtir   83 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDN-MNE--SELFGRTIR   83 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhc-Cch--hhhcceeEE
Confidence            34568999999999999999999999999999999999999999999999999999999999999 998  778888887


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |-.
T Consensus        84 VN~   86 (298)
T KOG0111|consen   84 VNL   86 (298)
T ss_pred             Eee
Confidence            654

>KOG0131|consensus

Probab=99.19  E-value=2.6e-11  Score=98.01  Aligned_cols=80  Identities=26%  Similarity=0.454  Sum_probs=74.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ...+|||+||++.++++.|.++|-+.|+|..+.+++++.+...+||||++|.++++|+-|++- +|+  ..+-|++|+|.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAiki-ln~--VkLYgrpIrv~   84 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKI-LNM--VKLYGRPIRVN   84 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHH-HHH--HHhcCceeEEE
Confidence            457999999999999999999999999999999999999999999999999999999999998 887  88889999987


Q ss_pred             eec
Q psy3930         275 SRL  277 (299)
Q Consensus       275 ~k~  277 (299)
                      ...
T Consensus        85 kas   87 (203)
T KOG0131|consen   85 KAS   87 (203)
T ss_pred             ecc
Confidence            644

>KOG0108|consensus

Probab=99.19  E-value=4.5e-11  Score=111.40  Aligned_cols=80  Identities=30%  Similarity=0.469  Sum_probs=76.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      +.+||||+|+++++++|..+|+..|.|..++++.|+.+|.++||||++|.+.++|..|++. +||  .++.|++|+|..+
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~-lNg--~~~~gr~l~v~~~   95 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRN-LNG--AEFNGRKLRVNYA   95 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHh-cCC--cccCCceEEeecc
Confidence            8999999999999999999999999999999999999999999999999999999999999 999  9999999999876


Q ss_pred             ccc
Q psy3930         277 LSF  279 (299)
Q Consensus       277 ~~~  279 (299)
                      ...
T Consensus        96 ~~~   98 (435)
T KOG0108|consen   96 SNR   98 (435)
T ss_pred             ccc
Confidence            554

>KOG1855|consensus

Probab=99.18  E-value=1.5e-11  Score=110.98  Aligned_cols=119  Identities=32%  Similarity=0.419  Sum_probs=97.7

Q ss_pred             hHHHHHHHHHHhhhhcCCCCcchhHHHHHhhhcCC--CeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceee
Q psy3930         106 KKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESP--EIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVR  183 (299)
Q Consensus       106 ~~~~~~~i~~q~efyfsd~nL~~d~fl~~~~~~~~--~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~  183 (299)
                      .+++..+|..|+||||||+||.+|.||..+++++.  +|+++++++|++|+.++.++..+..||+.+..+++++++.+|+
T Consensus       137 sedl~~kIv~QVEyyFSDenL~~d~fLlkhvrrnkeGyVpv~~vaSFKKvK~LTrd~~~va~ALr~S~kL~vseDgkKVr  216 (484)
T KOG1855|consen  137 SEDLAAKIVDQVEYYFSDENLLKDAFLLKHVRRNKEGYVPVKLVASFKKVKALTRDWKLVADALRKSSKLEVSEDGKKVR  216 (484)
T ss_pred             cHHHHHHHHHHhheeeccccccchHHHHHHHhcCCCCceeeehhhhHHHHHHHhhhhHHHHHHHhhcceEEEccCCceee
Confidence            47888999999999999999999999999999875  5999999999999999999999999999999999999999999


Q ss_pred             eeecccCCCCCCCcEEEEecCC------CCCCHHHHHHHh-hcCCceEEEEeeccC
Q psy3930         184 RTVVVQDKPDVDECTIYVEKLP------PEAEHDYIESVF-SKYGKVTYVSLPKFK  232 (299)
Q Consensus       184 r~~~~~~~~~~~~~~l~V~nLp------~~~t~e~L~~~F-~~~G~i~~v~i~~~~  232 (299)
                      |..|.++.        =..+||      .+..++...+-. .-||.+-.|..++.-
T Consensus       217 RisPlp~~--------~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIc  264 (484)
T KOG1855|consen  217 RISPLPEF--------DEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRIC  264 (484)
T ss_pred             ecCCCCCc--------cccccccceEEEecCCcchHHHHHHHHhhcccceeeeeec
Confidence            98877752        122344      333444444444 448888888777754

>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=99.18  E-value=2.3e-10  Score=79.91  Aligned_cols=73  Identities=42%  Similarity=0.669  Sum_probs=64.7

Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      +|+|+|||..+++++|+.+|+.||.|..+.+..+. .+.++|+|||+|.+.++|..|++. ++|  ..++|+.+.+.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~-~~~~~~~~~v~f~s~~~a~~a~~~-~~~--~~~~~~~~~v~   73 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDK-DTKSKGFAFVEFEDEEDAEKALEA-LNG--KELGGRPLRVE   73 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCC-CCCcceEEEEEECCHHHHHHHHHH-hCC--CeECCeEEEEe
Confidence            48999999999999999999999999999998876 446789999999999999999999 887  55778887664

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG0145|consensus

Probab=99.17  E-value=7.5e-11  Score=100.25  Aligned_cols=87  Identities=25%  Similarity=0.426  Sum_probs=74.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      +.....+.|.-||..+|+++++.+|+..|+|++|.++||+.+|++-|||||.|.++++|++|+.. +||  +.+....| 
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~Aint-lNG--LrLQ~KTI-  113 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINT-LNG--LRLQNKTI-  113 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhh-hcc--eeeccceE-
Confidence            34456799999999999999999999999999999999999999999999999999999999999 999  55555555 


Q ss_pred             EEeecccCCCCCCC
Q psy3930         273 TTSRLSFGITPLGF  286 (299)
Q Consensus       273 v~~k~~~~~~~r~~  286 (299)
                         |++|++|....
T Consensus       114 ---KVSyARPSs~~  124 (360)
T KOG0145|consen  114 ---KVSYARPSSDS  124 (360)
T ss_pred             ---EEEeccCChhh
Confidence               55666555443

>KOG0110|consensus

Probab=99.16  E-value=7e-11  Score=112.68  Aligned_cols=115  Identities=23%  Similarity=0.342  Sum_probs=96.7

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC-------CCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeecc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD-------KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKF  231 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~-------~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~  231 (299)
                      +.++|+.|++.+++..|.|..+.++.+...+.       ........|+|.|+|+.++..+++.+|..||.+..|++|.-
T Consensus       569 ~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK  648 (725)
T KOG0110|consen  569 KPESAQAALKALQGTVLDGHKLELKISENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKK  648 (725)
T ss_pred             CHHHHHHHHHHhcCceecCceEEEEeccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchh
Confidence            38999999999999999999998877651111       01233568999999999999999999999999999999986


Q ss_pred             CCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         232 KSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       232 ~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      ...+.++|||||+|-++.+|..|+.+ |.+  .++-|+.|.++..
T Consensus       649 ~~k~a~rGF~Fv~f~t~~ea~nA~~a-l~S--THlyGRrLVLEwA  690 (725)
T KOG0110|consen  649 IGKGAHRGFGFVDFLTPREAKNAFDA-LGS--THLYGRRLVLEWA  690 (725)
T ss_pred             hcchhhccceeeeccCcHHHHHHHHh-hcc--cceechhhheehh
Confidence            55677899999999999999999999 555  8888998887654

>KOG0146|consensus

Probab=99.15  E-value=5.1e-11  Score=101.61  Aligned_cols=87  Identities=18%  Similarity=0.299  Sum_probs=80.8

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       192 ~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      +.+++|+|||-.||.+....+|...|-.||.|.+..+-.|+.|+.+++||||.|+++.+|+.||.+ +||  ..++-.+|
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqA-MNG--FQIGMKRL  357 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQA-MNG--FQIGMKRL  357 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHH-hcc--hhhhhhhh
Confidence            468899999999999999999999999999999999888999999999999999999999999999 999  89999999


Q ss_pred             EEEeecccCC
Q psy3930         272 TTTSRLSFGI  281 (299)
Q Consensus       272 ~v~~k~~~~~  281 (299)
                      +|++|..+..
T Consensus       358 KVQLKRPkda  367 (371)
T KOG0146|consen  358 KVQLKRPKDA  367 (371)
T ss_pred             hhhhcCcccc
Confidence            9988766543

>smart00361 RRM_1 RNA recognition motif

Probab=99.08  E-value=4.6e-10  Score=79.02  Aligned_cols=61  Identities=21%  Similarity=0.345  Sum_probs=52.9

Q ss_pred             HHHHHHHhh----cCCceEEEE-eeccCCC--CCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         210 HDYIESVFS----KYGKVTYVS-LPKFKST--GKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       210 ~e~L~~~F~----~~G~i~~v~-i~~~~~~--g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      +++|+++|+    +||.|..|. ++.++.+  |.++|||||+|.+.++|.+|++. |||  ..+.|++|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~-l~g--~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVD-LNG--RYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHH-hCC--CEECCEEEEe
Confidence            578888888    999999985 6666555  89999999999999999999999 998  7888888865

>KOG0123|consensus

Probab=99.08  E-value=1.6e-10  Score=106.56  Aligned_cols=113  Identities=26%  Similarity=0.369  Sum_probs=94.9

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccCCC------CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeecc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP------DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKF  231 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~------~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~  231 (299)
                      .++++|.+|+..+|+..+.++++.+.......++.      ......+|+.+++.+.+.+.|..+|..+|.|..+.++.+
T Consensus       123 ~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~  202 (369)
T KOG0123|consen  123 ESEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRD  202 (369)
T ss_pred             CCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeec
Confidence            44899999999999999999999887655433322      233567999999999999999999999999999999988


Q ss_pred             CCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         232 KSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       232 ~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      . .|.++|||||.|.+.++|..|++. ++|  ..+.+..+.|.
T Consensus       203 ~-~g~~~~~gfv~f~~~e~a~~av~~-l~~--~~~~~~~~~V~  241 (369)
T KOG0123|consen  203 S-IGKSKGFGFVNFENPEDAKKAVET-LNG--KIFGDKELYVG  241 (369)
T ss_pred             C-CCCCCCccceeecChhHHHHHHHh-ccC--CcCCccceeec
Confidence            6 777999999999999999999999 998  55556665553

>KOG0124|consensus

Probab=99.03  E-value=2.3e-10  Score=101.49  Aligned_cols=78  Identities=31%  Similarity=0.464  Sum_probs=72.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      .-.|.||||.+.++..++.|+..|..||+|.+|.+-.|..||+++||+||+|+-++.|+-|++. +||  ..++|+.|+|
T Consensus       111 aiMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEq-MNg--~mlGGRNiKV  187 (544)
T KOG0124|consen  111 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ-MNG--QMLGGRNIKV  187 (544)
T ss_pred             HHhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHH-hcc--ccccCccccc
Confidence            3468999999999999999999999999999999999999999999999999999999999999 999  7777888877


Q ss_pred             E
Q psy3930         274 T  274 (299)
Q Consensus       274 ~  274 (299)
                      -
T Consensus       188 g  188 (544)
T KOG0124|consen  188 G  188 (544)
T ss_pred             c
Confidence            4

>KOG4212|consensus

Probab=99.00  E-value=1.2e-09  Score=99.09  Aligned_cols=79  Identities=28%  Similarity=0.436  Sum_probs=72.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhh-cCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFS-KYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~-~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ...+.+||.|+|+++.|++|+.+|. +.|+|++|.+..|. +|+.+|||.|+|++++.+++|++. ||.  +.++|++|.
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~-lnk--~~~~GR~l~  117 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEK-LNK--YEVNGRELV  117 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHH-hhh--ccccCceEE
Confidence            3456799999999999999999996 58999999999987 999999999999999999999999 887  899999999


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |+--
T Consensus       118 vKEd  121 (608)
T KOG4212|consen  118 VKED  121 (608)
T ss_pred             Eecc
Confidence            9653

>KOG4205|consensus

Probab=98.92  E-value=6.1e-10  Score=99.67  Aligned_cols=114  Identities=23%  Similarity=0.417  Sum_probs=91.3

Q ss_pred             HHHHHHHHHhcCccccccccceeeeeecccCCCCCC----CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCC
Q psy3930         160 PDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVD----ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG  235 (299)
Q Consensus       160 ~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~----~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g  235 (299)
                      .+.+.+++ ......+.++.+.+.++.+..+.....    ...|||++||+++++++++++|.+||.|..+.++.|..+.
T Consensus        58 ~~~v~~vl-~~~~h~~dgr~ve~k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~  136 (311)
T KOG4205|consen   58 PEGVDAVL-NARTHKLDGRSVEPKRAVSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTS  136 (311)
T ss_pred             Ccchheee-cccccccCCccccceeccCcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeeccccc
Confidence            34455555 334456788888777777766554333    4589999999999999999999999999999999999999


Q ss_pred             CcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeecc
Q psy3930         236 KLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLS  278 (299)
Q Consensus       236 ~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~  278 (299)
                      +.+|||||.|.+++++.+++..    +-+.++++.+.|+....
T Consensus       137 ~~rgFgfv~~~~e~sVdkv~~~----~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen  137 RPRGFGFVTFDSEDSVDKVTLQ----KFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             ccccceeeEeccccccceeccc----ceeeecCceeeEeeccc
Confidence            9999999999999999999876    44778888888866543

>KOG0109|consensus

Probab=98.89  E-value=2.9e-09  Score=92.08  Aligned_cols=76  Identities=24%  Similarity=0.376  Sum_probs=67.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      ..+||||||..+++.+|+.+|++||+|..|+|+++        ||||+.++...|+.|+.. |+|  ..+.|..|.|+-.
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairN-Lhg--YtLhg~nInVeaS   71 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRN-LHG--YTLHGVNINVEAS   71 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhh-ccc--ceecceEEEEEec
Confidence            36899999999999999999999999999999865        899999999999999999 898  8888999999876


Q ss_pred             cccCCCC
Q psy3930         277 LSFGITP  283 (299)
Q Consensus       277 ~~~~~~~  283 (299)
                      .++.++.
T Consensus        72 ksKsk~s   78 (346)
T KOG0109|consen   72 KSKSKAS   78 (346)
T ss_pred             cccCCCc
Confidence            6554333

>PF13893 RRM_5: RNA recognition motif

Probab=98.87  E-value=7.8e-09  Score=69.28  Aligned_cols=55  Identities=40%  Similarity=0.648  Sum_probs=47.5

Q ss_pred             HHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         213 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       213 L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      |.++|++||+|..+.+....     +++|||+|.+.++|..|++. +||  ..+.|++|.|..
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~-l~~--~~~~g~~l~V~~   55 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQ-LNG--RQFNGRPLKVSY   55 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHH-HTT--SEETTEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHH-hCC--CEECCcEEEEEE
Confidence            67899999999999997653     57999999999999999999 898  778999988764

(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 ....

>KOG4208|consensus

Probab=98.86  E-value=9.7e-09  Score=84.90  Aligned_cols=79  Identities=33%  Similarity=0.432  Sum_probs=70.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcC-CceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKY-GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~-G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      .....+|+..+|..+.+.++..+|.+| |.+..+++-|++.||.++|||||+|++++.|.-|-+. ||+  +-+.++.|.
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAET-MNN--YLl~e~lL~  123 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAET-MNN--YLLMEHLLE  123 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHH-hhh--hhhhhheee
Confidence            445678999999999999999999998 6888899989999999999999999999999999999 887  777788887


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      +..
T Consensus       124 c~v  126 (214)
T KOG4208|consen  124 CHV  126 (214)
T ss_pred             eEE
Confidence            654

>KOG0153|consensus

Probab=98.83  E-value=1.1e-08  Score=90.41  Aligned_cols=80  Identities=30%  Similarity=0.392  Sum_probs=69.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      +....+|||+||-..+++.+|+..|.+||+|.++++...      +++|||+|.+.++|+.|.++++|.  +.++|.+|.
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~--lvI~G~Rl~  296 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNK--LVINGFRLK  296 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcce--eeecceEEE
Confidence            556689999999999999999999999999999998764      358999999999999999997874  888999887


Q ss_pred             EEeecccCCCCC
Q psy3930         273 TTSRLSFGITPL  284 (299)
Q Consensus       273 v~~k~~~~~~~r  284 (299)
                      +.    |+.+.+
T Consensus       297 i~----Wg~~~~  304 (377)
T KOG0153|consen  297 IK----WGRPKQ  304 (377)
T ss_pred             EE----eCCCcc
Confidence            76    666544

>COG5193 LHP1 La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]

Probab=98.81  E-value=5.6e-10  Score=100.30  Aligned_cols=54  Identities=22%  Similarity=0.422  Sum_probs=52.0

Q ss_pred             CeeecCCCCcCcChHHHHhhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcC
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKS   54 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s   54 (299)
                      ||||||.+||+.|.|||++|+++|+||+++|..|.|..++..|.++|.+||+.+
T Consensus       278 iEyYFseenl~~d~~lrkk~~kaGf~plsfi~kf~Rn~Sf~gd~nLilaa~ke~  331 (438)
T COG5193         278 IEYYFSEENLKSDEFLRKKFKKAGFIPLSFIGKFYRNLSFGGDKNLILAAMKEV  331 (438)
T ss_pred             hHhhhhHHhhhhhhHHHhhhhhcccccHhhhhhhhhccccCCchhhhHHHHHHH
Confidence            799999999999999999999999999999999999999999999999999965

>KOG0116|consensus

Probab=98.79  E-value=2.3e-08  Score=92.94  Aligned_cols=80  Identities=26%  Similarity=0.425  Sum_probs=68.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      ..+|||+|||.+++..+|+++|..||.|...+|..-...+...+||||+|.+.++++.|+.+    .++.++++.+.|+-
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A----sp~~ig~~kl~Vee  363 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA----SPLEIGGRKLNVEE  363 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc----CccccCCeeEEEEe
Confidence            45699999999999999999999999999888765432344449999999999999999998    36899999999988


Q ss_pred             eccc
Q psy3930         276 RLSF  279 (299)
Q Consensus       276 k~~~  279 (299)
                      |...
T Consensus       364 k~~~  367 (419)
T KOG0116|consen  364 KRPG  367 (419)
T ss_pred             cccc
Confidence            7653

>KOG2590|consensus

Probab=98.74  E-value=2e-09  Score=100.06  Aligned_cols=58  Identities=36%  Similarity=0.563  Sum_probs=53.4

Q ss_pred             CeeecCCCCcCcChHHHHhhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCc
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDG   63 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~   63 (299)
                      ||||||.+||++|.|+++     +||||.+|++|+||..|+.|+++|.+||+.|.+|++..|-
T Consensus       308 ie~~FSeE~~~~d~~n~~-----k~~~l~~ia~F~r~ad~s~d~nli~~alr~s~ive~~~d~  365 (448)
T KOG2590|consen  308 IEFYFSEENLQRDRFNRE-----KFVPLRVIAKFKRVADLSSDINLILAALRNSLIVEETGDL  365 (448)
T ss_pred             cccccchHHHhhhhhhhc-----ccchhhhhhhhhhhhhcccCHHHHHHHHhhhhhhhccchh
Confidence            699999999999999887     4578999999999999999999999999999998887763

>KOG0415|consensus

Probab=98.73  E-value=2e-08  Score=89.03  Aligned_cols=81  Identities=23%  Similarity=0.378  Sum_probs=73.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      .++...|||-.|.+-++.++|.-+|+.||.|..|.+++|..||.+..||||+|++.+++++|.-+ |++  .-+.++.|-
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFK-MdN--vLIDDrRIH  312 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFK-MDN--VLIDDRRIH  312 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhh-hcc--eeeccceEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999 665  777888888


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |-..
T Consensus       313 VDFS  316 (479)
T KOG0415|consen  313 VDFS  316 (479)
T ss_pred             eehh
Confidence            8543

>KOG4205|consensus

Probab=98.70  E-value=1.9e-08  Score=90.11  Aligned_cols=81  Identities=23%  Similarity=0.385  Sum_probs=72.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      +.+++||++|+++++++.|++.|.+||+|..|.+++++.+++++||+||+|++.+...+++..    ..+.+.|+.+.++
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~----~~h~~dgr~ve~k   80 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA----RTHKLDGRSVEPK   80 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc----cccccCCccccce
Confidence            578999999999999999999999999999999999999999999999999998888888765    3477888888777


Q ss_pred             eeccc
Q psy3930         275 SRLSF  279 (299)
Q Consensus       275 ~k~~~  279 (299)
                      .....
T Consensus        81 ~av~r   85 (311)
T KOG4205|consen   81 RAVSR   85 (311)
T ss_pred             eccCc
Confidence            66554

>KOG4206|consensus

Probab=98.67  E-value=7.6e-08  Score=80.83  Aligned_cols=76  Identities=29%  Similarity=0.433  Sum_probs=68.1

Q ss_pred             CcEEEEecCCCCCCHHHHHH----HhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         196 ECTIYVEKLPPEAEHDYIES----VFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~----~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      +.||||.||++.+..++|+.    +|++||.|..|...+   +.+.+|-|||.|.+.+.|-.|+.+ ++|  .-+-|.++
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~-l~g--fpFygK~m   82 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRA-LQG--FPFYGKPM   82 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHH-hcC--CcccCchh
Confidence            34999999999999999988    999999999988754   777899999999999999999999 999  88889999


Q ss_pred             EEEeec
Q psy3930         272 TTTSRL  277 (299)
Q Consensus       272 ~v~~k~  277 (299)
                      +++...
T Consensus        83 riqyA~   88 (221)
T KOG4206|consen   83 RIQYAK   88 (221)
T ss_pred             heeccc
Confidence            887654

>KOG0132|consensus

Probab=98.61  E-value=7.8e-08  Score=92.97  Aligned_cols=89  Identities=17%  Similarity=0.339  Sum_probs=69.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ..++|||||+|+..+++.+|..+|+.||+|.+|.++..      +|||||......+|.+|+.+ |+.  ..+.+..|  
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqk-l~n--~kv~~k~I--  487 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQK-LSN--VKVADKTI--  487 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHH-Hhc--ccccceee--
Confidence            45789999999999999999999999999999998754      67999999999999999999 665  55555555  


Q ss_pred             EeecccCCCCCCCCCCCCcccC
Q psy3930         274 TSRLSFGITPLGFESGGWWFKS  295 (299)
Q Consensus       274 ~~k~~~~~~~r~~~~g~~~~~~  295 (299)
                        |..|+...+-...-..+|..
T Consensus       488 --ki~Wa~g~G~kse~k~~wD~  507 (894)
T KOG0132|consen  488 --KIAWAVGKGPKSEYKDYWDV  507 (894)
T ss_pred             --EEeeeccCCcchhhhhhhhc
Confidence              45554433333333445554

>KOG0146|consensus

Probab=98.60  E-value=1.1e-07  Score=81.55  Aligned_cols=79  Identities=27%  Similarity=0.395  Sum_probs=67.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCC-CCCCCceEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCP-PDYQSSILTT  273 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~-~~~~g~~l~v  273 (299)
                      +.+++|||-|...-.|++++.+|..||.|.+|.+.+.. .|.++||+||.|.+..+|+.||.. ++|.. .-.....|.|
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~a-LHgSqTmpGASSSLVV   95 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINA-LHGSQTMPGASSSLVV   95 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHH-hcccccCCCCccceEE
Confidence            56899999999999999999999999999999999987 899999999999999999999999 77632 2333445555


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      +.
T Consensus        96 K~   97 (371)
T KOG0146|consen   96 KF   97 (371)
T ss_pred             Ee
Confidence            54

>KOG0533|consensus

Probab=98.58  E-value=2.8e-07  Score=79.65  Aligned_cols=79  Identities=19%  Similarity=0.299  Sum_probs=72.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      ...|+|.|||..++.++|+++|..||.+..+.+..++ .|.+.|.|-|.|...++|.+|++. +||  ..++|+++.+.+
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~-~~g--v~ldG~~mk~~~  158 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKK-YNG--VALDGRPMKIEI  158 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHH-hcC--cccCCceeeeEE
Confidence            4689999999999999999999999999999888887 899999999999999999999999 998  888899988876


Q ss_pred             ecc
Q psy3930         276 RLS  278 (299)
Q Consensus       276 k~~  278 (299)
                      ...
T Consensus       159 i~~  161 (243)
T KOG0533|consen  159 ISS  161 (243)
T ss_pred             ecC
Confidence            543

>KOG4212|consensus

Probab=98.55  E-value=1.8e-07  Score=85.14  Aligned_cols=75  Identities=27%  Similarity=0.459  Sum_probs=66.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....|+|||.|||.++||+.|++-|..||.|.++.|.   ..|+++|  .|.|.++++|+.|+.. +||  ..+.|+.|.
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~edAEra~a~-Mng--s~l~Gr~I~  604 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPEDAERACAL-MNG--SRLDGRNIK  604 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHHHHHHHHHH-hcc--CcccCceee
Confidence            3567899999999999999999999999999999983   3677775  9999999999999998 999  788899988


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |++
T Consensus       605 V~y  607 (608)
T KOG4212|consen  605 VTY  607 (608)
T ss_pred             eee
Confidence            864

>KOG0110|consensus

Probab=98.51  E-value=3.8e-07  Score=87.65  Aligned_cols=77  Identities=29%  Similarity=0.372  Sum_probs=67.8

Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCC---CCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKST---GKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~---g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ++||.||+++++.++|...|...|.|..+.|...+..   --+.|||||+|.+.++|+.|++. |+|  ..++|+.|.++
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~-lqg--tvldGH~l~lk  593 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKA-LQG--TVLDGHKLELK  593 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHH-hcC--ceecCceEEEE
Confidence            4999999999999999999999999999988765411   22569999999999999999999 999  88889999988


Q ss_pred             eec
Q psy3930         275 SRL  277 (299)
Q Consensus       275 ~k~  277 (299)
                      +..
T Consensus       594 ~S~  596 (725)
T KOG0110|consen  594 ISE  596 (725)
T ss_pred             ecc
Confidence            865

>KOG4209|consensus

Probab=98.46  E-value=5.6e-07  Score=77.80  Aligned_cols=82  Identities=29%  Similarity=0.413  Sum_probs=74.6

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       192 ~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ...+...+||+|+...++-++++..|+.||.+..+.++.++.+|.++||+||+|.+.+.++.|+.  +||  -.+.++.+
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~--l~g--s~i~~~~i  172 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK--LDG--SEIPGPAI  172 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh--cCC--cccccccc
Confidence            35667899999999999999999999999999999999999889999999999999999999999  788  78888888


Q ss_pred             EEEeec
Q psy3930         272 TTTSRL  277 (299)
Q Consensus       272 ~v~~k~  277 (299)
                      .+..+.
T Consensus       173 ~vt~~r  178 (231)
T KOG4209|consen  173 EVTLKR  178 (231)
T ss_pred             eeeeee
Confidence            887654

>KOG2591|consensus

Probab=98.46  E-value=1.4e-07  Score=88.16  Aligned_cols=76  Identities=30%  Similarity=0.509  Sum_probs=71.9

Q ss_pred             HHHHHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceee
Q psy3930         108 QLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVR  183 (299)
Q Consensus       108 ~~~~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~  183 (299)
                      ++.+.+++||||||+.+||..|.||..+|..+.+|+|-+++.|..|..++.|.+.+.++|+++.+++++++..+|+
T Consensus        95 ~~kq~lk~qlEy~fSreNlssD~YL~sQMDSDqyVPI~tva~~~~i~klttDvdLI~Evlresp~VqvDekgekVr  170 (684)
T KOG2591|consen   95 DLKQLLKKQLEYYFSRENLSSDRYLISQMDSDQYVPINTVANFPEIMKLTTDVDLIVEVLRESPNVQVDEKGEKVR  170 (684)
T ss_pred             hHHHHHHHHHHHhhccccccchhhhhhhcccccccchhhhccchhhhhhccchHHHHHHHhcCCCceeccCccccc
Confidence            5667788999999999999999999999999999999999999999999999999999999999999999988874

>KOG4661|consensus

Probab=98.46  E-value=3.7e-07  Score=85.63  Aligned_cols=79  Identities=23%  Similarity=0.374  Sum_probs=69.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ..++++||++|...+--.+|+.+|++||.|+-..++++.-+--.++||||++.+.++|.+||.. |+.  ..+.|+.|.|
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~h-LHr--TELHGrmISV  479 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEH-LHR--TELHGRMISV  479 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHH-hhh--hhhcceeeee
Confidence            3467899999999999999999999999999999988765666789999999999999999999 654  8888999998


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      ..
T Consensus       480 Ek  481 (940)
T KOG4661|consen  480 EK  481 (940)
T ss_pred             ee
Confidence            65

>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=98.44  E-value=3.9e-07  Score=69.17  Aligned_cols=74  Identities=27%  Similarity=0.370  Sum_probs=45.3

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhc--CCCCCCCCCCceEEE
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG--LNPCPPDYQSSILTT  273 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~--lng~~~~~~g~~l~v  273 (299)
                      ++.|.+.|++..++.++|++.|+.||+|.+|.+.+..      ..|||+|.+++.|+.|++++  .++..+.+.+..+.+
T Consensus         1 G~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~   74 (105)
T PF08777_consen    1 GCILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTL   74 (105)
T ss_dssp             --EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEE
T ss_pred             CeEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEE
Confidence            4679999999999999999999999999999997643      25999999999999999872  222356666766665


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      ++
T Consensus        75 ~v   76 (105)
T PF08777_consen   75 EV   76 (105)
T ss_dssp             E-
T ss_pred             EE
Confidence            54

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

>KOG4206|consensus

Probab=98.42  E-value=1.1e-06  Score=73.88  Aligned_cols=101  Identities=17%  Similarity=0.290  Sum_probs=80.4

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeeccc------------------------------------------------
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ------------------------------------------------  189 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~------------------------------------------------  189 (299)
                      .+.+.|..|+..+++.-+.|+..++.++....                                                
T Consensus        60 k~~~~As~A~r~l~gfpFygK~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~  139 (221)
T KOG4206|consen   60 KETEAASAALRALQGFPFYGKPMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFL  139 (221)
T ss_pred             cChhHHHHHHHHhcCCcccCchhheecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCcc
Confidence            34788999999999988888887776543210                                                


Q ss_pred             CCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCC
Q psy3930         190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPP  264 (299)
Q Consensus       190 ~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~  264 (299)
                      ....+....+|+.|||.+++.+.+..+|.+|+....|+++...     .+.|||+|.+...|..|.+. ++|.++
T Consensus       140 ~~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~-lq~~~i  208 (221)
T KOG4206|consen  140 AQMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQA-LQGFKI  208 (221)
T ss_pred             ccCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhh-hcccee
Confidence            0113445789999999999999999999999999999988754     46899999999999999998 887433

>KOG0105|consensus

Probab=98.41  E-value=1.4e-06  Score=70.97  Aligned_cols=114  Identities=18%  Similarity=0.187  Sum_probs=87.9

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccC------------------------CCCCCCcEEEEecCCCCCCHHHH
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD------------------------KPDVDECTIYVEKLPPEAEHDYI  213 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~------------------------~~~~~~~~l~V~nLp~~~t~e~L  213 (299)
                      ++..+|..||..-++..+.+-.++|+.+..-..                        ..-.....|.|.+||++.+|++|
T Consensus        53 Ed~RDAeDAiygRdGYdydg~rLRVEfprggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDL  132 (241)
T KOG0105|consen   53 EDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDL  132 (241)
T ss_pred             cCccchhhhhhcccccccCcceEEEEeccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHH
Confidence            568889999999999999998888875431100                        00122357999999999999999


Q ss_pred             HHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeeccc
Q psy3930         214 ESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSF  279 (299)
Q Consensus       214 ~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~~  279 (299)
                      +....+-|.|.+..+.+|       |+|.|+|-..++.+-|+.+ +......-.|...-+.++...
T Consensus       133 KDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~-ld~~~~~seGe~~yirv~~~~  190 (241)
T KOG0105|consen  133 KDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRK-LDDQKFRSEGETAYIRVRGDE  190 (241)
T ss_pred             HHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHh-hccccccCcCcEeeEEecccC
Confidence            999999999999988776       3799999999999999999 554455556776666665443

>KOG1457|consensus

Probab=98.38  E-value=2.4e-06  Score=71.63  Aligned_cols=95  Identities=22%  Similarity=0.157  Sum_probs=70.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccC-CCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCC-CCceE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFK-STGKLKGFAFVEFSTKEEAAKALELGLNPCPPDY-QSSIL  271 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~-~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~-~g~~l  271 (299)
                      ..-+||||.|||.++..-+|..+|..|-.-+.+.+.... ...-.+.+|||.|.+..+|.+|+.+ +||.+.+. .+..|
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamna-LNGvrFDpE~~stL  110 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNA-LNGVRFDPETGSTL  110 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHH-hcCeeeccccCcee
Confidence            336899999999999999999999998666655554322 1122457999999999999999999 99966655 56777


Q ss_pred             EEEeecccCCCCCCCCCC
Q psy3930         272 TTTSRLSFGITPLGFESG  289 (299)
Q Consensus       272 ~v~~k~~~~~~~r~~~~g  289 (299)
                      .++...+-.+..|+.++|
T Consensus       111 hiElAKSNtK~kr~k~sg  128 (284)
T KOG1457|consen  111 HIELAKSNTKRKRRKGSG  128 (284)
T ss_pred             EeeehhcCcccccCCCCC
Confidence            777765554545555544

>KOG4211|consensus

Probab=98.36  E-value=1.9e-06  Score=79.77  Aligned_cols=140  Identities=19%  Similarity=0.260  Sum_probs=93.1

Q ss_pred             HhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeec--------
Q psy3930         116 LMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVV--------  187 (299)
Q Consensus       116 q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~--------  187 (299)
                      .++| |++.++..    -.+.+.++--..+.++.|..       .+++.+|++. +...++.+-+.|-...+        
T Consensus        27 i~~F-f~~~~I~~----~~~~r~~Gr~sGeA~Ve~~s-------eedv~~Alkk-dR~~mg~RYIEVf~~~~~e~d~~~~   93 (510)
T KOG4211|consen   27 ILDF-FSNCGIEN----LEIPRRNGRPSGEAYVEFTS-------EEDVEKALKK-DRESMGHRYIEVFTAGGAEADWVMR   93 (510)
T ss_pred             HHHH-HhcCceeE----EEEeccCCCcCcceEEEeec-------hHHHHHHHHh-hHHHhCCceEEEEccCCcccccccc
Confidence            4455 78777654    11223334455567777766       7899999964 33344444444433221        


Q ss_pred             -ccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEE-EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCC
Q psy3930         188 -VQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPD  265 (299)
Q Consensus       188 -~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~-v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~  265 (299)
                       ...........|-+.+||+.||+++|.++|+..-.+.. |-++.+. .|++.|-|||.|++.+.|++|+..    ++..
T Consensus        94 ~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r----hre~  168 (510)
T KOG4211|consen   94 PGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR----HREN  168 (510)
T ss_pred             CCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH----HHHh
Confidence             11111234567899999999999999999998664444 5566665 778889999999999999999987    3355


Q ss_pred             CCCceEEE
Q psy3930         266 YQSSILTT  273 (299)
Q Consensus       266 ~~g~~l~v  273 (299)
                      +..+=|.|
T Consensus       169 iGhRYIEv  176 (510)
T KOG4211|consen  169 IGHRYIEV  176 (510)
T ss_pred             hccceEEe
Confidence            55665555

>KOG4660|consensus

Probab=98.34  E-value=3.8e-07  Score=85.48  Aligned_cols=72  Identities=26%  Similarity=0.460  Sum_probs=63.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      +...++|+|-|||..++.++|..+|+.||+|..|+.-+.     .+|.+||+|-+.-+|++|+++ +|+  ..+.|..+.
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~-l~~--~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKA-LNR--REIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHH-HHH--HHhhhhhhc
Confidence            456789999999999999999999999999999876444     478899999999999999999 898  777777765

>KOG1548|consensus

Probab=98.32  E-value=2.1e-06  Score=76.29  Aligned_cols=78  Identities=27%  Similarity=0.387  Sum_probs=69.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEE--------EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCC
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTY--------VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPD  265 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~--------v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~  265 (299)
                      ..+..|||+|||.++|-+++.++|++||-|..        |.+.++. .|..+|-|.+.|...++..-|++. |++  ..
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~i-lDe--~~  207 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKI-LDE--DE  207 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHH-hCc--cc
Confidence            44567999999999999999999999997754        7788876 699999999999999999999999 998  78


Q ss_pred             CCCceEEEEe
Q psy3930         266 YQSSILTTTS  275 (299)
Q Consensus       266 ~~g~~l~v~~  275 (299)
                      +.|+.|+|+.
T Consensus       208 ~rg~~~rVer  217 (382)
T KOG1548|consen  208 LRGKKLRVER  217 (382)
T ss_pred             ccCcEEEEeh
Confidence            8899999975

>KOG4454|consensus

Probab=98.32  E-value=3.7e-07  Score=76.20  Aligned_cols=80  Identities=23%  Similarity=0.279  Sum_probs=71.4

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|+...++++-|.++|-+-|+|..|.|+.++ .+..+ ||||.|.++-+..-|++. +||  ..+.+..+.+
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~   81 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQL-ENG--DDLEEDEEQR   81 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhh-ccc--chhccchhhc
Confidence            345899999999999999999999999999999999887 66666 999999999999999998 999  7777888888


Q ss_pred             Eeecc
Q psy3930         274 TSRLS  278 (299)
Q Consensus       274 ~~k~~  278 (299)
                      ++++.
T Consensus        82 ~~r~G   86 (267)
T KOG4454|consen   82 TLRCG   86 (267)
T ss_pred             ccccC
Confidence            87754

>KOG0151|consensus

Probab=98.21  E-value=2.8e-06  Score=81.75  Aligned_cols=81  Identities=21%  Similarity=0.423  Sum_probs=65.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccC---CCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCc
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFK---STGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~---~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      ++...++||+||++.++++.|-..|+.||+|..++|+..+   .....+-||||-|.+..+|++|++. |+|  ..+.+.
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~-lqg--~iv~~~  247 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKE-LQG--IIVMEY  247 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHH-hcc--eeeeee
Confidence            4556789999999999999999999999999999987644   2344566899999999999999999 998  333333


Q ss_pred             eEEEEeecccC
Q psy3930         270 ILTTTSRLSFG  280 (299)
Q Consensus       270 ~l~v~~k~~~~  280 (299)
                          +.|..|+
T Consensus       248 ----e~K~gWg  254 (877)
T KOG0151|consen  248 ----EMKLGWG  254 (877)
T ss_pred             ----eeeeccc
Confidence                4455554

>KOG0226|consensus

Probab=98.21  E-value=2.6e-06  Score=72.72  Aligned_cols=79  Identities=25%  Similarity=0.390  Sum_probs=71.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..+...||+|.|.-+++.+-|...|.+|-.....++++++-||+++|||||.|.+.+++..|+.. +||  .-++.++|.
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmre-m~g--kyVgsrpik  263 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMRE-MNG--KYVGSRPIK  263 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHh-hcc--cccccchhH
Confidence            45567899999999999999999999999888889999988999999999999999999999999 998  667777776


Q ss_pred             EE
Q psy3930         273 TT  274 (299)
Q Consensus       273 v~  274 (299)
                      .+
T Consensus       264 lR  265 (290)
T KOG0226|consen  264 LR  265 (290)
T ss_pred             hh
Confidence            54

>KOG0106|consensus

Probab=98.20  E-value=6.3e-07  Score=75.90  Aligned_cols=107  Identities=26%  Similarity=0.371  Sum_probs=84.6

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecc-------c-----------CCCCCCCcEEEEecCCCCCCHHHHHHHhhc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVV-------Q-----------DKPDVDECTIYVEKLPPEAEHDYIESVFSK  219 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~-------~-----------~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~  219 (299)
                      .+..+|..|+..+++.++.+..+.+..+...       .           .......+.+.|.+++..+.+.+|...|.+
T Consensus        43 ed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~  122 (216)
T KOG0106|consen   43 EDPRDADDAVHDLDGKELCGERLVVEHARGKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRP  122 (216)
T ss_pred             CchhhhhcccchhcCceecceeeeeecccccccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcc
Confidence            4577888899889998888776655544321       0           011355678999999999999999999999


Q ss_pred             CCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         220 YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       220 ~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      +|.+.+..+.        .+++||+|++.++|..|+.. ++|  .++.+++|.+..
T Consensus       123 ~g~~~~~~~~--------~~~~~v~Fs~~~da~ra~~~-l~~--~~~~~~~l~~~~  167 (216)
T KOG0106|consen  123 AGEVTYVDAR--------RNFAFVEFSEQEDAKRALEK-LDG--KKLNGRRISVEK  167 (216)
T ss_pred             cCCCchhhhh--------ccccceeehhhhhhhhcchh-ccc--hhhcCceeeecc
Confidence            9998555442        45799999999999999999 888  899999999844

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

Probab=98.14  E-value=2.5e-05  Score=58.07  Aligned_cols=68  Identities=19%  Similarity=0.321  Sum_probs=60.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhc--CCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCC
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSK--YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPD  265 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~--~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~  265 (299)
                      +||.+.|+|-..|.++|.+++..  .|..-.+.+|.|-.++.+.|||||.|.+++.|.+..+. .+|..+.
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~-f~g~~w~   71 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKA-FNGKKWP   71 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHH-HcCCccc
Confidence            58999999999999999998865  46777888999988899999999999999999999999 8986654

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

>KOG0106|consensus

Probab=98.06  E-value=5.1e-06  Score=70.40  Aligned_cols=69  Identities=28%  Similarity=0.495  Sum_probs=59.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      ..+|||+||+.+.+.+|+.+|..||.+..+.+.        .||+||+|.+.-+|..|+.. +||  ..+.+..+.++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~-l~~--~~l~~e~~vve~~   70 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHD-LDG--KELCGERLVVEHA   70 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccch-hcC--ceecceeeeeecc
Confidence            468999999999999999999999999988874        35899999999999999999 888  6666666555443

>KOG4211|consensus

Probab=97.88  E-value=4.7e-05  Score=70.77  Aligned_cols=73  Identities=25%  Similarity=0.398  Sum_probs=60.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      ...|-+.+||+++|+++|.++|+.++ |..+.+++.  +|+..|-|||+|.+++++++|+++    .+..+..+=|.|-.
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alkk----dR~~mg~RYIEVf~   82 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR--NGRPSGEAYVEFTSEEDVEKALKK----DRESMGHRYIEVFT   82 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc--CCCcCcceEEEeechHHHHHHHHh----hHHHhCCceEEEEc
Confidence            45677899999999999999999998 777777765  799999999999999999999997    23555566666643

>KOG0120|consensus

Probab=97.80  E-value=3.4e-05  Score=73.09  Aligned_cols=114  Identities=22%  Similarity=0.279  Sum_probs=91.2

Q ss_pred             HHHHHHHHHhcCccccccccceeeeeeccc---------------------CCCCCCCcEEEEecCCCCCCHHHHHHHhh
Q psy3930         160 PDDVVKALRKSKLLEVTEDGTKVRRTVVVQ---------------------DKPDVDECTIYVEKLPPEAEHDYIESVFS  218 (299)
Q Consensus       160 ~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~---------------------~~~~~~~~~l~V~nLp~~~t~e~L~~~F~  218 (299)
                      .+.|.+|+ .+++....+...++.+.....                     .......+.+||++||...++.++.++..
T Consensus       233 ~~~at~~~-~~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~  311 (500)
T KOG0120|consen  233 ISEATEAM-ALDGIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLD  311 (500)
T ss_pred             CCchhhhh-cccchhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHH
Confidence            45566665 566666777776665432100                     00123456899999999999999999999


Q ss_pred             cCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeec
Q psy3930         219 KYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRL  277 (299)
Q Consensus       219 ~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~  277 (299)
                      .||++...+++.+..+|.++||||.+|-+......|+.. +||  ..+.+..+.|+..+
T Consensus       312 ~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~ag-LnG--m~lgd~~lvvq~A~  367 (500)
T KOG0120|consen  312 SFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAG-LNG--MQLGDKKLVVQRAI  367 (500)
T ss_pred             hcccchhheeecccccccccceeeeeeeCCcchhhhhcc-cch--hhhcCceeEeehhh
Confidence            999999999999998899999999999999999999999 999  88889999887654

>KOG1190|consensus

Probab=97.71  E-value=0.0017  Score=59.40  Aligned_cols=73  Identities=25%  Similarity=0.303  Sum_probs=63.4

Q ss_pred             CcEEEEecCCCC-CCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         196 ECTIYVEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       196 ~~~l~V~nLp~~-~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ++.|.|.||.+. +|.+.|..+|+-||+|.+|.|...+.     --|.|.+.+...|+-|+.+ |+|  ..+-|++|+|.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~h-L~g--~~l~gk~lrvt  368 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEH-LEG--HKLYGKKLRVT  368 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHH-hhc--ceecCceEEEe
Confidence            467889999765 89999999999999999999998753     2499999999999999999 999  66668999887


Q ss_pred             ee
Q psy3930         275 SR  276 (299)
Q Consensus       275 ~k  276 (299)
                      ..
T Consensus       369 ~S  370 (492)
T KOG1190|consen  369 LS  370 (492)
T ss_pred             ec
Confidence            64

>KOG0120|consensus

Probab=97.55  E-value=0.00014  Score=69.02  Aligned_cols=114  Identities=19%  Similarity=0.312  Sum_probs=76.7

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccCCCC---C--CCcEE-------EEecCCCCC-------C---------
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPD---V--DECTI-------YVEKLPPEA-------E---------  209 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~---~--~~~~l-------~V~nLp~~~-------t---------  209 (299)
                      .+......|+..+|+..+.+..+.+.++..-.....   .  +....       -..+.|..+       +         
T Consensus       339 ~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~E  418 (500)
T KOG0120|consen  339 CDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEE  418 (500)
T ss_pred             eCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHH
Confidence            345666788889999999999988877643211110   0  00001       111222111       1         


Q ss_pred             ----HHHHHHHhhcCCceEEEEeeccCCC---CCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         210 ----HDYIESVFSKYGKVTYVSLPKFKST---GKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       210 ----~e~L~~~F~~~G~i~~v~i~~~~~~---g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                          -|+++.-+++||.|..|.++++...   .-..|-.||+|.+.++++.|.++ |+|  ..|.++.+...
T Consensus       419 yeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~-L~G--rKF~nRtVvts  487 (500)
T KOG0120|consen  419 YEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEE-LTG--RKFANRTVVAS  487 (500)
T ss_pred             HHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHH-ccC--ceeCCcEEEEE
Confidence                2567778899999999999987212   22345679999999999999999 999  88999987654

>KOG0147|consensus

Probab=97.55  E-value=3.1e-05  Score=72.79  Aligned_cols=81  Identities=22%  Similarity=0.299  Sum_probs=73.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..+.+++|+-.++...+.-+|.++|+.+|.|..|+++.|+.++.++|.|||+|.+.++...||.  |.|  .-+.|.++.
T Consensus       176 ERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia--LsG--qrllg~pv~  251 (549)
T KOG0147|consen  176 ERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA--LSG--QRLLGVPVI  251 (549)
T ss_pred             HHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh--hcC--CcccCceeE
Confidence            4556899999999999999999999999999999999999999999999999999999999995  788  777799988


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |+...
T Consensus       252 vq~sE  256 (549)
T KOG0147|consen  252 VQLSE  256 (549)
T ss_pred             ecccH
Confidence            87753

>KOG1457|consensus

Probab=97.54  E-value=9.6e-05  Score=62.18  Aligned_cols=60  Identities=23%  Similarity=0.453  Sum_probs=50.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCC
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNP  261 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng  261 (299)
                      .|+||.||.+++++++|+.+|+.|.....++|...  .|  .+.+|++|++.+.|..|+.. ++|
T Consensus       211 stlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~~~~~at~am~~-lqg  270 (284)
T KOG1457|consen  211 STLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADFEEIEQATDAMNH-LQG  270 (284)
T ss_pred             hhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecHHHHHHHHHHHHH-hhc
Confidence            47999999999999999999999987776666421  33  45799999999999999998 887

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

Probab=97.45  E-value=0.00043  Score=45.64  Aligned_cols=52  Identities=21%  Similarity=0.565  Sum_probs=41.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHH
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL  255 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al  255 (299)
                      +.|-|.|+|++..+. +...|..||+|..+.+...      ..+.||.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            468899999876644 5558889999999998722      237999999999999985

>KOG1995|consensus

Probab=97.42  E-value=0.00019  Score=64.38  Aligned_cols=80  Identities=23%  Similarity=0.277  Sum_probs=69.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEE--------EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCC
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY--------VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPP  264 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~--------v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~  264 (299)
                      .....+|||.++|..+++++|.++|.++|.|..        |.+-+++.|+..+|-|-|.|.+...|+.|+.- +++  .
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~-~ag--k  139 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEW-FAG--K  139 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhh-hcc--c
Confidence            345678999999999999999999999997753        66778888999999999999999999999998 888  7


Q ss_pred             CCCCceEEEEe
Q psy3930         265 DYQSSILTTTS  275 (299)
Q Consensus       265 ~~~g~~l~v~~  275 (299)
                      .+.+..|+|..
T Consensus       140 df~gn~ikvs~  150 (351)
T KOG1995|consen  140 DFCGNTIKVSL  150 (351)
T ss_pred             cccCCCchhhh
Confidence            78887777643

>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=97.41  E-value=0.001  Score=47.62  Aligned_cols=67  Identities=24%  Similarity=0.362  Sum_probs=44.8

Q ss_pred             cEEEEecCCCCCCHH----HHHHHhhcCC-ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         197 CTIYVEKLPPEAEHD----YIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e----~L~~~F~~~G-~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ..|||.|||.+.+..    -|+.++..+| .|..|.          .+.|.|.|.+++.|.+|.+. |+|  -++-|..|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KR-meg--EdVfG~kI   69 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKR-MEG--EDVFGNKI   69 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHH-HTT----SSSS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHh-hcc--cccccceE
Confidence            368999999988765    4567777887 566552          24699999999999999999 787  67778888


Q ss_pred             EEEee
Q psy3930         272 TTTSR  276 (299)
Q Consensus       272 ~v~~k  276 (299)
                      .|...
T Consensus        70 ~v~~~   74 (90)
T PF11608_consen   70 SVSFS   74 (90)
T ss_dssp             EEESS
T ss_pred             EEEEc
Confidence            77654

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

>KOG1190|consensus

Probab=97.36  E-value=0.001  Score=60.69  Aligned_cols=111  Identities=17%  Similarity=0.142  Sum_probs=79.2

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecc---------cC--------------------CC----CCCCcEEEEecC
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVV---------QD--------------------KP----DVDECTIYVEKL  204 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~---------~~--------------------~~----~~~~~~l~V~nL  204 (299)
                      .|...|+-|+..+++..+.++.++|...+-.         ++                    +.    -+...++.+.|+
T Consensus       343 sd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsni  422 (492)
T KOG1190|consen  343 SDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNI  422 (492)
T ss_pred             cchhHHHHHHHHhhcceecCceEEEeeccCccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccC
Confidence            5788899999999999999998888654310         00                    00    145568999999


Q ss_pred             CCCCCHHHHHHHhhcCCce-EEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         205 PPEAEHDYIESVFSKYGKV-TYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       205 p~~~t~e~L~~~F~~~G~i-~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      |+++++++|+..|..-|-. ....+     -++.+.++++.+.+.++|..|+-.+.| + ....+..++|..
T Consensus       423 p~svsee~lk~~f~~~g~~vkafkf-----f~kd~kmal~q~~sveeA~~ali~~hn-h-~lgen~hlRvSF  487 (492)
T KOG1190|consen  423 PPSVSEEDLKNLFQEPGGQVKAFKF-----FQKDRKMALPQLESVEEAIQALIDLHN-H-YLGENHHLRVSF  487 (492)
T ss_pred             CcccchhHHHHhhhcCCceEEeeee-----cCCCcceeecccCChhHhhhhcccccc-c-cCCCCceEEEEe
Confidence            9999999999999988754 43333     222345899999999999999988333 2 222444666543

>KOG2314|consensus

Probab=97.33  E-value=0.00037  Score=65.91  Aligned_cols=72  Identities=29%  Similarity=0.453  Sum_probs=58.3

Q ss_pred             CcEEEEecCCCCC--C----HHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCc
Q psy3930         196 ECTIYVEKLPPEA--E----HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       196 ~~~l~V~nLp~~~--t----~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      ...|+|.|+|---  .    ..-|..+|+++|++....+|.+. .|.++||.|++|.+..+|+.|++. +||+.+..++.
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e-~ggtkG~lf~E~~~~~~A~~aVK~-l~G~~ldknHt  135 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDE-EGGTKGYLFVEYASMRDAKKAVKS-LNGKRLDKNHT  135 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCc-cCCeeeEEEEEecChhhHHHHHHh-cccceecccce
Confidence            4578899998532  2    34567899999999999999887 455999999999999999999999 99976665443

>KOG4210|consensus

Probab=97.31  E-value=0.00054  Score=61.31  Aligned_cols=76  Identities=29%  Similarity=0.388  Sum_probs=63.6

Q ss_pred             CCcEEE-EecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         195 DECTIY-VEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       195 ~~~~l~-V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++| |++++.++++++|+..|..+|.|..++++.+..+|..+|||||+|.....+..++..  +.  ..+.++++.+
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~--~~--~~~~~~~~~~  258 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND--QT--RSIGGRPLRL  258 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc--cc--CcccCccccc
Confidence            345566 999999999999999999999999999999999999999999999999988888773  22  4455666555


Q ss_pred             E
Q psy3930         274 T  274 (299)
Q Consensus       274 ~  274 (299)
                      .
T Consensus       259 ~  259 (285)
T KOG4210|consen  259 E  259 (285)
T ss_pred             c
Confidence            3

>KOG0112|consensus

Probab=97.24  E-value=0.00037  Score=69.20  Aligned_cols=144  Identities=15%  Similarity=0.199  Sum_probs=94.8

Q ss_pred             HHHHHhhhcCCCeee-eeeecccccccCCC-----------------CHHHHHHHHHhcCccccccccceeeeeecccCC
Q psy3930         130 RFFSQLLQESPEIEV-SVFLKCNKLARLTH-----------------DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDK  191 (299)
Q Consensus       130 ~fl~~~~~~~~~~~l-~~f~~F~~i~~~~~-----------------~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~  191 (299)
                      .|+.++-.+.+.-.| -+|..+|.+.++.-                 +...+-.|.-.+.+..|.....++....+    
T Consensus       375 Lf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~~----  450 (975)
T KOG0112|consen  375 LFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQP----  450 (975)
T ss_pred             hhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccccc----
Confidence            455555555555556 56778877776651                 11111222222222333333333322211    


Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       192 ~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      .......+++++|++++....|...|..||.|..|.+-.    |.  .|+||.|++...|+.|+.. +.|..++...+.+
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h----gq--~yayi~yes~~~aq~a~~~-~rgap~G~P~~r~  523 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH----GQ--PYAYIQYESPPAAQAATHD-MRGAPLGGPPRRL  523 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc----CC--cceeeecccCccchhhHHH-HhcCcCCCCCccc
Confidence            234457899999999999999999999999999988743    32  3899999999999999999 8887888778887


Q ss_pred             EEEeecccCCCCC
Q psy3930         272 TTTSRLSFGITPL  284 (299)
Q Consensus       272 ~v~~k~~~~~~~r  284 (299)
                      +|-..-..+++|.
T Consensus       524 rvdla~~~~~~Pq  536 (975)
T KOG0112|consen  524 RVDLASPPGATPQ  536 (975)
T ss_pred             ccccccCCCCChh
Confidence            7766544444443

>KOG0129|consensus

Probab=97.19  E-value=0.0011  Score=62.28  Aligned_cols=65  Identities=23%  Similarity=0.286  Sum_probs=60.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhh-cCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHh
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFS-KYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL  257 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~-~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~  257 (299)
                      ....+|||||+||.-++-++|..+|+ -||.|.++-|-.|..-+.++|-|=|.|.+..+-.+||.+
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            45578999999999999999999999 599999999999976788999999999999999999987

>KOG1548|consensus

Probab=97.18  E-value=0.0037  Score=56.05  Aligned_cols=109  Identities=18%  Similarity=0.258  Sum_probs=82.7

Q ss_pred             HHHHHHHHHhcCccccccccceeeeeecc--------------------------------cCC----CCCCCcEEEEec
Q psy3930         160 PDDVVKALRKSKLLEVTEDGTKVRRTVVV--------------------------------QDK----PDVDECTIYVEK  203 (299)
Q Consensus       160 ~~~a~~Al~~~~~~~~~~~~~~v~r~~~~--------------------------------~~~----~~~~~~~l~V~n  203 (299)
                      .+++.-|++.++...+.+..++|.++.-.                                ++.    .....++|.+.|
T Consensus       193 ~ESVeLA~~ilDe~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn  272 (382)
T KOG1548|consen  193 RESVELAIKILDEDELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKN  272 (382)
T ss_pred             ccHHHHHHHHhCcccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeee
Confidence            57778888888998898988888765310                                000    023467899988


Q ss_pred             CCC----CCC-------HHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         204 LPP----EAE-------HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       204 Lp~----~~t-------~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      +=.    ..+       +++|++-+.+||.|..|.+--    ..+.|.+-|.|.+.++|..||+. |+|  ..|.|+.|.
T Consensus       273 ~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~-m~G--R~fdgRql~  345 (382)
T KOG1548|consen  273 MFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQT-MDG--RWFDGRQLT  345 (382)
T ss_pred             cCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHH-hcC--eeecceEEE
Confidence            732    122       467788899999999997753    23467899999999999999999 999  899999998


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      ..+
T Consensus       346 A~i  348 (382)
T KOG1548|consen  346 ASI  348 (382)
T ss_pred             EEE
Confidence            766

>KOG2590|consensus

Probab=97.04  E-value=0.00019  Score=67.31  Aligned_cols=160  Identities=18%  Similarity=0.189  Sum_probs=111.6

Q ss_pred             CCCcCcChHHHHhhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeeccccccccccccccccc-c
Q psy3930           7 DSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGNIIRHFLVPISMETEA-S   85 (299)
Q Consensus         7 ~~nl~~d~~l~~~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr~~~~~~~~p~~~~~~~-~   85 (299)
                      +.+++.+.|.-.+++..+|.|=.....|.|.+..+.+......+.--+..++.-.+..+.+-+..  ...|.+..... .
T Consensus       204 ~n~~~~~~~~~~~~~n~~~~~~~~ss~~q~~k~~~~~~~~~q~~~G~~~~~~~l~~~~~~~~k~~--~~~~~~~~~~~~~  281 (448)
T KOG2590|consen  204 PNSVPGQRGQNQHHDNSSQNPHHNSSGFQRVKNMNGNSNHYQYSRGFSNSLPDLGNQNRNRVKNS--SYRPAPQKSQSGE  281 (448)
T ss_pred             cCCCCccccccccccccCcCCCCCCCCccchhhcccCccccccCCCcCCccccccCccccccccc--ccccchhhcCCCC
Confidence            46788899999999999999999999999999999998888888876666776666666655431  12232222211 1


Q ss_pred             ccccCccccccccCCCCcCchHHHHHHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCCCCHHHHHH
Q psy3930          86 DNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVK  165 (299)
Q Consensus        86 ~~~~~~~~~~~~~~~k~r~r~~~~~~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~~~~~~a~~  165 (299)
                      +..+-+...-.....-     ...-+-+.++++|||+.+||.+|.|++..     +++|++...|.++.+++.|.+.+.+
T Consensus       282 p~~~~~~~~~~s~~pi-----~~~~~~~~~~ie~~FSeE~~~~d~~n~~k-----~~~l~~ia~F~r~ad~s~d~nli~~  351 (448)
T KOG2590|consen  282 PIQPGDKNQIPSVQPI-----GNVIAFIQEPIEFYFSEENLQRDRFNREK-----FVPLRVIAKFKRVADLSSDINLILA  351 (448)
T ss_pred             ccccCccccCCCcccc-----cccccccccccccccchHHHhhhhhhhcc-----cchhhhhhhhhhhhhcccCHHHHHH
Confidence            1111111100000000     11113456799999999999988877655     5669999999999999999999999


Q ss_pred             HHHhcCccccccc
Q psy3930         166 ALRKSKLLEVTED  178 (299)
Q Consensus       166 Al~~~~~~~~~~~  178 (299)
                      ||++.-.+++.+.
T Consensus       352 alr~s~ive~~~d  364 (448)
T KOG2590|consen  352 ALRNSLIVEETGD  364 (448)
T ss_pred             HHhhhhhhhccch
Confidence            9998877665544

>KOG3152|consensus

Probab=97.04  E-value=0.00048  Score=59.19  Aligned_cols=71  Identities=27%  Similarity=0.407  Sum_probs=56.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCC--------CCc----ceEEEEEecCHHHHHHHHHhcCCCCC
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKST--------GKL----KGFAFVEFSTKEEAAKALELGLNPCP  263 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~--------g~~----kg~~fV~F~~~~~A~~Al~~~lng~~  263 (299)
                      ...||+++||+.+...-|+++|+.||.|-.|.+.....+        |..    -.-|+|+|.+...|..+... |||  
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~-Lnn--  150 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAEL-LNN--  150 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHH-hCC--
Confidence            468999999999999999999999999999988654332        221    22379999999999999998 887  


Q ss_pred             CCCCCc
Q psy3930         264 PDYQSS  269 (299)
Q Consensus       264 ~~~~g~  269 (299)
                      ..++|+
T Consensus       151 ~~Iggk  156 (278)
T KOG3152|consen  151 TPIGGK  156 (278)
T ss_pred             CccCCC
Confidence            444444

>KOG0128|consensus

Probab=97.00  E-value=0.00033  Score=69.20  Aligned_cols=133  Identities=18%  Similarity=0.201  Sum_probs=89.3

Q ss_pred             HHHHHhhhcCCCeee-eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeec--------ccCCCCCCCcEEE
Q psy3930         130 RFFSQLLQESPEIEV-SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVV--------VQDKPDVDECTIY  200 (299)
Q Consensus       130 ~fl~~~~~~~~~~~l-~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~--------~~~~~~~~~~~l~  200 (299)
                      .|++++..+....++ ..|..++.+.       ..+.++ ..+...+-|..- +....+        ...........++
T Consensus       670 ~fvsnl~~~~~~~dl~~~~~~~~~~e-------~vqi~~-h~n~~~~rG~~Y-~~F~~~~~~~aaV~f~d~~~~gK~~v~  740 (881)
T KOG0128|consen  670 IFVSNLSPKMSEEDLSERFSPSGTIE-------VVQIVI-HKNEKRFRGKAY-VEFLKPEHAGAAVAFRDSCFFGKISVA  740 (881)
T ss_pred             HHHhhcchhhcCchhhhhcCccchhh-------hHHHHH-Hhhcccccccee-eEeecCCchhhhhhhhhhhhhhhhhhh
Confidence            477777766667777 4577777753       333443 222222222211 111111        0111122356799


Q ss_pred             EecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         201 VEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       201 V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      |.|.|+..|.++++.++..+|.+..++++..+ .|.++|.++|.|.++.+|.+++.. ..+  ..++...+.+.+
T Consensus       741 i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s-~d~--~~~rE~~~~v~v  811 (881)
T KOG0128|consen  741 ISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVAS-VDV--AGKRENNGEVQV  811 (881)
T ss_pred             eeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhccc-chh--hhhhhcCccccc
Confidence            99999999999999999999999999988877 899999999999999999999877 555  444455555544

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.78  E-value=0.0042  Score=55.45  Aligned_cols=77  Identities=23%  Similarity=0.458  Sum_probs=57.7

Q ss_pred             CcEEEEecCCCCCCHHH----H--HHHhhcCCceEEEEeeccCCC-CCcce-E-EEEEecCHHHHHHHHHhcCCCCCCCC
Q psy3930         196 ECTIYVEKLPPEAEHDY----I--ESVFSKYGKVTYVSLPKFKST-GKLKG-F-AFVEFSTKEEAAKALELGLNPCPPDY  266 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~----L--~~~F~~~G~i~~v~i~~~~~~-g~~kg-~-~fV~F~~~~~A~~Al~~~lng~~~~~  266 (299)
                      ..-+||-+||+.+..|+    |  .++|++||.|..|.+-+...+ ....+ + .||+|.+.++|.+||.+ .+|  .-.
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~-vDg--s~~  190 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAE-VDG--SLL  190 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHH-hcc--ccc
Confidence            35689999999876665    2  489999999998877553211 11112 2 49999999999999999 888  777


Q ss_pred             CCceEEEEe
Q psy3930         267 QSSILTTTS  275 (299)
Q Consensus       267 ~g~~l~v~~  275 (299)
                      +|+.|+...
T Consensus       191 DGr~lkatY  199 (480)
T COG5175         191 DGRVLKATY  199 (480)
T ss_pred             cCceEeeec
Confidence            899886643

>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=96.74  E-value=0.0084  Score=44.92  Aligned_cols=72  Identities=17%  Similarity=0.254  Sum_probs=46.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEE-eeccC------CCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCC
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVS-LPKFK------STGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQS  268 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~-i~~~~------~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g  268 (299)
                      .+.|.|-|+|+. .-..+...|++||+|.... +.++.      .......+-.|+|.++.+|.+||..  ||  ..+.|
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~--NG--~i~~g   80 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK--NG--TIFSG   80 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT--TT--EEETT
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh--CC--eEEcC
Confidence            467889999988 5567778899999987764 11110      0011234789999999999999995  77  66767


Q ss_pred             ceEE
Q psy3930         269 SILT  272 (299)
Q Consensus       269 ~~l~  272 (299)
                      ..+.
T Consensus        81 ~~mv   84 (100)
T PF05172_consen   81 SLMV   84 (100)
T ss_dssp             CEEE
T ss_pred             cEEE
Confidence            5544

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=96.70  E-value=0.007  Score=52.20  Aligned_cols=101  Identities=21%  Similarity=0.175  Sum_probs=74.9

Q ss_pred             HHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEe
Q psy3930         166 ALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEF  245 (299)
Q Consensus       166 Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F  245 (299)
                      |-..+++....++.++|+.+..         ..|||.||+..++.+.+...|+.||+|....+..|. .|+..+-++|+|
T Consensus        10 ak~eLd~~~~~~~~lr~rfa~~---------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~   79 (275)
T KOG0115|consen   10 AKRELDGRFPKGRSLRVRFAMH---------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEF   79 (275)
T ss_pred             HHHhcCCCCCCCCceEEEeecc---------ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhh
Confidence            3335566667777888876542         579999999999999999999999999876555554 677777899999


Q ss_pred             cCHHHHHHHHHhcC-CCCCCCCCCceEEEEee
Q psy3930         246 STKEEAAKALELGL-NPCPPDYQSSILTTTSR  276 (299)
Q Consensus       246 ~~~~~A~~Al~~~l-ng~~~~~~g~~l~v~~k  276 (299)
                      ...-.|.+|+.... .|......+++..|.+-
T Consensus        80 ~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   80 AKKPNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             hcchhHHHHHHHhccCccccCCCCCccCCChh
Confidence            99999999998732 33234445666555443

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.45  E-value=0.012  Score=46.84  Aligned_cols=75  Identities=21%  Similarity=0.291  Sum_probs=52.2

Q ss_pred             CCCCcEEEEecCCC------CCC---HHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCC
Q psy3930         193 DVDECTIYVEKLPP------EAE---HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCP  263 (299)
Q Consensus       193 ~~~~~~l~V~nLp~------~~t---~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~  263 (299)
                      .+...||.|.-..+      ...   -.+|-+.|..||.+.=||++-+        .-+|+|.+..+|.+|+.  ++|  
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals--~dg--   91 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS--LDG--   91 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH--GCC--
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc--cCC--
Confidence            45567777765551      122   2367788899999988888754        37899999999999999  587  


Q ss_pred             CCCCCceEEEEeec-cc
Q psy3930         264 PDYQSSILTTTSRL-SF  279 (299)
Q Consensus       264 ~~~~g~~l~v~~k~-~~  279 (299)
                      ..++|+.+.++.|. .|
T Consensus        92 ~~v~g~~l~i~LKtpdW  108 (146)
T PF08952_consen   92 IQVNGRTLKIRLKTPDW  108 (146)
T ss_dssp             SEETTEEEEEEE-----
T ss_pred             cEECCEEEEEEeCCccH
Confidence            89999999999985 45

; PDB: 1UFW_A 2DNR_A.

>KOG1365|consensus

Probab=96.39  E-value=0.008  Score=54.65  Aligned_cols=76  Identities=18%  Similarity=0.259  Sum_probs=59.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCC-ceEE--EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYG-KVTY--VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G-~i~~--v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..+|-+.|||.+++.++|-.+|+.|. .|..  |.++.+. .|+..|-|||+|.+.++|..|... ...  ...+.+-|.
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk-~hk--~~mk~RYiE  355 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQK-CHK--KLMKSRYIE  355 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHH-HHH--hhcccceEE
Confidence            45788999999999999999999987 4544  7777664 899999999999999999999887 322  233566666


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |-.
T Consensus       356 vfp  358 (508)
T KOG1365|consen  356 VFP  358 (508)
T ss_pred             Eee
Confidence            644

>KOG1456|consensus

Probab=96.30  E-value=0.045  Score=49.79  Aligned_cols=119  Identities=16%  Similarity=0.176  Sum_probs=82.7

Q ss_pred             eeeecccccccCC-------------CCHHHHHHHHHhcCccccccccceeeeeecc-----------------c-----
Q psy3930         145 SVFLKCNKLARLT-------------HDPDDVVKALRKSKLLEVTEDGTKVRRTVVV-----------------Q-----  189 (299)
Q Consensus       145 ~~f~~F~~i~~~~-------------~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~-----------------~-----  189 (299)
                      .+|.-||.+..+.             -|..+.++|+..+|+..+-+..+.+.-++..                 +     
T Consensus       307 Nl~ClYGNV~rvkFmkTk~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSfKdys~S  386 (494)
T KOG1456|consen  307 NLFCLYGNVERVKFMKTKPGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQNFVSPVQPFLLPDGSPSFKDYSGS  386 (494)
T ss_pred             hhhhhcCceeeEEEeecccceeEEEcCcHHHHHHHHHHhccCccccceEEEeeccccccccCCceecCCCCcchhhcccc
Confidence            3456666655544             5688889999999998888877765433210                 0     


Q ss_pred             --------C-----CCCCCCcEEEEecCCCCCCHHHHHHHhhcCC-ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHH
Q psy3930         190 --------D-----KPDVDECTIYVEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL  255 (299)
Q Consensus       190 --------~-----~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G-~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al  255 (299)
                              +     +-....++|..-|.|..+||+.|..+|..-+ ....|++-..+ +-++ .-|.++|++.++|..||
T Consensus       387 kNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvFp~k-serS-ssGllEfe~~s~Aveal  464 (494)
T KOG1456|consen  387 KNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVFPLK-SERS-SSGLLEFENKSDAVEAL  464 (494)
T ss_pred             cccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEeeccc-cccc-ccceeeeehHHHHHHHH
Confidence                    0     0135678899999999999999999998766 34455554433 2222 24899999999999999


Q ss_pred             HhcCCCCCCCC
Q psy3930         256 ELGLNPCPPDY  266 (299)
Q Consensus       256 ~~~lng~~~~~  266 (299)
                      .. +|-.....
T Consensus       465 ~~-~NH~pi~~  474 (494)
T KOG1456|consen  465 MK-LNHYPIEG  474 (494)
T ss_pred             HH-hccccccC
Confidence            99 77544433

>KOG4307|consensus

Probab=96.30  E-value=0.013  Score=57.15  Aligned_cols=76  Identities=17%  Similarity=0.261  Sum_probs=62.7

Q ss_pred             Cc-EEEEecCCCCCCHHHHHHHhhcCCceE-EEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         196 EC-TIYVEKLPPEAEHDYIESVFSKYGKVT-YVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       196 ~~-~l~V~nLp~~~t~e~L~~~F~~~G~i~-~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ++ .|-+.|+|.+++-+||-++|..|-.+- +|++.++ ..|...|-|-|.|++.++|.+|... +++  ..+..+.+.+
T Consensus       866 Gp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~d-l~~--~~i~nr~V~l  941 (944)
T KOG4307|consen  866 GPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMD-LDG--QKIRNRVVSL  941 (944)
T ss_pred             CCeEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhc-ccc--CcccceeEEE
Confidence            45 678899999999999999999997543 4555554 4888899999999999999999998 888  7777777766


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      .+
T Consensus       942 ~i  943 (944)
T KOG4307|consen  942 RI  943 (944)
T ss_pred             Ee
Confidence            53

>KOG0129|consensus

Probab=96.15  E-value=0.012  Score=55.50  Aligned_cols=64  Identities=25%  Similarity=0.420  Sum_probs=49.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccC-CCC--Ccce---EEEEEecCHHHHHHHHHh
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFK-STG--KLKG---FAFVEFSTKEEAAKALEL  257 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~-~~g--~~kg---~~fV~F~~~~~A~~Al~~  257 (299)
                      ..-.+.||||+||++++++.|...|..||.+ .|..+... ..+  -.+|   |+|+-|+++.+.+.-+.+
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~a  325 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSA  325 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHH
Confidence            4456889999999999999999999999975 34454211 111  2455   999999999888887776

>KOG1456|consensus

Probab=96.02  E-value=0.041  Score=50.03  Aligned_cols=75  Identities=25%  Similarity=0.299  Sum_probs=63.2

Q ss_pred             CCCcEEEEecCCCC-CCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         194 VDECTIYVEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       194 ~~~~~l~V~nLp~~-~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..++.+.|-||... +.-+.|..+|-.||.|..|.+++.+     .|.|.|+..+..+.++|+.. ||+  ..+-|..|.
T Consensus       285 ~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~h-Lnn--~~lfG~kl~  356 (494)
T KOG1456|consen  285 APGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTH-LNN--IPLFGGKLN  356 (494)
T ss_pred             CCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHH-hcc--CccccceEE
Confidence            35688999999876 6788999999999999999999876     45799999999999999999 887  444677777


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      +.+.
T Consensus       357 v~~S  360 (494)
T KOG1456|consen  357 VCVS  360 (494)
T ss_pred             Eeec
Confidence            7654

>KOG4849|consensus

Probab=95.86  E-value=0.0095  Score=53.51  Aligned_cols=62  Identities=15%  Similarity=0.284  Sum_probs=53.8

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCC--ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHh
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL  257 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G--~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~  257 (299)
                      ...+|||||-+.+|.++|.+.....|  .+..+.+-.++.+|+++|||.|...+..+.++.++.
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~Mei  143 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEI  143 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHh
Confidence            35799999999999999999988777  566677777777999999999999998888888887

>PF09421 FRQ: Frequency clock protein; InterPro: IPR018554 The frequency clock protein, is the central component of the frq-based circadian negative feedback loop, regulates various aspects of the circadian clock in Neurospora crassa []

Probab=95.80  E-value=0.0062  Score=61.76  Aligned_cols=50  Identities=20%  Similarity=0.276  Sum_probs=45.5

Q ss_pred             hccCCCEEeeeeecchhhhhccCCHHHHHHHHh-cCcceeeccCcceeecc
Q psy3930          20 LQESPEIEVSVFLKCNKLARLTHDPDDVVKALR-KSKLLEVTEDGTKVKGN   69 (299)
Q Consensus        20 ~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~-~s~~~~v~~~~~~vrr~   69 (299)
                      .+.+|||.|.+||+--.|--|..+++.|..|+. .|+.+||+.||.+||=+
T Consensus       473 pDaeGWVYLNLL~NmAQLHiiNVTPdFVRsAV~E~StKfQLSpDGrKIRWR  523 (989)
T PF09421_consen  473 PDAEGWVYLNLLCNMAQLHIINVTPDFVRSAVSEKSTKFQLSPDGRKIRWR  523 (989)
T ss_pred             cccccceehHHHHHHHHHHhhccCHHHHHHHHHhcccceeeCCCCCeeeec
Confidence            366799999999999999989999999999997 88999999999999844

This protein has been shown to interact with itself via a coiled-coil [].

>KOG0128|consensus

Probab=95.72  E-value=0.00071  Score=66.95  Aligned_cols=64  Identities=28%  Similarity=0.467  Sum_probs=57.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHh
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL  257 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~  257 (299)
                      .+.+++|++||+..+.+++|...|..+|.+..+++.....+++.+|.||++|..++.|.+|+..
T Consensus       665 R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f  728 (881)
T KOG0128|consen  665 RDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAF  728 (881)
T ss_pred             HHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhh
Confidence            3457899999999999999999999999988888776666899999999999999999999986

>KOG1365|consensus

Probab=95.37  E-value=0.05  Score=49.61  Aligned_cols=60  Identities=27%  Similarity=0.274  Sum_probs=48.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcC----CceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHh
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKY----GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL  257 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~----G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~  257 (299)
                      -.|-+.|||++++..++.++|..-    |....|-+++.. +|+..|-|||.|..+++|+.|+.+
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k  225 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK  225 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH
Confidence            456778999999999999999631    244555555543 788888899999999999999987

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

Probab=95.32  E-value=0.12  Score=35.07  Aligned_cols=53  Identities=25%  Similarity=0.233  Sum_probs=43.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcC---CceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHh
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKY---GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL  257 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~---G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~  257 (299)
                      ..|+|.|+. +.+-++|+.+|..|   .....|..+-|.       -|-|.|.+.+.|.+||.+
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~   61 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVA   61 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHc
Confidence            579999985 58889999999998   124567666664       389999999999999986

>KOG4454|consensus

Probab=95.28  E-value=0.0059  Score=51.51  Aligned_cols=86  Identities=22%  Similarity=0.305  Sum_probs=70.5

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEec----CCCCCCHHHHHHHhhcCCceEEEEeeccCCC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEK----LPPEAEHDYIESVFSKYGKVTYVSLPKFKST  234 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~n----Lp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~  234 (299)
                      ++..+.-|++-+|++.+.++++.+               +++.|+    |....+++.+...|+.-|++..+++.++. .
T Consensus        58 ~E~sv~~a~~L~ng~~l~~~e~q~---------------~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~-d  121 (267)
T KOG4454|consen   58 NENSVQLAGQLENGDDLEEDEEQR---------------TLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDN-D  121 (267)
T ss_pred             cccchhhhhhhcccchhccchhhc---------------ccccCCCcchhhhhcchhhheeeecccCCCCCccccccc-c
Confidence            366778899999999998888765               344454    66778999999999999999999999987 6


Q ss_pred             CCcceEEEEEecCHHHHHHHHHhcCCC
Q psy3930         235 GKLKGFAFVEFSTKEEAAKALELGLNP  261 (299)
Q Consensus       235 g~~kg~~fV~F~~~~~A~~Al~~~lng  261 (299)
                      |+.+.++|+.+....+.-.++.. ..|
T Consensus       122 ~rnrn~~~~~~qr~~~~P~~~~~-y~~  147 (267)
T KOG4454|consen  122 GRNRNFGFVTYQRLCAVPFALDL-YQG  147 (267)
T ss_pred             CCccCccchhhhhhhcCcHHhhh-hcc
Confidence            88899999999887777777776 554

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

Probab=94.72  E-value=0.17  Score=36.27  Aligned_cols=52  Identities=25%  Similarity=0.409  Sum_probs=38.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHh
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL  257 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~  257 (299)
                      +..||+ +|......||.++|+.||.| .|..+.+.       -|||.....+.|..|+..
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~   61 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNT   61 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHH
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHH
Confidence            445555 99999999999999999976 45555443       599999999999999887

; 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.

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

Probab=94.58  E-value=0.032  Score=48.29  Aligned_cols=89  Identities=19%  Similarity=0.233  Sum_probs=65.2

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeee----cccC------------------CCCCCCcEEEEecCCCCCCHHHHHH
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTV----VVQD------------------KPDVDECTIYVEKLPPEAEHDYIES  215 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~----~~~~------------------~~~~~~~~l~V~nLp~~~t~e~L~~  215 (299)
                      .+.+++..|+..+++..+.++.+.|....    +...                  ........+++++++..++...+..
T Consensus       165 ~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (306)
T COG0724         165 ESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELAD  244 (306)
T ss_pred             cCHHHHHHHHHHcCCCeECCceeEeeccccccccccccccccchhhhccccccccccccccceeeccccccccchhHHHH
Confidence            56899999999999999999999888742    1111                  1134567899999999999999999


Q ss_pred             HhhcCCceEEEEeeccCCCCCcceEEEEEec
Q psy3930         216 VFSKYGKVTYVSLPKFKSTGKLKGFAFVEFS  246 (299)
Q Consensus       216 ~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~  246 (299)
                      .|..+|.+....+.............++.+.
T Consensus       245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  275 (306)
T COG0724         245 LFKSRGDIVRASLPPSKDGKIPKSRSFVGNE  275 (306)
T ss_pred             hccccccceeeeccCCCCCcccccccccchh
Confidence            9999999977777655433333333444333

>KOG2202|consensus

Probab=94.24  E-value=0.025  Score=48.85  Aligned_cols=62  Identities=24%  Similarity=0.342  Sum_probs=48.6

Q ss_pred             HHHHHHhh-cCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         211 DYIESVFS-KYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       211 e~L~~~F~-~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      ++|...|+ +||+|..+.+-.+. .-...|=+||.|...++|++|++. |||  ..+.|++|.....
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~-lnn--Rw~~G~pi~ae~~  145 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALED-LNN--RWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHH-HcC--ccccCCcceeeec
Confidence            45555555 89999988665432 334567799999999999999999 888  8999999988764

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

Probab=93.64  E-value=0.012  Score=47.34  Aligned_cols=31  Identities=13%  Similarity=0.062  Sum_probs=26.4

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .+.++|++|++.+++.++.++.++|..+.+.
T Consensus        84 ~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~  114 (144)
T PLN03134         84 NDEGAATAAISEMDGKELNGRHIRVNPANDR  114 (144)
T ss_pred             CCHHHHHHHHHHcCCCEECCEEEEEEeCCcC
Confidence            4589999999999999999999999876543

>KOG4676|consensus

Probab=93.47  E-value=0.13  Score=47.05  Aligned_cols=76  Identities=20%  Similarity=0.294  Sum_probs=56.8

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCC---CCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKS---TGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~---~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ..|.|.||.++++.+++..+|+..|.|..+++..+..   -......|||.|.+...+..|--. .|   ..+-++.|-|
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhL-tn---tvfvdraliv   83 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHL-TN---TVFVDRALIV   83 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhh-cc---ceeeeeeEEE
Confidence            4789999999999999999999999999998765321   122445899999998888777553 55   4555555555


Q ss_pred             Eee
Q psy3930         274 TSR  276 (299)
Q Consensus       274 ~~k  276 (299)
                      .+-
T Consensus        84 ~p~   86 (479)
T KOG4676|consen   84 RPY   86 (479)
T ss_pred             Eec
Confidence            443

>KOG0112|consensus

Probab=93.03  E-value=0.034  Score=55.77  Aligned_cols=68  Identities=18%  Similarity=0.166  Sum_probs=57.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCC
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPC  262 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~  262 (299)
                      ....++||+||++..+++.+|+..|..+|.+..|+|-+.. -+....||||.|.+...+-.|... +.|.
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e-~s~~  436 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFE-ESGP  436 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchh-hcCC
Confidence            3557899999999999999999999999999999987654 344455899999999999888887 6663

>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=92.52  E-value=0.25  Score=41.05  Aligned_cols=68  Identities=15%  Similarity=0.157  Sum_probs=43.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhc-CCce---EEEEeeccC-CC-CCcceEEEEEecCHHHHHHHHHhcCCCCC
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSK-YGKV---TYVSLPKFK-ST-GKLKGFAFVEFSTKEEAAKALELGLNPCP  263 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~-~G~i---~~v~i~~~~-~~-g~~kg~~fV~F~~~~~A~~Al~~~lng~~  263 (299)
                      ....|.|++||++.|++++.+.++. +|.-   .++.-.... .. -....-|||.|.+.+++...... ++|+.
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~-~~g~~   79 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDR-FDGHV   79 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHH-CTTEE
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHh-cCCcE
Confidence            3568999999999999999997776 6655   344311211 11 11233489999999999999998 88843

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.

>KOG0111|consensus

Probab=92.28  E-value=0.043  Score=46.40  Aligned_cols=46  Identities=11%  Similarity=0.174  Sum_probs=36.6

Q ss_pred             eeeecccccccCC------------------CCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         145 SVFLKCNKLARLT------------------HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       145 ~~f~~F~~i~~~~------------------~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      ..|..||.|+.+.                  .-.++|++||.++|.-++.++.++|..+.|..-
T Consensus        29 aAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~ki   92 (298)
T KOG0111|consen   29 AAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPEKI   92 (298)
T ss_pred             hccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCccc
Confidence            4566677666655                  337889999999999999999999998877654

>PF13893 RRM_5: RNA recognition motif

Probab=92.20  E-value=0.059  Score=35.40  Aligned_cols=26  Identities=19%  Similarity=0.130  Sum_probs=22.9

Q ss_pred             CHHHHHHHHHhcCccccccccceeee
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      +.++|..|++.+++..+.++.++|..
T Consensus        30 ~~~~A~~a~~~l~~~~~~g~~l~V~~   55 (56)
T PF13893_consen   30 SVEDAQKAIEQLNGRQFNGRPLKVSY   55 (56)
T ss_dssp             SHHHHHHHHHHHTTSEETTEEEEEEE
T ss_pred             CHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            48999999999999999998888764

(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 ....

>KOG2416|consensus

Probab=91.86  E-value=0.16  Score=48.93  Aligned_cols=75  Identities=19%  Similarity=0.188  Sum_probs=56.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhc-CCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCC-CCceE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSK-YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDY-QSSIL  271 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~-~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~-~g~~l  271 (299)
                      .....|||.||=.-+|.-+|++++++ .|.|....|  |+    .+..|||.|.+.++|.+...+ |+|..+-. +.+.|
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--Dk----IKShCyV~yss~eEA~atr~A-lhnV~WP~sNPK~L  514 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DK----IKSHCYVSYSSVEEAAATREA-LHNVQWPPSNPKHL  514 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHHH--HH----hhcceeEecccHHHHHHHHHH-HhccccCCCCCcee
Confidence            45678999999999999999999996 555655533  32    244699999999999999999 77754433 55555


Q ss_pred             EEEe
Q psy3930         272 TTTS  275 (299)
Q Consensus       272 ~v~~  275 (299)
                      .+..
T Consensus       515 ~adf  518 (718)
T KOG2416|consen  515 IADF  518 (718)
T ss_pred             Eeee
Confidence            5543

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=91.48  E-value=0.74  Score=36.54  Aligned_cols=72  Identities=24%  Similarity=0.262  Sum_probs=50.1

Q ss_pred             CCCCcEEEEecCCCCC-CHH---HHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCC
Q psy3930         193 DVDECTIYVEKLPPEA-EHD---YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQS  268 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~-t~e---~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g  268 (299)
                      ++.-.||.|.=|..++ ..+   .+...++.||+|.+|..     .|+  ..|.|.|.+..+|=.|+.+ +..       
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~-----cGr--qsavVvF~d~~SAC~Av~A-f~s-------  147 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTL-----CGR--QSAVVVFKDITSACKAVSA-FQS-------  147 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeee-----cCC--ceEEEEehhhHHHHHHHHh-hcC-------
Confidence            5566788887666664 234   44556678999999976     343  2599999999999999998 552       


Q ss_pred             ceEEEEeeccc
Q psy3930         269 SILTTTSRLSF  279 (299)
Q Consensus       269 ~~l~v~~k~~~  279 (299)
                      +.-..+..|+|
T Consensus       148 ~~pgtm~qCsW  158 (166)
T PF15023_consen  148 RAPGTMFQCSW  158 (166)
T ss_pred             CCCCceEEeec
Confidence            22234456666

>KOG4307|consensus

Probab=91.31  E-value=0.14  Score=50.23  Aligned_cols=81  Identities=20%  Similarity=0.117  Sum_probs=62.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEE-EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~-v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..+..|||.+||..+++.++-.+|..--.|+. |.|.+.. ++..++-|||.|..++++..|..- .  ++...+.+.|+
T Consensus       432 ~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~-~--~k~y~G~r~ir  507 (944)
T KOG4307|consen  432 GAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSV-K--TKFYPGHRIIR  507 (944)
T ss_pred             CccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhc-c--cccccCceEEE
Confidence            44678999999999999999999998766665 6666554 788888999999998877777654 2  33556678888


Q ss_pred             EEeecc
Q psy3930         273 TTSRLS  278 (299)
Q Consensus       273 v~~k~~  278 (299)
                      |..-..
T Consensus       508 v~si~~  513 (944)
T KOG4307|consen  508 VDSIAD  513 (944)
T ss_pred             eechhh
Confidence            865433

>KOG2193|consensus

Probab=91.09  E-value=0.16  Score=46.98  Aligned_cols=75  Identities=23%  Similarity=0.288  Sum_probs=55.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      ..+|++||.+.++..+|+.+|+..-.-..-.+..      ..||+||...+...|.+|++. ++| ...+.|.++.+...
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~-~sg-k~elqGkr~e~~~s   73 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIET-LSG-KVELQGKRQEVEHS   73 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHh-hch-hhhhcCceeeccch
Confidence            3589999999999999999997541100101111      246999999999999999999 776 67778888877655


Q ss_pred             ccc
Q psy3930         277 LSF  279 (299)
Q Consensus       277 ~~~  279 (299)
                      +..
T Consensus        74 v~k   76 (584)
T KOG2193|consen   74 VPK   76 (584)
T ss_pred             hhH
Confidence            443

>KOG1996|consensus

Probab=90.92  E-value=0.7  Score=40.92  Aligned_cols=62  Identities=29%  Similarity=0.302  Sum_probs=46.4

Q ss_pred             HHHHHHHhhcCCceEEEEeeccCCCCCcc-eEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         210 HDYIESVFSKYGKVTYVSLPKFKSTGKLK-GFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       210 ~e~L~~~F~~~G~i~~v~i~~~~~~g~~k-g~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ++++++-+++||.|..|-|.-...--... ---||+|...++|.+|+-. +||  .-|+|+.+...
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~Vd-lnG--RyFGGr~v~A~  362 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVD-LNG--RYFGGRVVSAC  362 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHh-cCC--ceecceeeehe
Confidence            46788899999999988765543211111 1269999999999999998 999  88888887543

>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=90.87  E-value=3.1  Score=31.67  Aligned_cols=64  Identities=16%  Similarity=0.256  Sum_probs=45.4

Q ss_pred             cEEEEecCCCC-CCHHHHHHHhhcCC-ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCC
Q psy3930         197 CTIYVEKLPPE-AEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCP  263 (299)
Q Consensus       197 ~~l~V~nLp~~-~t~e~L~~~F~~~G-~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~  263 (299)
                      ..+.+=..|+. ++-++|..+.+.+- .|..++++++.  ...+-.+.+.|.+..+|...... .||..
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~-fNGk~   78 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEE-FNGKP   78 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHH-hCCCc
Confidence            44444444544 55666765555554 57789999874  22455789999999999999999 99954

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2278|consensus

Probab=90.05  E-value=0.25  Score=40.26  Aligned_cols=52  Identities=15%  Similarity=0.220  Sum_probs=41.4

Q ss_pred             HhhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCc----ceeeccCcceeecc
Q psy3930          18 QLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSK----LLEVTEDGTKVKGN   69 (299)
Q Consensus        18 ~~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~----~~~v~~~~~~vrr~   69 (299)
                      =+|+.|||||+..+++.|+.+-.....++|..+++.-.    .+..-++..-||.+
T Consensus        27 L~m~~dGfvpv~~lL~lnq~r~~~~t~ddi~riVk~ndKqRF~l~d~~~el~IrAn   82 (207)
T KOG2278|consen   27 LNMRGDGFVPVEDLLNLNQFRGANHTIDDIRRIVKRNDKQRFSLIDEAGELLIRAN   82 (207)
T ss_pred             ccccCCCceEHHHHhccchhcccCCcHHHHHHHHhccccceEEeecCCCcEEEEec
Confidence            35888999999999999999999888999999998554    34444555566654

>KOG2068|consensus

Probab=88.38  E-value=0.23  Score=44.72  Aligned_cols=71  Identities=21%  Similarity=0.375  Sum_probs=51.8

Q ss_pred             cEEEEecCCCCCCHH-HHH--HHhhcCCceEEEEeeccCC----CCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCc
Q psy3930         197 CTIYVEKLPPEAEHD-YIE--SVFSKYGKVTYVSLPKFKS----TGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e-~L~--~~F~~~G~i~~v~i~~~~~----~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      .-+||-+||.....+ .|+  +.|++||.|..|.+-++..    .|.+ .-++|+|...++|..||.. .+|  ....|+
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~-~s~yITy~~~eda~rci~~-v~g--~~~dg~  153 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGT-CSVYITYEEEEDADRCIDD-VDG--FVDDGR  153 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCC-CcccccccchHhhhhHHHH-hhh--HHhhhh
Confidence            568899999886544 443  6899999999998877652    2222 2379999999999999998 776  444555


Q ss_pred             eE
Q psy3930         270 IL  271 (299)
Q Consensus       270 ~l  271 (299)
                      .+
T Consensus       154 ~l  155 (327)
T KOG2068|consen  154 AL  155 (327)
T ss_pred             hh
Confidence            53

>PF00076 RRM_1: RNA recognition motif

Probab=87.81  E-value=0.035  Score=37.81  Aligned_cols=24  Identities=17%  Similarity=0.198  Sum_probs=20.1

Q ss_pred             CCHHHHHHHHHhcCccccccccce
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTK  181 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~  181 (299)
                      .+.++|.+|+..+++..+.+..++
T Consensus        47 ~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen   47 ESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             SSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCHHHHHHHHHHcCCCEECccCcC
Confidence            458999999999999988887653

(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 ....

>PF01885 PTS_2-RNA: RNA 2'-phosphotransferase, Tpt1 / KptA family; InterPro: IPR002745 The final step of tRNA splicing in Saccharomyces cerevisiae (Baker's yeast) requires 2'-phosphotransferase (Tpt1) to transfer the 2'-phosphate from ligated tRNA to NAD, producing mature tRNA and ADP ribose-1' '-2' '-cyclic phosphate

Probab=87.41  E-value=0.36  Score=40.50  Aligned_cols=52  Identities=13%  Similarity=0.278  Sum_probs=34.4

Q ss_pred             hhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCc--ceeec---cCcceeeccc
Q psy3930          19 LLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSK--LLEVT---EDGTKVKGNI   70 (299)
Q Consensus        19 ~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~--~~~v~---~~~~~vrr~~   70 (299)
                      .|+.+|||+|..|+...+++....+.+.|.+.+..++  -.++.   +++..||-+-
T Consensus        26 ~~d~~G~v~v~dLL~~~~~~~~~~t~~~i~~vV~~~~K~Rfel~~~~~~~~~IRA~q   82 (186)
T PF01885_consen   26 VMDPDGWVSVDDLLRALRFKGLWVTEEDIREVVETDDKQRFELRYEDPGGWRIRANQ   82 (186)
T ss_dssp             ---TT--EEHHHHHHHHHHT-TT--HHHHHHHHHH-SS--EEEE-----TTEEEESS
T ss_pred             ccCCCCCEeHHHHHHHHHHcCCCCCHHHHHHHHhhCCCCCeeEEcccccCceEEECC
Confidence            3788999999999999999887778899999998666  56777   7788998753

Yeast and Mus musculus (Mouse) Tpt1 protein and bacterial KptA protein can catalyze the conversion of the generated intermediate to both product and the original substrate, these enzymes likely use the same reaction mechanism. Step 1 of this reaction is strikingly similar to the ADP-ribosylation of proteins catalyzed by a number of bacterial toxins. KptA, a functional Tpt1 protein homologue from Escherichia coli is strikingly similar to yeast Tpt1 in its kinetic parameters, although E. coli is not known to have a 2'-phosphorylated RNA substrate [,].; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation; PDB: 1WFX_A.

>KOG0130|consensus

Probab=85.35  E-value=0.17  Score=39.71  Aligned_cols=45  Identities=9%  Similarity=0.049  Sum_probs=35.8

Q ss_pred             hhhcCCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeee
Q psy3930         135 LLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       135 ~~~~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      +-+..+++++-.++.|.+       .+.|++|+..+|+.++-+..+.|.++-
T Consensus       106 LDRRtGy~KGYaLvEYet-------~keAq~A~~~~Ng~~ll~q~v~VDw~F  150 (170)
T KOG0130|consen  106 LDRRTGYVKGYALVEYET-------LKEAQAAIDALNGAELLGQNVSVDWCF  150 (170)
T ss_pred             cccccccccceeeeehHh-------HHHHHHHHHhccchhhhCCceeEEEEE
Confidence            345566777766677766       788999999999999999999998764

>KOG4210|consensus

Probab=84.56  E-value=0.82  Score=41.03  Aligned_cols=63  Identities=22%  Similarity=0.176  Sum_probs=55.2

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHh
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL  257 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~  257 (299)
                      ..++.|++++...+.+.+...++..+|......+........++|++++.|...+.+..|+..
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~  149 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEE  149 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHh
Confidence            467899999999999999999999999877777666555788899999999999999999986

>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=84.40  E-value=4.4  Score=27.82  Aligned_cols=45  Identities=16%  Similarity=0.268  Sum_probs=35.4

Q ss_pred             CCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCC
Q psy3930         207 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNP  261 (299)
Q Consensus       207 ~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng  261 (299)
                      .++-++++..+..|+ ...  +..++ +|     -||.|.+..+|+++... .+|
T Consensus        11 ~~~v~d~K~~Lr~y~-~~~--I~~d~-tG-----fYIvF~~~~Ea~rC~~~-~~~   55 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WDR--IRDDR-TG-----FYIVFNDSKEAERCFRA-EDG   55 (66)
T ss_pred             CccHHHHHHHHhcCC-cce--EEecC-CE-----EEEEECChHHHHHHHHh-cCC
Confidence            478899999999997 233  33344 33     58999999999999998 787

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4285|consensus

Probab=83.75  E-value=7  Score=34.98  Aligned_cols=69  Identities=22%  Similarity=0.376  Sum_probs=48.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCC-ceEEEE
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQS-SILTTT  274 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g-~~l~v~  274 (299)
                      ..-|-|-|+|+... .-|...|++||.|.......   +|   .|-+|+|.+..+|++||..  ||  .-++| ..|.|+
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~---ng---NwMhirYssr~~A~KALsk--ng--~ii~g~vmiGVk  265 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPS---NG---NWMHIRYSSRTHAQKALSK--NG--TIIDGDVMIGVK  265 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecCC---CC---ceEEEEecchhHHHHhhhh--cC--eeeccceEEeee
Confidence            44566778887754 45667899999988776542   33   3789999999999999986  65  44434 445555


Q ss_pred             e
Q psy3930         275 S  275 (299)
Q Consensus       275 ~  275 (299)
                      .
T Consensus       266 p  266 (350)
T KOG4285|consen  266 P  266 (350)
T ss_pred             e
Confidence            5

>PLN03213 repressor of silencing 3; Provisional

Probab=83.54  E-value=0.17  Score=47.80  Aligned_cols=58  Identities=2%  Similarity=-0.024  Sum_probs=37.0

Q ss_pred             HHHHHhhhcCCCeee-eee----ecccccccCCCCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         130 RFFSQLLQESPEIEV-SVF----LKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       130 ~fl~~~~~~~~~~~l-~~f----~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .-|...+..+|.|.- .+.    ..|+-|.-...+..++.+||..+|+.+..|+.++|..+.+
T Consensus        25 DDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213         25 DDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             HHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            345666666665222 221    1222222222445789999999999999999999998775

>KOG4574|consensus

Probab=81.18  E-value=1.2  Score=44.83  Aligned_cols=71  Identities=20%  Similarity=0.156  Sum_probs=57.7

Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      +.++.|.+-..+-..|..+|+.||.|...+..++-      ..+.|+|.+.+.|..|+++ ++|.....-|-+.+|..
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dA-l~gkevs~~g~Ps~V~~  370 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDA-LQGKEVSVTGAPSRVSF  370 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhh-hcCCcccccCCceeEEe
Confidence            34455555566778899999999999999987764      2699999999999999999 99987777888876644

>PRK00819 RNA 2'-phosphotransferase; Reviewed

Probab=80.84  E-value=1.2  Score=37.00  Aligned_cols=50  Identities=10%  Similarity=0.187  Sum_probs=37.2

Q ss_pred             hhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCc--ceeeccCcceeeccc
Q psy3930          19 LLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSK--LLEVTEDGTKVKGNI   70 (299)
Q Consensus        19 ~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~--~~~v~~~~~~vrr~~   70 (299)
                      .|+.+|||+|..|+...+.+....+.+.|.+.+..++  -.+++  +.+||-+-
T Consensus        27 ~ld~~G~v~v~~Ll~~~~~~~~~~t~~~l~~vV~~d~K~Rf~l~--~~~IRA~q   78 (179)
T PRK00819         27 TLDEEGWVDIDALIEALAKAYKWVTRELLEAVVESDDKGRFEIS--GDRIRARQ   78 (179)
T ss_pred             ccCCCCCEEHHHHHHHHHHccCCCCHHHHHHHHHcCCCcceEec--CceEEecc
Confidence            3788999999999987664433347888999998776  45665  56888763

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	299
2vod_A	193	Crystal Structure Of N-Terminal Domains Of Human La		2e-13
1zh5_A	195	Structural Basis For Recognition Of Uuuoh 3'-Termin		2e-12
1yty_A	194	Structural Basis For Recognition Of Uuuoh 3'-Termin		2e-12
1s7a_A	103	Nmr Structure Of The La Motif Of Human La Protein L		1e-08
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		1e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		2e-06
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		3e-06
1sxl_A	97	Resonance Assignments And Solution Structure Of The		6e-06
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		2e-05
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		2e-05
1s29_A	92	La Autoantigen N-Terminal Domain Length = 92		3e-05
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		3e-05
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		5e-05
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		5e-05
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		9e-05
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		9e-05
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		1e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		1e-04
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		2e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		2e-04
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		2e-04
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		2e-04
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-04
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		2e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		2e-04
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		2e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-04
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		2e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		2e-04
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-04
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		2e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		3e-04
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		3e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		3e-04
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		5e-04
2cqk_A	101	Solution Structure Of The La Domain Of C-Mpl Bindin		6e-04
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		6e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		6e-04
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		7e-04

>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La Protein Complexed With Rna Oligomer Auauuuu Length = 193

Iteration: 1
 Score = 72.8 bits (177), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 51/167 (30%), Positives = 88/167 (52%), Gaps = 11/167 (6%)
Query: 100 GGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQ-ESPEIEVSVFLKCNKLARLTH 158
            G   +   L  +I + +E+Y  D NL +D+F  + ++ +   + + + +K N+L RLT 
Sbjct: 3   NGDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTT 62
Query: 159 DPDDVVKALRKSK--LLEVTEDGTKVRRT-------VVVQDKPDVDECTIYVEKLPPEAE 209
           D + +V+AL KSK  L+E++ED TK+RR+       V  + K DV   ++Y++  P +A 
Sbjct: 63  DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDAT 122
Query: 210 HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            D I+      G+V  + + +       KG  FV F + E A K +E
Sbjct: 123 LDDIKEWLEDKGQVLNIQMRRTLHKA-FKGSIFVVFDSIESAKKFVE 168

>pdb|1ZH5|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of Nascent Rna Pol Iii Transcripts By La Autoantigen Length = 195

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 51/168 (30%), Positives = 87/168 (51%), Gaps = 11/168 (6%)
Query: 99  DGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQ-ESPEIEVSVFLKCNKLARLT 157
           + G   +   L  +I + +E+Y  D NL +D+F  + ++ +   + + + +K N+L RLT
Sbjct: 4   ENGDNEKXAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIXIKFNRLNRLT 63
Query: 158 HDPDDVVKALRKSK--LLEVTEDGTKVRRT-------VVVQDKPDVDECTIYVEKLPPEA 208
            D + +V+AL KSK  L E++ED TK+RR+       V  + K DV   ++Y++  P +A
Sbjct: 64  TDFNVIVEALSKSKAELXEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDA 123
Query: 209 EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             D I+      G+V  +   +       KG  FV F + E A K +E
Sbjct: 124 TLDDIKEWLEDKGQVLNIQXRRTLHKA-FKGSIFVVFDSIESAKKFVE 170

>pdb|1YTY|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of Nascent Rna Pol Iii Transcripts By La Autoantigen Length = 194

Iteration: 1
 Score = 69.3 bits (168), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 51/168 (30%), Positives = 87/168 (51%), Gaps = 11/168 (6%)
Query: 99  DGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQ-ESPEIEVSVFLKCNKLARLT 157
           + G   +   L  +I + +E+Y  D NL +D+F  + ++ +   + + + +K N+L RLT
Sbjct: 3   ENGDNEKXAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIXIKFNRLNRLT 62
Query: 158 HDPDDVVKALRKSK--LLEVTEDGTKVRRT-------VVVQDKPDVDECTIYVEKLPPEA 208
            D + +V+AL KSK  L E++ED TK+RR+       V  + K DV   ++Y++  P +A
Sbjct: 63  TDFNVIVEALSKSKAELXEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDA 122
Query: 209 EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             D I+      G+V  +   +       KG  FV F + E A K +E
Sbjct: 123 TLDDIKEWLEDKGQVLNIQXRRTLHKA-FKGSIFVVFDSIESAKKFVE 169

>pdb|1S7A|A Chain A, Nmr Structure Of The La Motif Of Human La Protein Length = 103

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 32/90 (35%), Positives = 55/90 (61%), Gaps = 3/90 (3%)
Query: 99  DGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFF-SQLLQESPEIEVSVFLKCNKLARLT 157
           + G   +   L  +I + +E+Y  D NL +D+F   Q+  +   + + + +K N+L RLT
Sbjct: 3   ENGDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLT 62
Query: 158 HDPDDVVKALRKSK--LLEVTEDGTKVRRT 185
            D + +V+AL KSK  L+E++ED TK+RR+
Sbjct: 63  TDFNVIVEALSKSKAELMEISEDKTKIRRS 92

>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 = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           + +  +YV  LP     D ++++F KYG +   ++ + K TG+ +G AFV ++ +EEA +
Sbjct: 98  IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 157
Query: 254 ALELGLNPCPPDYQSSILT 272
           A+   LN   P+  S  L+
Sbjct: 158 AIS-ALNNVIPEGGSQPLS 175

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           + +  +YV  LP     D ++++F KYG +   ++ + K TG+ +G AFV ++ +EEA +
Sbjct: 87  IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 146
Query: 254 ALELGLNPCPPDYQSSILT 272
           A+   LN   P+  S  L+
Sbjct: 147 AIS-ALNNVIPEGGSQPLS 164

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 37/61 (60%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           D  TI V  L  +     ++ +F  +G ++ + L K K+TG+ KGFAF+ F  +E+AA+A
Sbjct: 14  DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 255 L 255
           +
Sbjct: 74  I 74

>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 = 48.1 bits (113), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/79 (31%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           + +  +YV  LP     D ++++F KYG +   ++ + K TG+ +G AFV ++ +EEA +
Sbjct: 11  IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 70
Query: 254 ALELGLNPCPPDYQSSILT 272
           A+   LN   P+  S  L+
Sbjct: 71  AIS-ALNNVIPEGGSQPLS 88

>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 107

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPK-FKSTGKLKGFAFVEFSTKEEAAKALE 256
           I V  +P +A    I  +FS +G++  V LPK    TG  +GF FV+F TK++A KA  
Sbjct: 18  ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 192 PDVDECT-IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
           PDV+  T + V+ L      D +  VF KYG+V  V +P+ + T + +GFAFV F  K +
Sbjct: 42  PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101
Query: 251 AAKALE 256
           A  A++
Sbjct: 102 AEDAMD 107

>pdb|1S29|A Chain A, La Autoantigen N-Terminal Domain Length = 92

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 44/76 (57%), Gaps = 2/76 (2%)
Query: 111 QQIMNLMEFYLSDSNLRKDRFFSQLLQESPE--IEVSVFLKCNKLARLTHDPDDVVKALR 168
           Q++   +EFY SD N+++D F      E+ E  + +   L   ++  +T D  +VV+A+R
Sbjct: 12  QKLQKQVEFYFSDVNVQRDIFLKGKXAENAEGFVSLETLLTFKRVNSVTTDVKEVVEAIR 71
Query: 169 KSKLLEVTEDGTKVRR 184
            S+ L ++EDG  VRR
Sbjct: 72  PSEKLVLSEDGLXVRR 87

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/106 (27%), Positives = 51/106 (48%), Gaps = 3/106 (2%)
Query: 159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFS 218
           DP+D  KA+     L++     KV  +        + +  +YV  LP       +E +FS
Sbjct: 55  DPNDADKAINTLNGLKLQTKTIKV--SYARPSSASIRDANLYVSGLPKTMSQKEMEQLFS 112
Query: 219 KYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPP 264
           +YG++    +   ++TG  +G  F+ F  + EA +A++ GLN   P
Sbjct: 113 QYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK-GLNGQKP 157

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           DE  ++V  L  +     +E VFSKYG+++ V + K + T + +GF FV F   ++A  A
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 255 LELGLNPCPPD 265
           + + +N    D
Sbjct: 71  M-MAMNGKSVD 80

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 24/54 (44%), Positives = 33/54 (61%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
           T+YV  LP    ++ +  +FSKYGKV  V++ K K T K KG AF+ F  K+ A
Sbjct: 18  TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 192 PDVDE-CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
           PDVD   T+ V+ L      D +  VF KYG+V  V +P+   T   +GFAFV F  + +
Sbjct: 8   PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD 67
Query: 251 AAKA 254
           A  A
Sbjct: 68  AQDA 71

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/59 (35%), Positives = 33/59 (55%)
Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            +YV  L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+AA A++
Sbjct: 65  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 187 VVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFS 246
           V++     ++C IYV  LPP+     IE VF KYG +  + L K +  G    FAFVEF 
Sbjct: 13  VIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFE 69
Query: 247 TKEEAAKAL 255
              +A  A+
Sbjct: 70  DPRDAEDAV 78

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           V+   ++V  +  EA  + I   F++YG++  + L   + TG LKG+  VE+ T +EA  
Sbjct: 20  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 79
Query: 254 ALELGLN 260
           A+E GLN
Sbjct: 80  AME-GLN 85

>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 = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/121 (26%), Positives = 59/121 (48%), Gaps = 10/121 (8%)
Query: 145 SVFLKCNKLARLTHD-PDDVVKALRKSKLLEVTEDGTKVRR-TVVVQDKPDVDECT---- 198
           SV +K    A + ++ P+    AL +   + +     KV R + + Q +P +D+      
Sbjct: 64  SVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEAR 123
Query: 199 ----IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
               IYV  +  +   D I+SVF  +GK+   +L +  +TGK KG+ F+E+   + +  A
Sbjct: 124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDA 183
Query: 255 L 255
           +
Sbjct: 184 V 184

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           V+   ++V  +  EA  + I   F++YG++  + L   + TG LKG+  VE+ T +EA  
Sbjct: 7   VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 66
Query: 254 ALELGLN 260
           A+E GLN
Sbjct: 67  AME-GLN 72

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           V+   ++V  +  EA  + I   F++YG++  + L   + TG LKG+  VE+ T +EA  
Sbjct: 5   VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 64
Query: 254 ALELGLN 260
           A+E GLN
Sbjct: 65  AME-GLN 70

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 33/58 (56%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +YV  L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+AA A++
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/114 (26%), Positives = 51/114 (44%), Gaps = 3/114 (2%)
Query: 159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFS 218
           DP D  KA+     L +     KV  +        + +  +YV  LP       +E +FS
Sbjct: 53  DPKDAEKAINTLNGLRLQTKTIKV--SYARPSSASIRDANLYVSGLPKTMTQKELEQLFS 110
Query: 219 KYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT 272
           +YG++    +   + TG  +G  F+ F  + EA +A++ GLN   P   +  +T
Sbjct: 111 QYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK-GLNGQKPSGATEPIT 163

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           V+   ++V  +  EA  + I   F++YG++  + L   + TG LKG+  VE+ T +EA  
Sbjct: 5   VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 64
Query: 254 ALELGLN 260
           A+E GLN
Sbjct: 65  AME-GLN 70

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           V+   ++V  +  EA  + I   F++YG++  + L   + TG LKG+  VE+ T +EA  
Sbjct: 21  VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 80
Query: 254 ALELGLN 260
           A+E GLN
Sbjct: 81  AME-GLN 86

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/59 (35%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL-KGFAFVEFSTKEEAAKALE 256
           +++ +L      D+I  +FS YGK+  + +P  +    L KG+A+VEF   +EA KAL+
Sbjct: 7   VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           V+   ++V  +  EA  + I   F++YG++  + L   + TG LKG+  VE+ T +EA  
Sbjct: 5   VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 64
Query: 254 ALELGLN 260
           A+E GLN
Sbjct: 65  AME-GLN 70

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 33/58 (56%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +YV  L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+AA A++
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 33/58 (56%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +YV  L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+AA A++
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 31/58 (53%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +YV  L      D +  +F  +GK+  + L K   TG+ KG+ F+ FS  E A +ALE
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 34/60 (56%)
Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            ++ V+ L      D +  VF KYG+V  V +P+ + T + +GFAFV F  K +A  A++
Sbjct: 71  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 33/58 (56%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +YV  L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+AA A++
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 32/121 (26%), Positives = 59/121 (48%), Gaps = 10/121 (8%)
Query: 145 SVFLKCNKLARLTHD-PDDVVKALRKSKLLEVTEDGTKVRR-TVVVQDKPDVDECT---- 198
           SV +K    A + ++ P+    AL +   + +     KV R + + Q +P +D+      
Sbjct: 49  SVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEAR 108
Query: 199 ----IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
               IYV  +  +   D I+SVF  +GK+   +L +  +TGK KG+ F+E+   + +  A
Sbjct: 109 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDA 168
Query: 255 L 255
           +
Sbjct: 169 V 169

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 37/67 (55%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           Q K   +   ++V  L PE   + I+S F+ +GK++   + K  +TGK KG+ FV F  K
Sbjct: 8   QKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNK 67
Query: 249 EEAAKAL 255
            +A  A+
Sbjct: 68  LDAENAI 74

>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 = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 28/105 (26%), Positives = 51/105 (48%), Gaps = 9/105 (8%)
Query: 160 PDDVVKALRKSKLLEVTEDGTKVRR-TVVVQDKPDVDECT--------IYVEKLPPEAEH 210
           P+    AL +   + +     KV R + + Q +P +D+          IYV  +  +   
Sbjct: 64  PEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSD 123
Query: 211 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           D I+SVF  +GK+   +L +  +TGK KG+ F+E+   + +  A+
Sbjct: 124 DDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168

>pdb|2CQK|A Chain A, Solution Structure Of The La Domain Of C-Mpl Binding Protein Length = 101

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 35/67 (52%)
Query: 117 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVT 176
           +EF  S  NL KD +    +     I +       ++ +LT DPD +++ LR S +++V 
Sbjct: 22  LEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSPMVQVD 81
Query: 177 EDGTKVR 183
           E G KVR
Sbjct: 82  EKGEKVR 88

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 30/58 (51%)
Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +YV  L      D +  +F  +G++  + L     TG+ KG+ F+ FS  E A KALE
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86

>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 = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 38/68 (55%)
Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           Q K   +   ++V  L PE   + I++ F+ +G+++   + K  +TGK KG+ FV F  K
Sbjct: 8   QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNK 67
Query: 249 EEAAKALE 256
            +A  A++
Sbjct: 68  WDAENAIQ 75

>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 = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 192 PDVDEC--TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
           P VD    +++V  +P EA  + ++ +FS+ G V    L   + TGK KG+ F E+  +E
Sbjct: 2   PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 250 EAAKAL 255
            A  A+
Sbjct: 62  TALSAM 67

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	299
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	4e-29
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-06
1s29_A	92	LA protein; winged helix-turn-helix, autoantigen,	6e-22
1s29_A	92	LA protein; winged helix-turn-helix, autoantigen,	9e-19
2cqk_A	101	C-MPL binding protein; LA domain, structural genom	7e-21
2cqk_A	101	C-MPL binding protein; LA domain, structural genom	3e-17
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-18
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-18
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	7e-18
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-18
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-17
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-17
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-17
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-17
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	4e-17
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-17
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	6e-17
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	6e-17
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	8e-17
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-16
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-16
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-16
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-16
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	4e-16
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-16
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	8e-16
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	9e-16
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-15
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-15
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-15
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-09
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-15
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-15
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-15
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	4e-15
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	5e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-09
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	7e-15
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-14
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-11
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-14
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-14
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-14
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-14
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-14
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-09
1x4e_A	85	RNA binding motif, single-stranded interacting pro	2e-14
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-14
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-14
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-12
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-14
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-13
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-14
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-13
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	6e-14
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	7e-14
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-14
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	7e-14
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	8e-14
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-13
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-13
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-13
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-13
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-13
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-13
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-06
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	6e-13
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-13
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-12
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-12
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-12
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-12
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-12
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-12
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-12
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-12
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-12
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-12
2div_A	99	TRNA selenocysteine associated protein; structural	3e-12
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-12
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-12
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-12
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	4e-12
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	5e-12
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-12
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	6e-12
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	6e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-11
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-10
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-11
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-11
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-11
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-11
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-11
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-11
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-11
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-11
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-11
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-11
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-11
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-11
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-10
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-10
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-11
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	4e-11
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	5e-11
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	5e-11
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	5e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	6e-11
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	6e-11
1x5o_A	114	RNA binding motif, single-stranded interacting pro	7e-11
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	8e-11
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-10
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-10
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-10
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-10
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-10
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-10
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-10
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-07
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-10
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	5e-10
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	6e-10
1x5p_A	97	Negative elongation factor E; structure genomics,	7e-10
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	8e-10
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	9e-10
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-09
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	3e-09
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-09
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	5e-09
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	6e-09
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	7e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	8e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-06
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	8e-09
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-08
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-08
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-08
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-08
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-08
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-08
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	6e-08
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	6e-08
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	7e-08
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	8e-08
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	8e-08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-07
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	1e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-07
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	3e-07
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-07
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	4e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	4e-07
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	5e-07
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	6e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	8e-07
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	8e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	9e-06
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	2e-05
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	3e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-05
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-04
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	1e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	2e-04
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	5e-04

>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 =  109 bits (272), Expect = 4e-29
 Identities = 43/167 (25%), Positives = 76/167 (45%), Gaps = 11/167 (6%)

Query: 101 GGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPE-IEVSVFLKCNKLARLTHD 159
           G   +   L  +I + +E+Y  D NL +D+F  + ++     + + + +K N+L RLT D
Sbjct: 4   GDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTD 63

Query: 160 PDDVVKALRKSKLLEVTEDGTKVRRTV---------VVQDKPDVDECTIYVEKLPPEAEH 210
            + +V+AL KSK   +     K +              + K DV   ++Y++  P +A  
Sbjct: 64  FNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATL 123

Query: 211 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           D I+      G+V  + + +       KG  FV F + E A K +E 
Sbjct: 124 DDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVET 169

>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 = 47.1 bits (111), Expect = 1e-06
 Identities = 20/64 (31%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 1  MEFYLSDSNLRKDRFFSQLLQESPE-IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEV 59
          +E+Y  D NL +D+F  + ++     + + + +K N+L RLT D + +V+AL KSK   +
Sbjct: 20 IEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELM 79

Query: 60 TEDG 63
              
Sbjct: 80 EISE 83

>1s29_A LA protein; winged helix-turn-helix, autoantigen, RNA-binding, RNA binding protein; 1.60A {Trypanosoma brucei} SCOP: a.4.5.46 Length = 92

 Score = 86.7 bits (215), Expect = 6e-22
 Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 2/79 (2%)

Query: 108 QLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPE--IEVSVFLKCNKLARLTHDPDDVVK 165
           +  Q++   +EFY SD N+++D F    + E+ E  + +   L   ++  +T D  +VV+
Sbjct: 9   ENKQKLQKQVEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVE 68

Query: 166 ALRKSKLLEVTEDGTKVRR 184
           A+R S+ L ++EDG  VRR
Sbjct: 69  AIRPSEKLVLSEDGLMVRR 87

>1s29_A LA protein; winged helix-turn-helix, autoantigen, RNA-binding, RNA binding protein; 1.60A {Trypanosoma brucei} SCOP: a.4.5.46 Length = 92

 Score = 78.3 bits (193), Expect = 9e-19
 Identities = 23/69 (33%), Positives = 41/69 (59%), Gaps = 2/69 (2%)

Query: 1  MEFYLSDSNLRKDRFFSQLLQESPE--IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLE 58
          +EFY SD N+++D F    + E+ E  + +   L   ++  +T D  +VV+A+R S+ L 
Sbjct: 18 VEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVEAIRPSEKLV 77

Query: 59 VTEDGTKVK 67
          ++EDG  V+
Sbjct: 78 LSEDGLMVR 86

>2cqk_A C-MPL binding protein; LA domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.5.46 Length = 101

 Score = 84.5 bits (209), Expect = 7e-21
 Identities = 23/80 (28%), Positives = 39/80 (48%)

Query: 105 RKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVV 164
             + L + +   +EF  S  NL KD +    +     I +       ++ +LT DPD ++
Sbjct: 10  STEDLKECLKKQLEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLIL 69

Query: 165 KALRKSKLLEVTEDGTKVRR 184
           + LR S +++V E G KVR 
Sbjct: 70  EVLRSSPMVQVDEKGEKVRP 89

>2cqk_A C-MPL binding protein; LA domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.5.46 Length = 101

 Score = 74.9 bits (184), Expect = 3e-17
 Identities = 24/79 (30%), Positives = 39/79 (49%)

Query: 1   MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVT 60
           +EF  S  NL KD +    +     I +       ++ +LT DPD +++ LR S +++V 
Sbjct: 22  LEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSPMVQVD 81

Query: 61  EDGTKVKGNIIRHFLVPIS 79
           E G KV+ +  R    P S
Sbjct: 82  EKGEKVRPSHKRCISGPSS 100

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 77.6 bits (192), Expect = 2e-18
 Identities = 23/66 (34%), Positives = 35/66 (53%)

Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
            + D  +IYV  +   A  + +E+ F   G V  V++   K +G  KGFA++EFS KE  
Sbjct: 2   MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 61

Query: 252 AKALEL 257
             +L L
Sbjct: 62  RTSLAL 67

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 77.6 bits (192), Expect = 3e-18
 Identities = 23/66 (34%), Positives = 40/66 (60%), Gaps = 1/66 (1%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           D  TI V  L  +     ++ +F  +G ++ + L K K+TG+ KGFAF+ F  +E+AA+A
Sbjct: 14  DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73

Query: 255 LELGLN 260
           +  G++
Sbjct: 74  IA-GVS 78

>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 = 77.1 bits (190), Expect = 7e-18
 Identities = 16/69 (23%), Positives = 39/69 (56%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           ++K ++D+ ++YV  +   +    +E+ FS  G +  +++   K +G  KG+A++EF+ +
Sbjct: 29  EEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAER 88

Query: 249 EEAAKALEL 257
                A+ +
Sbjct: 89  NSVDAAVAM 97

>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 = 76.6 bits (189), Expect = 7e-18
 Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPK-FKSTGKLKGFAFVEFST 247
           Q         I V  +P +A    I  +FS +G++  V LPK    TG  +GF FV+F T
Sbjct: 8   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67

Query: 248 KEEAAKALE 256
           K++A KA  
Sbjct: 68  KQDAKKAFN 76

>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 = 74.9 bits (185), Expect = 2e-17
 Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
            +  +YV  L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+AA A
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65

Query: 255 LELGLN 260
           ++  +N
Sbjct: 66  ID-NMN 70

>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 = 75.4 bits (186), Expect = 2e-17
 Identities = 18/67 (26%), Positives = 31/67 (46%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
             + D  T++  +L        +E  FS  GKV  V +   +++ + KG A+VEF   + 
Sbjct: 20  PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79

Query: 251 AAKALEL 257
              A+ L
Sbjct: 80  VPLAIGL 86

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 75.0 bits (185), Expect = 2e-17
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
            +  V+   ++V  +  EA  + I   F++YG++  + L   + TG LKG+  VE+ T +
Sbjct: 17  PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 76

Query: 250 EAAKALELGLN 260
           EA  A+E GLN
Sbjct: 77  EAQAAME-GLN 86

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 74.2 bits (183), Expect = 4e-17
 Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
            +  +YV  L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+AA A
Sbjct: 11  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70

Query: 255 LELGLN 260
           ++  +N
Sbjct: 71  ID-NMN 75

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 74.2 bits (183), Expect = 4e-17
 Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 192 PDVDE-CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
           PDVD   T+ V+ L      D +  VF KYG+V  V +P+   T   +GFAFV F  + +
Sbjct: 8   PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD 67

Query: 251 AAKALELGLN 260
           A  A    ++
Sbjct: 68  AQDAEA-AMD 76

>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 = 73.8 bits (182), Expect = 5e-17
 Identities = 25/66 (37%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
            + T+YV  LP    ++ +  +FSKYGKV  V++ K K T K KG AF+ F  K+ A   
Sbjct: 15  SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74

Query: 255 LELGLN 260
               +N
Sbjct: 75  TR-AIN 79

>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 = 74.3 bits (183), Expect = 6e-17
 Identities = 18/62 (29%), Positives = 32/62 (51%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           +  T+++  L  ++E + +  V  ++G + YV +     T   KG AF +F T+E A K 
Sbjct: 14  EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC 73

Query: 255 LE 256
           L 
Sbjct: 74  LA 75

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 74.8 bits (184), Expect = 6e-17
 Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
            +  +YV  L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+AA A
Sbjct: 62  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121

Query: 255 LELGLN 260
           ++  +N
Sbjct: 122 ID-NMN 126

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 73.9 bits (182), Expect = 8e-17
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
            +  V+   ++V  +  EA+ D I+  F  YG++  + L   + TG  KG+A VE+ T +
Sbjct: 20  PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 79

Query: 250 EAAKALELGLN 260
           +A  A E  LN
Sbjct: 80  QALAAKE-ALN 89

>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 = 73.6 bits (181), Expect = 1e-16
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
            +  V+   ++V  +  EA  + I   F++YG++  + L   + TG LKG+  VE+ T +
Sbjct: 16  PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 75

Query: 250 EAAKALELGLN 260
           EA  A+E GLN
Sbjct: 76  EAQAAME-GLN 85

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 72.6 bits (179), Expect = 1e-16
 Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
               +YV  L      D +  +F  +GK+  + L K   TG+ KG+ F+ FS  E A +A
Sbjct: 4   GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63

Query: 255 LELGLN 260
           LE  LN
Sbjct: 64  LE-QLN 68

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 72.3 bits (178), Expect = 2e-16
 Identities = 16/77 (20%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 184 RTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFV 243
            + V +    +++  +++  LP     + +E +   +G V  + L   +  GK KG A+V
Sbjct: 5   SSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYV 63

Query: 244 EFSTKEEAAKALELGLN 260
           E+  + +A++A+   ++
Sbjct: 64  EYENESQASQAVM-KMD 79

>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 = 72.2 bits (178), Expect = 2e-16
 Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
                    ++V  L   +  + +E +FS YG ++ +  P    T K KGFAFV F   E
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 250 EAAKALELGLN 260
            A KA    ++
Sbjct: 62  HAVKAYA-EVD 71

>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 = 71.0 bits (175), Expect = 4e-16
 Identities = 20/65 (30%), Positives = 36/65 (55%), Gaps = 2/65 (3%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKS-TGKLKGFAFVEFSTKEEAAKAL 255
             +++ +L      D+I  +FS YGK+  + +P  +      KG+A+VEF   +EA KAL
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 256 ELGLN 260
           +  ++
Sbjct: 65  K-HMD 68

>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 = 73.3 bits (180), Expect = 5e-16
 Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           V+   ++V  +  EA+ D I+  F  YG++  + L   + TG  KG+A VE+ T ++A  
Sbjct: 70  VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 129

Query: 254 ALELGLN 260
           A E  LN
Sbjct: 130 AKE-ALN 135

>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 = 70.8 bits (174), Expect = 8e-16
 Identities = 19/66 (28%), Positives = 37/66 (56%), Gaps = 1/66 (1%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
            + T+YV  L  +     +  +F + G V    +PK + TG+ +G+ FVEF ++E+A  A
Sbjct: 14  QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73

Query: 255 LELGLN 260
           ++  ++
Sbjct: 74  IK-IMD 78

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 71.7 bits (176), Expect = 9e-16
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
              ++ V+ L      D +  VF KYG+V  V +P+ + T + +GFAFV F  K +A  A
Sbjct: 46  GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 105

Query: 255 LELGLN 260
           ++  ++
Sbjct: 106 MD-AMD 110

>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 = 70.4 bits (173), Expect = 1e-15
 Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
           K       +YV  L      D +  +F  +G++  + L     TG+ KG+ F+ FS  E 
Sbjct: 21  KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC 80

Query: 251 AAKALELGLN 260
           A KALE  LN
Sbjct: 81  AKKALE-QLN 89

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 70.2 bits (172), Expect = 1e-15
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
           K DV   ++Y++  P +A  D I+      G+V  + + +       KG  FV F + E 
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIES 64

Query: 251 AAKALEL 257
           A K +E 
Sbjct: 65  AKKFVET 71

>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 = 70.0 bits (172), Expect = 2e-15
 Identities = 17/68 (25%), Positives = 36/68 (52%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
               D D   +++ ++P   +   ++ +F ++GK+  +++ K + TG  KG AF+ +  +
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCER 65

Query: 249 EEAAKALE 256
           E A KA  
Sbjct: 66  ESALKAQS 73

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 71.4 bits (176), Expect = 2e-15
 Identities = 20/99 (20%), Positives = 39/99 (39%), Gaps = 4/99 (4%)

Query: 159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFS 218
            P  V + ++   +L    DG  +     +          I+V  + P+      E  FS
Sbjct: 54  KPSSVDEVVKTQHIL----DGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFS 109

Query: 219 KYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           ++G +    L   K TG+ +GF FV + + +   +  + 
Sbjct: 110 QWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN 148

>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 = 55.2 bits (134), Expect = 1e-09
 Identities = 16/62 (25%), Positives = 31/62 (50%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           + C +++  L  +   D +   F KYG VT + + K  +TG+ +GF F+ F       + 
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 255 LE 256
           ++
Sbjct: 62  VK 63

>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 = 71.0 bits (174), Expect = 2e-15
 Identities = 26/94 (27%), Positives = 43/94 (45%), Gaps = 1/94 (1%)

Query: 164 VKALRKSKLLEVTED-GTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGK 222
           +KALR    +E+++      R     Q+K     CT+YV  L      + I  +FSK G 
Sbjct: 6   LKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGD 65

Query: 223 VTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +  + +   K      GF FVE+ ++ +A  A+ 
Sbjct: 66  IKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

>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 = 71.0 bits (174), Expect = 2e-15
 Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 1/66 (1%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
              ++ V+ L      D +  VF KYG+V  V +P+ + T + +GFAFV F  K +A  A
Sbjct: 69  GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128

Query: 255 LELGLN 260
           ++  ++
Sbjct: 129 MD-AMD 133

>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 = 69.2 bits (170), Expect = 3e-15
 Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 1/66 (1%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           DE  ++V  L  +     +E VFSKYG+++ V + K + T + +GF FV F   ++A  A
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70

Query: 255 LELGLN 260
           +   +N
Sbjct: 71  MM-AMN 75

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 69.3 bits (170), Expect = 4e-15
 Identities = 13/59 (22%), Positives = 26/59 (44%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            +   +L       +++ +  KYG+V  V +     T K  G A V F++   A + ++
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

>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 = 68.4 bits (168), Expect = 4e-15
 Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 1/64 (1%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             +Y+  +P +   + I  + S  G V  + +     TG+ KG+AF+EF   E +A A+ 
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 257 LGLN 260
             LN
Sbjct: 63  -NLN 65

>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 = 68.8 bits (169), Expect = 5e-15
 Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
            D    +++V  +P EA  + ++ +FS+ G V    L   + TGK KG+ F E+  +E A
Sbjct: 4   VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 252 AKALELGLN 260
             A+   LN
Sbjct: 64  LSAMR-NLN 71

>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 = 72.3 bits (178), Expect = 7e-15
 Identities = 23/100 (23%), Positives = 42/100 (42%), Gaps = 10/100 (10%)

Query: 158 HDPDDVVKALRKSKLLEVTEDGTKVR-RTVVVQDKPDVDECTIYVEKLPPEAEHDYIESV 216
            + +    A+            +++R R + VQ +P   +  + V  LPP       E +
Sbjct: 65  LNGEQAEAAINAF-------HQSRLRERELSVQLQPT--DALLCVANLPPSLTQQQFEEL 115

Query: 217 FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
              +G +    L   + TG+ KG+ F E+  K+ AA+A  
Sbjct: 116 VRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 155

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 70.4 bits (173), Expect = 3e-14
 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 2/60 (3%)

Query: 198 TIYVEKLPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            + V++LPP   + D +    S     T+  L      G+LKGFA +E+ T E A +A +
Sbjct: 186 CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLAC-GQDGQLKGFAVLEYETAEMAEEAQQ 244

>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 = 56.1 bits (136), Expect = 3e-09
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 7/79 (8%)

Query: 178 DGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL 237
           D  ++R+ +   ++   +   I +  LP +  +  +  + S Y         K+    K 
Sbjct: 4   DPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKY 56

Query: 238 KGFAFVEFSTKEEAAKALE 256
           KG AFV     E+A  A+ 
Sbjct: 57  KGTAFVTLLNGEQAEAAIN 75

>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 = 68.1 bits (167), Expect = 7e-15
 Identities = 20/72 (27%), Positives = 31/72 (43%), Gaps = 7/72 (9%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
            +K       ++V  LPP+   + +  +F KYGK   V +       K KGF F+   T+
Sbjct: 8   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLETR 61

Query: 249 EEAAKALELGLN 260
             A  A    L+
Sbjct: 62  TLAEIAKV-ELD 72

>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 = 68.1 bits (167), Expect = 1e-14
 Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
               +++  L  E     +++VF K+G ++ V L K + T K +GFAF+ F    +A  A
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNA 64

Query: 255 LELGLN 260
            +  +N
Sbjct: 65  AK-DMN 69

>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 = 70.1 bits (172), Expect = 1e-14
 Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 1/87 (1%)

Query: 174 EVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKS 233
               +   V    VV          +++  LP     D ++ + + +G +   +L K  +
Sbjct: 92  PGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA 151

Query: 234 TGKLKGFAFVEFSTKEEAAKALELGLN 260
           TG  KG+AF E+       +A+  GLN
Sbjct: 152 TGLSKGYAFCEYVDINVTDQAIA-GLN 177

>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 = 61.6 bits (150), Expect = 1e-11
 Identities = 12/66 (18%), Positives = 27/66 (40%), Gaps = 5/66 (7%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKF-----KSTGKLKGFAFVEFSTKEEA 251
             +YV  +P     + +   F+   ++  ++             + K FAF+EF + +E 
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 252 AKALEL 257
            +A+  
Sbjct: 65  TQAMAF 70

>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 = 68.1 bits (167), Expect = 1e-14
 Identities = 21/68 (30%), Positives = 38/68 (55%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           Q K   +   ++V  L PE   + I++ F+ +G+++   + K  +TGK KG+ FV F  K
Sbjct: 8   QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNK 67

Query: 249 EEAAKALE 256
            +A  A++
Sbjct: 68  WDAENAIQ 75

>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 = 67.8 bits (166), Expect = 2e-14
 Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 183 RRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAF 242
            R V  +  PD   C + V  L        +  VFSKYG +  VS+   + + + +GFAF
Sbjct: 34  SRHVGNRANPD-PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 92

Query: 243 VEFSTKEEAAKALELGLN 260
           V F   ++A +A E   N
Sbjct: 93  VYFENVDDAKEAKE-RAN 109

>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 = 67.3 bits (165), Expect = 2e-14
 Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 4/69 (5%)

Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
              ++C IYV  LPP+     IE VF KYG +  + L   K+      FAFVEF    +A
Sbjct: 18  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDA 74

Query: 252 AKALELGLN 260
             A+  G +
Sbjct: 75  EDAVY-GRD 82

>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 = 66.9 bits (164), Expect = 2e-14
 Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 1/70 (1%)

Query: 188 VQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST 247
           V+         +++  L P      ++   S+      +++     TG  + F +V+F +
Sbjct: 9   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFES 67

Query: 248 KEEAAKALEL 257
            E+  KALEL
Sbjct: 68  AEDLEKALEL 77

>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 = 68.8 bits (169), Expect = 2e-14
 Identities = 24/106 (22%), Positives = 45/106 (42%), Gaps = 10/106 (9%)

Query: 158 HDPDDVVKALRKSKLLEVTEDGT--KVRRTVVVQDKPDVDECT-IYVEKLPPEAEHDYIE 214
              D+  +A+       +   G   K+RR     D   +     +++  LP     D ++
Sbjct: 59  RSVDETTQAM---AFDGIIFQGQSLKIRRP---HDYQPLPGAHKLFIGGLPNYLNDDQVK 112

Query: 215 SVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLN 260
            + + +G +   +L K  +TG  KG+AF E+       +A+  GLN
Sbjct: 113 ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA-GLN 157

>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 = 54.9 bits (133), Expect = 2e-09
 Identities = 12/65 (18%), Positives = 27/65 (41%), Gaps = 5/65 (7%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKF-----KSTGKLKGFAFVEFSTKEEAA 252
            +YV  +P     + +   F+   ++  ++             + K FAF+EF + +E  
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 253 KALEL 257
           +A+  
Sbjct: 66  QAMAF 70

>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 = 66.4 bits (163), Expect = 2e-14
 Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 1/66 (1%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
               +Y+  L P      +  +   YGK+        K+T K KG+ FV+F +   A KA
Sbjct: 4   GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63

Query: 255 LELGLN 260
           +   L 
Sbjct: 64  VT-ALK 68

>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 = 66.5 bits (163), Expect = 2e-14
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           +  PD   C + V  L        +  VFSKYG +  VS+   + + + +GFAFV F   
Sbjct: 9   RANPD-PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67

Query: 249 EEAAKALELGLN 260
           ++A +A E   N
Sbjct: 68  DDAKEAKE-RAN 78

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 68.8 bits (169), Expect = 2e-14
 Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 10/100 (10%)

Query: 159 DPDDVVKALRKSKLLEVTEDGTKVR--RTVVVQDKPDVDECTIYVEKLPPEAEHDYIESV 216
             +D+ KAL   +L  +   G +++  +      K      T+  + L      D ++ V
Sbjct: 63  SAEDLEKAL---ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEV 119

Query: 217 FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           F    ++  V        GK KG A++EF ++ +A K LE
Sbjct: 120 FEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLE 154

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 63.4 bits (155), Expect = 2e-12
 Identities = 15/70 (21%), Positives = 30/70 (42%), Gaps = 1/70 (1%)

Query: 188 VQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST 247
           V+         +++  L P      ++   S+      +++     TG  + F +V+F +
Sbjct: 5   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFES 63

Query: 248 KEEAAKALEL 257
            E+  KALEL
Sbjct: 64  AEDLEKALEL 73

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 66.9 bits (164), Expect = 2e-14
 Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           ++ P     T YV  LP       I+++F     +  V L + K T K KGF +VEF   
Sbjct: 8   KELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEV 66

Query: 249 EEAAKALEL 257
           +   +AL  
Sbjct: 67  DSLKEALTY 75

>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 = 70.0 bits (172), Expect = 5e-14
 Identities = 18/99 (18%), Positives = 34/99 (34%), Gaps = 6/99 (6%)

Query: 158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVF 217
           H   D  + L +              +        + +  T+ V+ LP     + +   F
Sbjct: 7   HARPDSKRPLDEGSPAAAGL----TSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYF 62

Query: 218 SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
              G + +V +    S  K   FA +EF+  + A  A+ 
Sbjct: 63  KHCGPIIHVDVAD--SLKKNFRFARIEFARYDGALAAIT 99

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 69.2 bits (170), Expect = 9e-14
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 2/70 (2%)

Query: 190 DKPDVDECTIYVEKLPPEA-EHDYIESVFSKYGKVTYVSLPK-FKSTGKLKGFAFVEFST 247
           D   ++   I +  L  E  + + +   F  +G +  +++P   K        AF+ F  
Sbjct: 204 DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFEN 263

Query: 248 KEEAAKALEL 257
           K+ A +AL++
Sbjct: 264 KDSAERALQM 273

>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 = 66.9 bits (164), Expect = 5e-13
 Identities = 19/99 (19%), Positives = 39/99 (39%), Gaps = 12/99 (12%)

Query: 159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFS 218
             D  + A+ K+            +  ++V     + ECT+++   PP      I  +  
Sbjct: 90  RYDGALAAITKTH-------KVVGQNEIIVSH---LTECTLWMTNFPPSYTQRNIRDLLQ 139

Query: 219 KYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
               V   + LP        + FA+++ ++KE+A   +E
Sbjct: 140 DINVVALSIRLPS-LRFNTSRRFAYIDVTSKEDARYCVE 177

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 68.5 bits (168), Expect = 6e-14
 Identities = 19/59 (32%), Positives = 33/59 (55%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            IYV  +  +   D I+SVF  +GK+   +L +  +TGK KG+ F+E+   + +  A+ 
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 66.2 bits (162), Expect = 5e-13
 Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 179 GTKVRRTVVVQDKPDVDE-CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL 237
           G ++ R    Q +  +     +YV  +  E   D I   F+ +G +  + +     T K 
Sbjct: 10  GQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKH 69

Query: 238 KGFAFVEFSTKEEAAKALE 256
           KGFAFVE+   E A  ALE
Sbjct: 70  KGFAFVEYEVPEAAQLALE 88

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 66.3 bits (162), Expect = 6e-14
 Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 8/76 (10%)

Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY--------VSLPKFKSTGKLKGFA 241
           ++ + D  TI+V+ L      + +   F + G +          ++L   + TGKLKG A
Sbjct: 1   EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60

Query: 242 FVEFSTKEEAAKALEL 257
            V F     A  A++ 
Sbjct: 61  TVSFDDPPSAKAAIDW 76

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 65.4 bits (160), Expect = 7e-14
 Identities = 19/77 (24%), Positives = 30/77 (38%), Gaps = 8/77 (10%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVT--------YVSLPKFKSTGKLKGF 240
                 D  TI+V+ L      + +   F + G +          ++L   + TGKLKG 
Sbjct: 6   HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65

Query: 241 AFVEFSTKEEAAKALEL 257
           A V F     A  A++ 
Sbjct: 66  ATVSFDDPPSAKAAIDW 82

>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 = 65.3 bits (160), Expect = 7e-14
 Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
             +  + T++V  L      + +  +F + G +T V++ K +  GK K F FV F   E 
Sbjct: 11  AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPES 69

Query: 251 AAKALELGLN 260
            + A+ L LN
Sbjct: 70  VSYAIAL-LN 78

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 65.0 bits (159), Expect = 7e-14
 Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 2/69 (2%)

Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGK--VTYVSLPKFKSTGKLKGFAFVEFST 247
                   TI +  + P    D I +  S Y    V  + L K K T + +GFAFV+ S+
Sbjct: 3   HHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSS 62

Query: 248 KEEAAKALE 256
             +A++ L+
Sbjct: 63  AMDASQLLQ 71

>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 = 66.3 bits (162), Expect = 8e-14
 Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
               + V  +P   +   +  +F +YG +  V +   + T + +G+ FV+F +   A +A
Sbjct: 41  VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100

Query: 255 LELGLN 260
           +  GLN
Sbjct: 101 IA-GLN 105

>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 = 65.0 bits (159), Expect = 1e-13
 Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
            +     +  ++V  L  +   + +  +F  +G +   ++ +    G  KG AFV+FS+ 
Sbjct: 8   SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLR-GPDGSSKGCAFVKFSSH 66

Query: 249 EEAAKALELGLN 260
            EA  A+   L+
Sbjct: 67  TEAQAAIH-ALH 77

>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 = 67.3 bits (165), Expect = 1e-13
 Identities = 22/105 (20%), Positives = 43/105 (40%), Gaps = 11/105 (10%)

Query: 159 DPDDVVKALR-KSKLLEVTEDGTKVR------RTVVVQDKPDVDECTIYVEKLPPEAEHD 211
             ++V  A+  +   +    DG  V       R    +    +    I+V  +  + E  
Sbjct: 64  TVEEVDAAMNARPHKV----DGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119

Query: 212 YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           ++   F +YGK+  + +   + +GK +GFAFV F   +   K + 
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164

>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 = 55.8 bits (135), Expect = 1e-09
 Identities = 15/62 (24%), Positives = 31/62 (50%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
               +++  L  E   + + S F ++G +T   + +  +T + +GF FV ++T EE   A
Sbjct: 12  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71

Query: 255 LE 256
           + 
Sbjct: 72  MN 73

>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 = 64.5 bits (158), Expect = 1e-13
 Identities = 23/63 (36%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
            IYV  L   A  + ++ +FS++GKV  V L   + T K KGF FVE    E  ++A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA- 60

Query: 258 GLN 260
            L+
Sbjct: 61  KLD 63

>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 = 65.1 bits (159), Expect = 1e-13
 Identities = 21/77 (27%), Positives = 28/77 (36%), Gaps = 8/77 (10%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVT--------YVSLPKFKSTGKLKGF 240
               D D   IYV+ L      D +   F + G V          + +   K TGK KG 
Sbjct: 8   DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 67

Query: 241 AFVEFSTKEEAAKALEL 257
           A V +     A  A+E 
Sbjct: 68  ATVSYEDPPTAKAAVEW 84

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 64.6 bits (158), Expect = 2e-13
 Identities = 16/60 (26%), Positives = 31/60 (51%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             +Y++ L P      + S+F+++ +     +     TG+++G AF+ F  KE A +AL 
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

>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 = 63.3 bits (155), Expect = 2e-13
 Identities = 11/62 (17%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           ++V  L    + + + + F  +       +     TG  +G+ FV F+++++A  A++  
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD-S 62

Query: 259 LN 260
           + 
Sbjct: 63  MQ 64

>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 = 63.3 bits (155), Expect = 3e-13
 Identities = 20/65 (30%), Positives = 34/65 (52%)

Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
           P      ++V  L PE     I + F+ +G+++   + K  +TGK KG+ FV F  K +A
Sbjct: 2   PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61

Query: 252 AKALE 256
             A++
Sbjct: 62  ENAIQ 66

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.9 bits (156), Expect = 3e-13
 Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 7/85 (8%)

Query: 176 TEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG 235
           +   TK  R   V ++     CT+Y   +        +   FS +G++  + +       
Sbjct: 5   SSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP----- 59

Query: 236 KLKGFAFVEFSTKEEAAKALELGLN 260
             KG++FV FST E AA A+   +N
Sbjct: 60  -EKGYSFVRFSTHESAAHAIV-SVN 82

>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 = 66.3 bits (161), Expect = 3e-13
 Identities = 14/91 (15%), Positives = 31/91 (34%), Gaps = 1/91 (1%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           +++       ++    P E   +    +  + G     S+  F    +      +E+ +K
Sbjct: 116 KNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSK 175

Query: 249 EEAAKALELGLNPCPPDYQSSILTTTSRLSF 279
            +A + L   LN       +     T +L F
Sbjct: 176 SDALETLGF-LNHYQMKNPNGPYPYTLKLCF 205

>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 = 46.2 bits (109), Expect = 3e-06
 Identities = 17/63 (26%), Positives = 23/63 (36%), Gaps = 6/63 (9%)

Query: 195 DECTIYVEKLPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAK 253
           D   + V  L       D + +VF  YG V  V   K K      G A VE +      +
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDR 57

Query: 254 ALE 256
           A+ 
Sbjct: 58  AIT 60

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 63.1 bits (154), Expect = 6e-13
 Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 9/72 (12%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           + + ++    ++V   P + +   +  +F  +G +  V +          GFAFVEF   
Sbjct: 24  RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEA 75

Query: 249 EEAAKALELGLN 260
           E AAKA+E  ++
Sbjct: 76  ESAAKAIE-EVH 86

>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 = 62.6 bits (153), Expect = 6e-13
 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 2/67 (2%)

Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKST-GKLKGFAFVEFSTKEE 250
           P     T ++  LP +   + I+  F     ++ V LP+  S   +LKGF + EF   + 
Sbjct: 15  PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDS 73

Query: 251 AAKALEL 257
              AL L
Sbjct: 74  LLSALSL 80

>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 = 64.5 bits (158), Expect = 7e-13
 Identities = 26/104 (25%), Positives = 50/104 (48%), Gaps = 12/104 (11%)

Query: 158 HDPDDVVKALRKSKLLEVTEDGTKVR-RTVVV----QDKPDVDECTIYVEKLPPEAEHDY 212
               D  +A++         +G  VR + + V         + +  +YV  LP     D 
Sbjct: 53  TSEMDSQRAIK-------VLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQ 105

Query: 213 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           ++++F KYG +   ++ + K TG+ +G AFV ++ +EEA +A+ 
Sbjct: 106 LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149

>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 = 61.8 bits (151), Expect = 7e-12
 Identities = 13/59 (22%), Positives = 31/59 (52%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            + V  LP +     + ++F   G +    + +   TG   G+AFV+F+++ ++ +A++
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 62.3 bits (152), Expect = 1e-12
 Identities = 14/73 (19%), Positives = 26/73 (35%), Gaps = 7/73 (9%)

Query: 188 VQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST 247
           +         T Y+  +P  A    +  +F  +G +              KG  F+++ T
Sbjct: 19  IIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDT 72

Query: 248 KEEAAKALELGLN 260
            E+AA  +   L 
Sbjct: 73  HEQAAVCIV-ALA 84

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 61.9 bits (151), Expect = 1e-12
 Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 3/65 (4%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL---KGFAFVEFSTKEEA 251
               ++++ L      + ++ VFSK G +   ++ K K+   +    GF FVE+   E+A
Sbjct: 4   GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 252 AKALE 256
            KAL+
Sbjct: 64  QKALK 68

>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 = 61.9 bits (151), Expect = 1e-12
 Identities = 19/72 (26%), Positives = 32/72 (44%), Gaps = 5/72 (6%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
                 +  T+ +  L   A  + ++ VF K   +           GK KG+AF+EF++ 
Sbjct: 8   NSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQ----NQNGKSKGYAFIEFASF 63

Query: 249 EEAAKALELGLN 260
           E+A +AL    N
Sbjct: 64  EDAKEALN-SCN 74

>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 = 61.9 bits (151), Expect = 1e-12
 Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 2/70 (2%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKS-TGKLKGFAFVEFST 247
              P     T ++  LP +   + I+  F     ++ V LP+  S   +LKGF + EF  
Sbjct: 8   SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED 66

Query: 248 KEEAAKALEL 257
            +    AL L
Sbjct: 67  LDSLLSALSL 76

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 62.0 bits (151), Expect = 1e-12
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 12/71 (16%)

Query: 192 PDVDECTIYVEKLPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
           P      +++  L      + D +E++FSKYG+V   S+ K        G+AFV++S + 
Sbjct: 23  PKSINSRVFIGNLNTALVKKSD-VETIFSKYGRVAGCSVHK--------GYAFVQYSNER 73

Query: 250 EAAKALELGLN 260
            A  A+  G N
Sbjct: 74  HARAAVL-GEN 83

>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 = 61.5 bits (150), Expect = 2e-12
 Identities = 18/67 (26%), Positives = 29/67 (43%), Gaps = 5/67 (7%)

Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
            K      T+  + L      D ++ VF    ++  V        GK KG A++EF ++ 
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEA 64

Query: 250 EAAKALE 256
           +A K LE
Sbjct: 65  DAEKNLE 71

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 61.4 bits (150), Expect = 2e-12
 Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 9/66 (13%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
               +++  LP EA    I S+F +YGKV    +        +K + FV    K  A  A
Sbjct: 7   GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI--------IKNYGFVHIEDKTAAEDA 58

Query: 255 LELGLN 260
           +   L+
Sbjct: 59  IR-NLH 63

>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 = 61.6 bits (150), Expect = 2e-12
 Identities = 16/62 (25%), Positives = 24/62 (38%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
               I V+ +P     D I   F  Y  +      K+   G   G A V F +++EA  A
Sbjct: 14  GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 255 LE 256
           + 
Sbjct: 74  VI 75

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 62.0 bits (151), Expect = 2e-12
 Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 1/64 (1%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             +++  LP E     +  +F  +G V    +   K T   K F FV +     A  A++
Sbjct: 26  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85

Query: 257 LGLN 260
             +N
Sbjct: 86  -SMN 88

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 62.0 bits (151), Expect = 2e-12
 Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           C +++  LP E     + S F  +G V    +   K T   K F FV F   + A  A++
Sbjct: 41  CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100

Query: 257 LGLN 260
             +N
Sbjct: 101 -AMN 103

>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 = 60.8 bits (148), Expect = 3e-12
 Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 2/65 (3%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
            ++++  L P  + ++I   F+  G  V  V + + + TG   G+ FVEF+    A K L
Sbjct: 10  ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69

Query: 256 ELGLN 260
              +N
Sbjct: 70  H-KIN 73

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 60.9 bits (148), Expect = 3e-12
 Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 184 RTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFV 243
           + +VV   P        +           + S+FSK GKV  +  P  ++TGK KGF FV
Sbjct: 7   QYIVVNGAP-------VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59

Query: 244 EFSTKEEAAKALE 256
           E  +  +A K ++
Sbjct: 60  ECGSMNDAKKIIK 72

>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 = 60.7 bits (148), Expect = 3e-12
 Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 9/69 (13%)

Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
                  ++V  + P   +  + + F +YG V    +         K +AFV     E+A
Sbjct: 6   SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDA 57

Query: 252 AKALELGLN 260
            +A+  GL+
Sbjct: 58  VEAIR-GLD 65

>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 = 60.7 bits (148), Expect = 4e-12
 Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 3/72 (4%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
             + D    T+YV  L  +     I  +FS+ G      +    ++     + FVEF   
Sbjct: 8   MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEH 65

Query: 249 EEAAKALELGLN 260
            +AA AL   +N
Sbjct: 66  RDAAAALA-AMN 76

>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 = 60.7 bits (148), Expect = 4e-12
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           ++V  +    +   I S F++YG V  V +     TG  KG+ FV F    +  K +E
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIIT-DRTGVSKGYGFVSFYNDVDVQKIVE 68

>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 = 60.8 bits (148), Expect = 5e-12
 Identities = 13/59 (22%), Positives = 29/59 (49%), Gaps = 3/59 (5%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            +Y+  LP +   + +  +F KYG +  + +     T + +G A+V +    +A  A++
Sbjct: 10  ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVD 65

>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 = 60.4 bits (147), Expect = 5e-12
 Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 3/72 (4%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
             +       ++V  +P       +  +F ++GK+  V +   +   K  GF FV F   
Sbjct: 8   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENS 65

Query: 249 EEAAKALELGLN 260
            +A +A E  L+
Sbjct: 66  ADADRARE-KLH 76

>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 = 60.0 bits (146), Expect = 6e-12
 Identities = 16/62 (25%), Positives = 24/62 (38%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
               I V+ +P     D I   F  Y  +      K+   G   G A V F +++EA  A
Sbjct: 14  GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 255 LE 256
           + 
Sbjct: 74  VI 75

>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 = 59.9 bits (146), Expect = 6e-12
 Identities = 14/66 (21%), Positives = 27/66 (40%), Gaps = 9/66 (13%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           +   I+V  +        + S+F + G+V    +        +K +AFV    + +A  A
Sbjct: 8   NTWKIFVGNVSAACTSQELRSLFERRGRVIECDV--------VKDYAFVHMEKEADAKAA 59

Query: 255 LELGLN 260
           +   LN
Sbjct: 60  IA-QLN 64

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 61.9 bits (151), Expect = 7e-12
 Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 2/64 (3%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL--KGFAFVEFSTKEEAA 252
           D   ++V ++P       +  +F +YG V  +++ + +S      KG  FV F T++ A 
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 253 KALE 256
           +A  
Sbjct: 62  EAQN 65

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 61.1 bits (149), Expect = 1e-11
 Identities = 20/107 (18%), Positives = 42/107 (39%), Gaps = 17/107 (15%)

Query: 159 DPDDVVKALRKSKLLEVTEDGTKV--RRTVVVQDKP-------DVDECTIYVEKLPPEAE 209
                ++A              KV       +Q KP        V++  +++  +  +  
Sbjct: 56  TRKAALEAQN-------ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCT 108

Query: 210 HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            + I  +FS +G++    + +    G  +G AFV F+T+  A  A++
Sbjct: 109 ENDIRVMFSSFGQIEECRILR-GPDGLSRGCAFVTFTTRAMAQTAIK 154

>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 = 62.3 bits (152), Expect = 8e-12
 Identities = 16/68 (23%), Positives = 30/68 (44%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
              P     ++YV  L P+     +   FS  G +  + + +   T +  G+A+V F   
Sbjct: 8   PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQP 67

Query: 249 EEAAKALE 256
            +A +AL+
Sbjct: 68  ADAERALD 75

>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 = 58.1 bits (141), Expect = 3e-10
 Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

Query: 193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
                 I+++ L    ++  +   FS +G +    +         KG+ FV F T+E A 
Sbjct: 100 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAE 157

Query: 253 KALE 256
           +A+E
Sbjct: 158 RAIE 161

>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 = 59.9 bits (145), Expect = 1e-11
 Identities = 18/69 (26%), Positives = 28/69 (40%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
                 ++  + +  LP     + I   FS    V           GK+ G AFV+F+++
Sbjct: 35  NSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQ 94

Query: 249 EEAAKALEL 257
           E A KAL  
Sbjct: 95  ELAEKALGK 103

>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 = 1e-11
 Identities = 10/59 (16%), Positives = 23/59 (38%), Gaps = 6/59 (10%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            ++V  L P      +   F ++G +  +         K   FA++++ + + A  A  
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACA 71

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 8/59 (13%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            ++V  L      + +E  FS++GK+  V         KLK +AF+ F  ++ A KA+E
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAME 63

>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 = 59.0 bits (143), Expect = 2e-11
 Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 2/67 (2%)

Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGK-VTYVSLPK-FKSTGKLKGFAFVEFSTKE 249
                C +++  +P   + + I    +K  + V  V +        K +GFAFVE+ +  
Sbjct: 4   GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63

Query: 250 EAAKALE 256
            AA A  
Sbjct: 64  AAAMARR 70

>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 = 59.5 bits (144), Expect = 2e-11
 Identities = 19/69 (27%), Positives = 28/69 (40%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
              P      +Y++ LP EAE+ ++   F K   V       +   GK  G  FVEF  +
Sbjct: 18  SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE 77

Query: 249 EEAAKALEL 257
            +   AL  
Sbjct: 78  ADYKAALCR 86

>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 = 59.3 bits (144), Expect = 2e-11
 Identities = 13/59 (22%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            + V  L        I+ +F+++G +   ++   + +G+  G A V F  + +A KA++
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMK 94

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 58.6 bits (142), Expect = 2e-11
 Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 11/79 (13%)

Query: 187 VVQDKPDVDE---CTIYVEKLP--PEAEHD----YIESVFSKYGKVTYVSLPKFKSTGKL 237
           V++D+P   +     I V+ +P       +     I  +FSK+GK+T    P+    GK 
Sbjct: 3   VLKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKT 60

Query: 238 KGFAFVEFSTKEEAAKALE 256
           KG+ F+E+++   A  A++
Sbjct: 61  KGYIFLEYASPAHAVDAVK 79

>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 = 58.0 bits (141), Expect = 2e-11
 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 7/63 (11%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
            +Y+  L P    D +  +F                     G+AFV++  +  A +A+E 
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGDRKLPLAGQ------VLLKSGYAFVDYPDQNWAIRAIE- 62

Query: 258 GLN 260
            L+
Sbjct: 63  TLS 65

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 58.6 bits (142), Expect = 2e-11
 Identities = 9/69 (13%), Positives = 23/69 (33%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           +   +  +   ++  +P       +                   + G+  G A V+F  +
Sbjct: 8   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 67

Query: 249 EEAAKALEL 257
           ++A K+  L
Sbjct: 68  DDARKSERL 76

>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 = 58.0 bits (141), Expect = 3e-11
 Identities = 11/64 (17%), Positives = 26/64 (40%), Gaps = 3/64 (4%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +Y+  L      + +       G   +  +   + ++ G+ KGFA V   ++  + K ++
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 257 LGLN 260
             L 
Sbjct: 64  -LLP 66

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 58.4 bits (142), Expect = 3e-11
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 3/69 (4%)

Query: 189 QDKPDVDE-CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST 247
            D+    +   +YV+ L    + + +   FS +G +T   +      G+ KGF FV FS+
Sbjct: 7   GDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKV--MMEGGRSKGFGFVCFSS 64

Query: 248 KEEAAKALE 256
            EEA KA+ 
Sbjct: 65  PEEATKAVT 73

>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 = 58.0 bits (141), Expect = 3e-11
 Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 7/64 (10%)

Query: 197 CTIYVEKLPPEAEHD----YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
            TIY+  L  + + D     + ++FS++G++  + + +   + K++G AFV F     A 
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 65

Query: 253 KALE 256
            AL 
Sbjct: 66  NALR 69

>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 = 3e-11
 Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 1/60 (1%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            T++V  L  +     ++ VFS  G V    + + K  GK +G   V F    EA +A+ 
Sbjct: 16  STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAIS 74

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 57.8 bits (140), Expect = 3e-11
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 8/67 (11%)

Query: 196 ECTIYVEKLP--PEAEHD----YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
           +  I V+ +P       +     I  +FSK+GK+T    P+    GK KG+ F+E+++  
Sbjct: 1   DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPA 58

Query: 250 EAAKALE 256
            A  A++
Sbjct: 59  HAVDAVK 65

>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 = 58.4 bits (142), Expect = 3e-11
 Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            + V  L        I+ +F+++G +   ++   + +G+  G A V F  K +A KA++
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMK 88

>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 = 59.9 bits (146), Expect = 3e-11
 Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 2/99 (2%)

Query: 158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVF 217
            DP D  KA+     L +      ++ +        + +  +YV  LP       +E +F
Sbjct: 52  IDPKDAEKAINTLNGLRL--QTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLF 109

Query: 218 SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           S+YG++    +   + TG  +G  F+ F  + EA +A++
Sbjct: 110 SQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148

>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 = 58.0 bits (141), Expect = 1e-10
 Identities = 16/59 (27%), Positives = 28/59 (47%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            + V  LP     +   S+F   G++    L + K TG+  G+ FV +   ++A KA+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

>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 = 58.0 bits (141), Expect = 3e-11
 Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 4/72 (5%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
            +       T++V+ L  +   + ++  F    +     +   + TG  KGF FV+F+++
Sbjct: 8   PNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETGSSKGFGFVDFNSE 64

Query: 249 EEAAKALELGLN 260
           E+A  A E  + 
Sbjct: 65  EDAKAAKE-AME 75

>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 = 59.8 bits (146), Expect = 3e-11
 Identities = 11/59 (18%), Positives = 28/59 (47%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            ++V  L    + + + + F  +       +     TG  +G+ FV F+++++A  A++
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 147

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 56.4 bits (137), Expect = 5e-10
 Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            +YV  L      D ++  F   G +  + +   K   K   +AFVE+    +A  AL+
Sbjct: 2   VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 57.6 bits (140), Expect = 3e-11
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           C I+V  LP +     ++  F++ G V Y  +      GK KG   V+F + E A +A  
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERACR 66

Query: 257 LGLN 260
             +N
Sbjct: 67  -MMN 69

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 58.1 bits (141), Expect = 4e-11
 Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 3/82 (3%)

Query: 179 GTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLK 238
              V R   +  +       ++V  +P       +  +F ++GK+  V +   +   K  
Sbjct: 12  SGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK-- 69

Query: 239 GFAFVEFSTKEEAAKALELGLN 260
           GF FV F    +A +A E  L+
Sbjct: 70  GFGFVTFENSADADRARE-KLH 90

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 57.2 bits (139), Expect = 5e-11
 Identities = 12/68 (17%), Positives = 29/68 (42%), Gaps = 12/68 (17%)

Query: 195 DECTIYVEKLPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
            +  +++  LP +   + D +  +FS YG +  +++           F F++F   +   
Sbjct: 9   PKSRLFIGNLPLKNVSKED-LFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVR 59

Query: 253 KALELGLN 260
            A+E   +
Sbjct: 60  DAIE-CES 66

>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 = 58.7 bits (142), Expect = 5e-11
 Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 2/69 (2%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
                     +++  LP +A  + I + FS    V  V +      G++ G A VEF+T 
Sbjct: 39  FTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR-VHIEI-GPDGRVTGEADVEFATH 96

Query: 249 EEAAKALEL 257
           EEA  A+  
Sbjct: 97  EEAVAAMSK 105

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 56.9 bits (138), Expect = 6e-11
 Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 6/68 (8%)

Query: 193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
           D    T+YV  L        + + F ++G++  +++ +       +  AF++F+T++ A 
Sbjct: 9   DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ------RQQCAFIQFATRQAAE 62

Query: 253 KALELGLN 260
            A E   N
Sbjct: 63  VAAEKSFN 70

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 57.3 bits (139), Expect = 6e-11
 Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 6/62 (9%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELG 258
           +YV  L   A    +E  FS YG +  V + +        GFAFVEF    +A  A+  G
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIAR-----NPPGFAFVEFEDPRDAEDAVR-G 56

Query: 259 LN 260
           L+
Sbjct: 57  LD 58

>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 = 57.6 bits (140), Expect = 7e-11
 Identities = 13/70 (18%), Positives = 30/70 (42%), Gaps = 2/70 (2%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
           + + D   +Y+  LP   +   +E++   +G+V    + +  S+G  +G  F    + E+
Sbjct: 20  QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILR-DSSGTSRGVGFARMESTEK 78

Query: 251 AAKALELGLN 260
               +    N
Sbjct: 79  CEAVIG-HFN 87

>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 = 56.4 bits (137), Expect = 8e-11
 Identities = 19/58 (32%), Positives = 29/58 (50%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           I+V  L P+   + I   F  +G+V  + LP    T K +GF F+ F  +E   K +E
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59

>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 = 56.6 bits (137), Expect = 1e-10
 Identities = 12/68 (17%), Positives = 29/68 (42%), Gaps = 11/68 (16%)

Query: 191 KPDVDECTIYVEKLPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           +    +  +++  LP +   + D +  +FS YG +  +++           F F++F   
Sbjct: 17  RGSHMKSRLFIGNLPLKNVSKED-LFRIFSPYGHIMQINI--------KNAFGFIQFDNP 67

Query: 249 EEAAKALE 256
           +    A+E
Sbjct: 68  QSVRDAIE 75

>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 = 58.0 bits (140), Expect = 1e-10
 Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 6/69 (8%)

Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
               +C +YV  L        +E  F  YG +  V + +        GFAFVEF    +A
Sbjct: 69  SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR-----NPPGFAFVEFEDPRDA 123

Query: 252 AKALELGLN 260
           A A+   L+
Sbjct: 124 ADAVR-ELD 131

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 57.9 bits (140), Expect = 2e-10
 Identities = 13/61 (21%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
              + V  L        I+ +F+++G +   ++  +  +G+  G A V F  + +A KA+
Sbjct: 88  GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAV-DYDRSGRSLGTADVHFERRADALKAM 146

Query: 256 E 256
           +
Sbjct: 147 K 147

>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 = 56.1 bits (136), Expect = 2e-10
 Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 6/59 (10%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            +YV  L      + IE  F+         + K      ++ +AFV FS +E+A +A++
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMK 69

>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 = 55.9 bits (135), Expect = 2e-10
 Identities = 17/63 (26%), Positives = 28/63 (44%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           ++  + +  LP     + I   FS    V           G+  G AFV+F+++E A KA
Sbjct: 14  NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKA 73

Query: 255 LEL 257
           L+ 
Sbjct: 74  LKK 76

>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 = 56.0 bits (136), Expect = 2e-10
 Identities = 14/59 (23%), Positives = 27/59 (45%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           I+V  +P       +   F K+G VT V +       + +GF F+ F  ++   +A+ +
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71

>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 = 58.6 bits (141), Expect = 2e-10
 Identities = 10/61 (16%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
            +Y+  L      + +       G   +  +   + ++ G+ KGFA V   ++  + K +
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 256 E 256
           +
Sbjct: 130 D 130

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 55.5 bits (134), Expect = 2e-10
 Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 4/66 (6%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
               + +  +PP  + + ++S+  +YG V         S         V +S+K++A +A
Sbjct: 14  RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQA 70

Query: 255 LELGLN 260
           L+  LN
Sbjct: 71  LD-KLN 75

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 59.1 bits (142), Expect = 3e-10
 Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 7/64 (10%)

Query: 197 CTIYVEKLPPEAEHD----YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
            TIY+  L  + + D     + ++FS++G++  + + +   + K++G AFV F     A 
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 66

Query: 253 KALE 256
            AL 
Sbjct: 67  NALR 70

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 49.1 bits (116), Expect = 6e-07
 Identities = 13/60 (21%), Positives = 25/60 (41%), Gaps = 5/60 (8%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             +++  LP E     +  +F+++     V L   +        AFVEF  + +A  A +
Sbjct: 208 HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARD 262

>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 = 55.2 bits (133), Expect = 4e-10
 Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 6/62 (9%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
            +  I  + LP       I+  FS++G +  V LP+          A VEF    EA KA
Sbjct: 9   SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG------GITAIVEFLEPLEARKA 62

Query: 255 LE 256
             
Sbjct: 63  FR 64

>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 = 54.5 bits (132), Expect = 5e-10
 Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 6/66 (9%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKF---KSTGKLKGFAFVEFSTKEEAAKA 254
            I++  L PE +   +   FS +G +  +  PK      TG  KG+AF+ F++ + +  A
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVI--LQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64

Query: 255 LELGLN 260
           +E  +N
Sbjct: 65  IE-AMN 69

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 54.9 bits (133), Expect = 6e-10
 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 3/66 (4%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
               I+++ L    ++  +   FS +G +  +S          KG+ FV F T+E A +A
Sbjct: 4   GSGNIFIKNLDKSIDNKALYDTFSAFGNI--LSCKVVCDENGSKGYGFVHFETQEAAERA 61

Query: 255 LELGLN 260
           +E  +N
Sbjct: 62  IE-KMN 66

>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 = 54.2 bits (131), Expect = 7e-10
 Identities = 13/68 (19%), Positives = 26/68 (38%), Gaps = 8/68 (11%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           + +      T+YV     +     +   FS +G +  +S+         +  AFV +   
Sbjct: 8   ERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKM 59

Query: 249 EEAAKALE 256
           E A +A+ 
Sbjct: 60  ESADQAVA 67

>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 = 54.3 bits (131), Expect = 8e-10
 Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
                     +++  LP  A  + I + FS       V +      G++ G A VEF+T 
Sbjct: 8   SSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEI-GPDGRVTGEADVEFATH 65

Query: 249 EEAAKALEL 257
           E+A  A+  
Sbjct: 66  EDAVAAMAK 74

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 57.9 bits (139), Expect = 9e-10
 Identities = 25/159 (15%), Positives = 53/159 (33%), Gaps = 9/159 (5%)

Query: 144 VSVFLKCNKLARLTHDPDDVVKAL--RKSKLLEVTEDGTKVRRTVVVQDKPDVD------ 195
           ++ +++  +  R    P          + K  E  E   +   T +    P  D      
Sbjct: 41  IAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGD 100

Query: 196 -ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
              T++V ++  +     +   F  YG +  + +   K +GK +G+AF+E+  + +   A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160

Query: 255 LELGLNPCPPDYQSSILTTTSRLSFGITPLGFESGGWWF 293
            +          +  +     R   G  P     G    
Sbjct: 161 YKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGT 199

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 55.3 bits (133), Expect = 1e-09
 Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 3/65 (4%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
            +YV           +  V    G   V  +   + ++ G+ KG+A V  +++    K L
Sbjct: 57  AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116

Query: 256 ELGLN 260
           E  L 
Sbjct: 117 E-LLP 120

>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 = 54.0 bits (130), Expect = 1e-09
 Identities = 15/61 (24%), Positives = 23/61 (37%), Gaps = 7/61 (11%)

Query: 196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           E  + V  LPP      ++    + G V Y  + +        G   VEF  KE+   A+
Sbjct: 15  ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYAV 67

Query: 256 E 256
            
Sbjct: 68  R 68

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 53.5 bits (129), Expect = 1e-09
 Identities = 13/61 (21%), Positives = 20/61 (32%), Gaps = 5/61 (8%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           +++V   P   +   +   F  +G V  V + K K       FA VE          L  
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGDVGAREAVLSQ 64

Query: 258 G 258
            
Sbjct: 65  S 65

>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 = 53.6 bits (129), Expect = 1e-09
 Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 2/63 (3%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           D+  + V  +P  A  + +   F    +V  V L K    G+  G   V+F + ++  +A
Sbjct: 15  DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLK-DHVGRNNGNGLVKFLSPQDTFEA 72

Query: 255 LEL 257
           L+ 
Sbjct: 73  LKR 75

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 53.3 bits (128), Expect = 2e-09
 Identities = 13/82 (15%), Positives = 26/82 (31%), Gaps = 6/82 (7%)

Query: 179 GTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLK 238
            +          +       +YV  LP +A    ++    + G V     P   +    +
Sbjct: 2   SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPR 56

Query: 239 GFAFVEFSTKEEAAKALELGLN 260
             AF+ +     A +A+   L 
Sbjct: 57  RRAFLHYPDSAAAQQAVS-CLQ 77

>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 = 55.4 bits (133), Expect = 3e-09
 Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 4/60 (6%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            T+++  +PP    + ++ +FS  G V  V   KF    +    A ++  + EEA +AL 
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGV--VKGFKFFQKDR--KMALIQMGSVEEAVQALI 207

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 45.8 bits (108), Expect = 4e-06
 Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 6/61 (9%)

Query: 197 CTIYVEKLPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
             + V  L PE      +  +F  YG V  V     K     K  A V+ +   +A  A+
Sbjct: 35  SVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQLAM 89

Query: 256 E 256
            
Sbjct: 90  S 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 = 52.3 bits (126), Expect = 3e-09
 Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 2/60 (3%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           T+ +   P       +    +   K   + + +  + G   G+ FV+FS +EE  +AL+ 
Sbjct: 12  TVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVR-NAHGNKTGYIFVDFSNEEEVKQALKC 69

>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 = 52.7 bits (127), Expect = 3e-09
 Identities = 15/68 (22%), Positives = 28/68 (41%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
             + D     I+V  LP       +   F  +G +    +   + TGK +G+ FV  + +
Sbjct: 10  GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 69

Query: 249 EEAAKALE 256
             A +A +
Sbjct: 70  AAAERACK 77

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 53.0 bits (127), Expect = 3e-09
 Identities = 11/64 (17%), Positives = 27/64 (42%), Gaps = 7/64 (10%)

Query: 197 CTIYVEKLPPEAEHD----YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
             + +  + PE   +     + ++ S  G +  + +     +    G A++ F+T+E A 
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQ 86

Query: 253 KALE 256
             +E
Sbjct: 87  AFVE 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 = 52.6 bits (126), Expect = 5e-09
 Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 6/69 (8%)

Query: 194 VDECTIYVEKLPP---EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLK---GFAFVEFST 247
           V +  ++V  L     + E       F K+GK+  V +    S    +     A+V +  
Sbjct: 13  VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIR 72

Query: 248 KEEAAKALE 256
            E+A +A++
Sbjct: 73  SEDALRAIQ 81

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 50.9 bits (123), Expect = 6e-09
 Identities = 17/58 (29%), Positives = 29/58 (50%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           I+V  L      + ++  F ++GKV    L   K+T + +GF FV F +++   K  E
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59

>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 = 51.3 bits (123), Expect = 7e-09
 Identities = 12/64 (18%), Positives = 27/64 (42%), Gaps = 5/64 (7%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKF-----KSTGKLKGFAFVEFSTKEEAAK 253
           +YV  +P     + +   F+   ++  ++             + K FAF+EF + +E  +
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 254 ALEL 257
           A+  
Sbjct: 69  AMAF 72

>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 = 53.7 bits (129), Expect = 8e-09
 Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 4/60 (6%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            T+++  +PP    + ++ +FS  G V       FK   K +  A ++  + EEA +AL 
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVV----KGFKFFQKDRKMALIQMGSVEEAVQALI 176

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 44.9 bits (106), Expect = 6e-06
 Identities = 15/64 (23%), Positives = 23/64 (35%), Gaps = 6/64 (9%)

Query: 194 VDECTIYVEKLPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
           +    + V  L PE      +  +F  YG V  V     K     K  A V+ +   +A 
Sbjct: 1   MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQ 55

Query: 253 KALE 256
            A+ 
Sbjct: 56  LAMS 59

>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 = 54.3 bits (131), Expect = 8e-09
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           + V+ L P   ++ +E  FS++G V    +      G+  G  FVEF+ K  A KALE
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVV-DDRGRATGKGFVEFAAKPPARKALE 155

>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 = 53.5 bits (129), Expect = 1e-08
 Identities = 14/76 (18%), Positives = 33/76 (43%), Gaps = 6/76 (7%)

Query: 181 KVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGF 240
            ++  +   +K     C ++V  LP +   +  + +F +YG+ + V + + +      GF
Sbjct: 7   DIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GF 60

Query: 241 AFVEFSTKEEAAKALE 256
            F+   ++  A  A  
Sbjct: 61  GFIRLESRTLAEIAKA 76

>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 = 51.4 bits (123), Expect = 1e-08
 Identities = 15/62 (24%), Positives = 23/62 (37%), Gaps = 7/62 (11%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
            E  + V  LPP      ++    + G V Y  + +        G   VEF  KE+   A
Sbjct: 15  SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-------DGTGVVEFVRKEDMTYA 67

Query: 255 LE 256
           + 
Sbjct: 68  VR 69

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 5/73 (6%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY----VSLPKFKSTGKLKGFAFVE 244
           Q     ++  + +  LP  A  + + + F ++  +T     +        G+  G AFV 
Sbjct: 16  QFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVT-YPDGRPTGDAFVL 74

Query: 245 FSTKEEAAKALEL 257
           F+ +E A  AL  
Sbjct: 75  FACEEYAQNALRK 87

>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 = 51.8 bits (124), Expect = 1e-08
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 5/65 (7%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLP-----KFKSTGKLKGFAFVEFSTKEEA 251
           C IYV+ L    +   ++ +F +Y   +  +       +    G++KG AF+    ++ A
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 252 AKALE 256
           AKAL+
Sbjct: 106 AKALK 110

>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 = 50.6 bits (121), Expect = 2e-08
 Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 6/59 (10%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            ++V  L        +     K+G + YV +  F      K  A VEF   + A + + 
Sbjct: 17  VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVT 69

>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 = 49.7 bits (119), Expect = 2e-08
 Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 7/62 (11%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
               I V+ LP ++    +  +   Y         K+    + K  AFV     E+A  A
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNA 56

Query: 255 LE 256
           ++
Sbjct: 57  IQ 58

>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 = 49.9 bits (120), Expect = 3e-08
 Identities = 19/66 (28%), Positives = 29/66 (43%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
           +       + V  LP +     ++  FS +G+V  V + K   TG  KGF FV F+  E 
Sbjct: 10  RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69

Query: 251 AAKALE 256
             K + 
Sbjct: 70  QVKVMS 75

>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 = 50.4 bits (120), Expect = 3e-08
 Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 4/82 (4%)

Query: 179 GTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKY---GKVTYVSLPKFKSTG 235
           G ++ R  ++      +   + +  LP     + +++  S          V        G
Sbjct: 27  GQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIY-TREG 85

Query: 236 KLKGFAFVEFSTKEEAAKALEL 257
           +  G AFVE  ++++   AL+ 
Sbjct: 86  RQSGEAFVELGSEDDVKMALKK 107

>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 = 5e-08
 Identities = 53/322 (16%), Positives = 96/322 (29%), Gaps = 81/322 (25%)

Query: 7   DSNLRKDRFF--SQLLQES--PEIEVSVFLKC-NKLARLTH--DPDDV-----VKALRKS 54
           +  LR +  F  S +  E   P +   ++++  ++L          +V        LR+ 
Sbjct: 84  EEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQ- 142

Query: 55  KLLEVTEDGTKVKGNIIRHFLVPISM-----ETEASDNVDKDLSDLQRKDG-------GG 102
            LLE+     +   N++        +        A D V        + D          
Sbjct: 143 ALLEL-----RPAKNVLID-----GVLGSGKTWVALD-VCLSYKVQCKMDFKIFWLNLKN 191

Query: 103 RHRKKQLYQQIMNLMEFYLSDSNL--RKDRFFS-QLLQESPEIEVSVFLKCNKLAR---- 155
            +  + + + +  L   Y  D N   R D   + +L   S + E+   LK          
Sbjct: 192 CNSPETVLEMLQKL--LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLV 249

Query: 156 LTHDPDDV-----VKALR-KSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAE 209
           L     +V       A     K+L +T   T  R   V           I ++       
Sbjct: 250 L----LNVQNAKAWNAFNLSCKIL-LT---T--RFKQVTDFLSAATTTHISLDHHSMTLT 299

Query: 210 HDYIESVFSKYGKVTYVSLPKFKSTG---KLKGFA-----------FVEFSTKEEAAKAL 255
            D ++S+  KY       LP+   T    +L   A             +    ++    +
Sbjct: 300 PDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTII 359

Query: 256 ELGLNPCPPD-----YQS-SIL 271
           E  LN   P      +   S+ 
Sbjct: 360 ESSLNVLEPAEYRKMFDRLSVF 381

>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 = 49.2 bits (118), Expect = 6e-08
 Identities = 14/74 (18%), Positives = 28/74 (37%)

Query: 183 RRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAF 242
              V          C +++  L  +   + +   F ++G+V    + +   T + +GF F
Sbjct: 12  SGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71

Query: 243 VEFSTKEEAAKALE 256
           V F  +    K L 
Sbjct: 72  VTFMDQAGVDKVLA 85

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 49.0 bits (117), Expect = 6e-08
 Identities = 11/60 (18%), Positives = 21/60 (35%), Gaps = 6/60 (10%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             +++  L        +     ++G ++YV +         K  A VEF     A  A+ 
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVN 75

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 48.8 bits (117), Expect = 7e-08
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 2/69 (2%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSK-YGKVTYVSLPKFKSTGKLKGFAFVEFST 247
                  E +++V  L P+ +   +   F K Y       +   + TG  KG+ FV+F+ 
Sbjct: 2   SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTD 60

Query: 248 KEEAAKALE 256
           + E  +AL 
Sbjct: 61  ELEQKRALT 69

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 47.9 bits (115), Expect = 8e-08
 Identities = 13/60 (21%), Positives = 27/60 (45%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           C +++  L  +   + +   F ++G+V    + +   T + +GF FV F  +    K L 
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

>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 = 47.9 bits (115), Expect = 8e-08
 Identities = 16/66 (24%), Positives = 32/66 (48%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
           K + D   ++V  L  +     ++  F+K+G+V   ++    +TG+ +GF F+ F     
Sbjct: 6   KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAAS 65

Query: 251 AAKALE 256
             K L+
Sbjct: 66  VEKVLD 71

>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 = 49.7 bits (118), Expect = 1e-07
 Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 4/58 (6%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           I VE L      D +  +FSK+G V  +      +  +    A ++++    A  A  
Sbjct: 49  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKL 102

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 48.9 bits (116), Expect = 1e-07
 Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 4/58 (6%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           I VE L      D +  +FSK+G V  +      +  +    A ++++    A  A  
Sbjct: 31  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKL 84

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 47.5 bits (113), Expect = 2e-07
 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 6/59 (10%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            I++ KLP +     + S+   +GKVT + + K       K  AF+E +T+E A   + 
Sbjct: 18  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVN 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 = 48.0 bits (114), Expect = 2e-07
 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 6/59 (10%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            I++ KLP +     + S+   +GKVT + + K       K  AF+E +T+E A   + 
Sbjct: 33  VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVN 85

>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 = 47.2 bits (113), Expect = 2e-07
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 5/58 (8%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           ++V +   +   D +   FS+YG V  V +PK       + FAFV F+  + A     
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG 60

>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 = 47.2 bits (113), Expect = 3e-07
 Identities = 17/67 (25%), Positives = 30/67 (44%)

Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
           +    +   ++V  L      + + S FS+YG+V    + K K+T + +GF FV+F    
Sbjct: 10  NSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPN 69

Query: 250 EAAKALE 256
                L 
Sbjct: 70  CVGTVLA 76

>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 = 47.6 bits (113), Expect = 3e-07
 Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 4/70 (5%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKY---GKVTYVSLPKFKSTGKLKGFAFVEFST 247
               +   + +  LP     + +++  S       V  V        G+  G AFVE  +
Sbjct: 12  PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIY-TREGRQSGEAFVELES 70

Query: 248 KEEAAKALEL 257
           +++   AL+ 
Sbjct: 71  EDDVKLALKK 80

>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 = 46.8 bits (111), Expect = 4e-07
 Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 6/58 (10%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +    L      + +  V  K G V  + +P        K ++F  + T EE+ +A  
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYV 81

>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 = 46.1 bits (110), Expect = 4e-07
 Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 5/68 (7%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
                     ++V +   +   + ++  F +YG+V  V +PK       + FAFV F+  
Sbjct: 4   SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK-----PFRAFAFVTFADD 58

Query: 249 EEAAKALE 256
           + A     
Sbjct: 59  KVAQSLCG 66

>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 = 46.4 bits (110), Expect = 5e-07
 Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 5/73 (6%)

Query: 188 VQDKPDVDECTIYVEKLPPEAEHDYIESVFSKY---GKVTYVSLPKFKSTGKLKGFAFVE 244
           ++++ D D   I  + LP     + + + FS          +        GK +G A +E
Sbjct: 4   LEEEVD-DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLL-NRDGKRRGDALIE 61

Query: 245 FSTKEEAAKALEL 257
             ++++  KALE 
Sbjct: 62  MESEQDVQKALEK 74

>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 = 46.5 bits (111), Expect = 6e-07
 Identities = 13/68 (19%), Positives = 33/68 (48%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           + +       +++  L  E   + + + + ++GK+T   + +  ++ + +GF FV FS+ 
Sbjct: 20  KKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM 79

Query: 249 EEAAKALE 256
            E   A+ 
Sbjct: 80  AEVDAAMA 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 = 45.6 bits (108), Expect = 8e-07
 Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 6/59 (10%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            +++ KLP E     + ++   +GKVT + + K       K  AF+E +T+E A   + 
Sbjct: 17  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVN 69

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 43.3 bits (102), Expect = 8e-06
 Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 5/67 (7%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
           K       I ++ LP       ++ +  +   + T+ S+    +T    G   +EF ++E
Sbjct: 23  KLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSV----NTRDFDGTGALEFPSEE 78

Query: 250 EAAKALE 256
              +ALE
Sbjct: 79  ILVEALE 85

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 43.0 bits (101), Expect = 9e-06
 Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 2/68 (2%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVT--YVSLPKFKSTGKLKGFAFVEFSTK 248
                   ++V  LPP+ + D I + F ++G +   +    + KS    KG+AF+ F  +
Sbjct: 3   SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEE 62

Query: 249 EEAAKALE 256
                 ++
Sbjct: 63  SSVQALID 70

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 41.7 bits (97), Expect = 2e-05
 Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 7/56 (12%)

Query: 210 HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL--ELGLNPCP 263
            D +  +  KYG+V  + L       K  G A VEF+T + A  A+  E+GL   P
Sbjct: 31  KDVLLRLLQKYGEVLNLVLSS-----KKPGTAVVEFATVKAAELAVQNEVGLVDNP 81

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 41.2 bits (96), Expect = 3e-05
 Identities = 13/67 (19%), Positives = 31/67 (46%), Gaps = 7/67 (10%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             + ++ L  + +   + ++  ++G +        +      G A  +++T+EEA KA +
Sbjct: 8   SWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ------GIALCKYTTREEANKA-Q 60

Query: 257 LGLNPCP 263
           + LN C 
Sbjct: 61  MALNNCV 67

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 5/58 (8%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           + ++        D + +V +  GKV      +     +    A VEF +   A KA  
Sbjct: 28  LSIQNPLYPITVDVLYTVCNPVGKV-----QRIVIFKRNGIQAMVEFESVLCAQKAKA 80

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 9/61 (14%)

Query: 198 TIYVEKLPPEA--EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
            I++  LP     +   +  +   YGK+    L       ++K  AF+E  T+E+A   +
Sbjct: 27  VIHLSNLPHSGYSDSA-VLKLAEPYGKIKNYIL------MRMKSQAFIEMETREDAMAMV 79

Query: 256 E 256
           +
Sbjct: 80  D 80

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 41.7 bits (97), Expect = 1e-04
 Identities = 14/74 (18%), Positives = 25/74 (33%), Gaps = 15/74 (20%)

Query: 192 PDVDECTIYVEKLPPEAEHDYIES---------VFSKYGKVTYVSLPKFKSTGKLKGFAF 242
                 T+YV  +       +++          VFS+ G +  +   + K         F
Sbjct: 130 FRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK------NCGF 183

Query: 243 VEFSTKEEAAKALE 256
           V+F  +  A  A E
Sbjct: 184 VKFKYQANAEFAKE 197

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 207 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLN 260
           E   +    +  KYG+V  +++        L G  +V+F  +E+A KA+   LN
Sbjct: 38  EFFEEVFTEMEEKYGEVEEMNVCD-NLGDHLVGNVYVKFRREEDAEKAVI-DLN 89

>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 = 39.6 bits (93), Expect = 2e-04
 Identities = 10/58 (17%), Positives = 24/58 (41%), Gaps = 8/58 (13%)

Query: 206 PEAEHDYIESVF---SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLN 260
              + +  + V    +K+G V ++ + K  + G      +V+  +   A  A+   L+
Sbjct: 24  VGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGN----VYVKCPSIAAAIAAVN-ALH 76

>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 = 38.1 bits (89), Expect = 5e-04
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 8/58 (13%)

Query: 206 PEAEHDYIESVF---SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLN 260
           P   ++  E +    SK+G++  + L      G     A V F   EEA   ++  L+
Sbjct: 33  PLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGV----ASVSFRDPEEADYCIQ-TLD 85

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	299
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	100.0
2cqk_A	101	C-MPL binding protein; LA domain, structural genom	99.96
1s29_A	92	LA protein; winged helix-turn-helix, autoantigen,	99.95
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.82
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.8
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.79
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.79
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.78
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.78
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.77
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.76
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.75
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.75
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.74
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.74
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.74
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.74
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.74
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.74
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.73
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.73
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.73
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.73
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.73
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.73
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.72
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.72
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.72
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.72
2div_A	99	TRNA selenocysteine associated protein; structural	99.72
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.72
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.72
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.71
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.71
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.71
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.71
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.71
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.71
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.71
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.71
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.71
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.71
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.7
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.7
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.7
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.7
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.7
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.7
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.7
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.69
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.69
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.52
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.69
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.69
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.69
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.69
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.69
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.69
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.68
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.68
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.68
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.68
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.68
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.68
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.68
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.68
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.67
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.67
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.67
1s29_A	92	LA protein; winged helix-turn-helix, autoantigen,	99.67
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.67
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.67
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.67
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.67
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.67
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.67
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.67
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.67
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.67
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.67
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.67
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.66
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.66
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.66
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.66
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.65
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.65
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.65
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.65
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.65
2cqk_A	101	C-MPL binding protein; LA domain, structural genom	99.65
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.65
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.65
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.65
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.64
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.64
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.64
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.64
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.64
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.64
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.64
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.64
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.64
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.64
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.64
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.64
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.64
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.64
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.63
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.63
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.63
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.63
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.63
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.63
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.63
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.63
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.63
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.63
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.62
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.62
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.62
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.62
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.61
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.61
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.61
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.61
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.61
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.61
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.6
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.6
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.6
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.6
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.6
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.6
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.59
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.59
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.59
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.59
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.58
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.58
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.58
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.58
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.57
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.57
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.56
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.56
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.56
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.56
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.56
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.56
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.55
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.55
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.55
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.55
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.55
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.55
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.55
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.55
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.55
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.55
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.54
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.54
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.54
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.53
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.53
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.53
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.53
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.53
1x5p_A	97	Negative elongation factor E; structure genomics,	99.52
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.52
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.52
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.52
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.51
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.51
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.51
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.51
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.5
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.5
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.49
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.48
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.47
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.47
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.47
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.46
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.45
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.44
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.42
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.42
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.41
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.4
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.4
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.39
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.36
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.34
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.32
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.31
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.29
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.28
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.28
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.27
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.27
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.25
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.23
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.23
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.22
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.21
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.18
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.1
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.93
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.83
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.59
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.58
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	98.21
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.8
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.5
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	97.27
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.02
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.86
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.81
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	96.8
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.78
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	96.47
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.12
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.24
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	95.16
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	95.01
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	95.01
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	94.98
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	94.75
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	94.63
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	94.54
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	94.4
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	94.39
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	94.34
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	94.29
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	94.28
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	94.26
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.17
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	94.17
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	94.17
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	94.16
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	94.15
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	94.11
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	94.1
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	94.09
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	94.05
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	93.91
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	93.9
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	93.9
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	93.82
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	93.81
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	92.88
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	93.76
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	93.75
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	93.73
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	93.7
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	93.69
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	93.6
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	93.51
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	93.49
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	93.43
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	93.38
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	93.35
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	93.35
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	93.34
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	93.32
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	93.28
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	93.28
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	93.27
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	93.27
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	93.19
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	93.16
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	93.15
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	93.14
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	93.09
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	93.07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	93.04
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	93.04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	93.01
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	92.99
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	92.99
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	92.93
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	92.87
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	92.86
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	92.81
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	92.64
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	92.61
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	92.56
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	92.48
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	92.46
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	92.4
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	92.4
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	92.39
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	92.37
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	92.36
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	92.28
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	92.27
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	92.25
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	92.24
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	92.19
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	92.11
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	92.03
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	92.01
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	92.0
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	91.96
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	91.94
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	91.85
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	91.79
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	91.74
1x4e_A	85	RNA binding motif, single-stranded interacting pro	91.71
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	91.7
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	91.68
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	91.64
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	91.3
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	91.28
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	91.22
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	91.22
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	91.17
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	91.16
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	91.11
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	90.98
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	90.97
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	90.77
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	90.66
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	90.56
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	90.56
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	90.54
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	90.48
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	90.38
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	90.38
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	90.32
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	90.3
1x5p_A	97	Negative elongation factor E; structure genomics,	90.21
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	90.16
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	90.07
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	89.91
2div_A	99	TRNA selenocysteine associated protein; structural	89.89
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	89.83
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	89.77
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	89.53
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	89.43
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	89.18
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	89.14
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	89.09
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	89.07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	88.93
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	88.82
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	88.75
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	88.46
1x5o_A	114	RNA binding motif, single-stranded interacting pro	88.38
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	88.33
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	88.25
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	88.1
2dis_A	109	Unnamed protein product; structural genomics, RRM	88.06
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	88.01
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	87.91
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	87.69
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	87.66
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	87.65
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	87.42
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	86.52
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	86.1
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	85.76
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	85.44
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	85.42
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	85.32
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	84.9
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	84.37
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	84.3
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	83.54
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	83.45
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	83.07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	81.07

>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=100.00  E-value=4.8e-36  Score=252.88  Aligned_cols=167  Identities=28%  Similarity=0.467  Sum_probs=142.6

Q ss_pred             CeeecCCCCcCcChHHHHhhc-cCCCEEeeeeecchhhhhccCCHHHHHHHHhcC--cceeeccCcceeecccccccccc
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQ-ESPEIEVSVFLKCNKLARLTHDPDDVVKALRKS--KLLEVTEDGTKVKGNIIRHFLVP   77 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~-~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s--~~~~v~~~~~~vrr~~~~~~~~p   77 (299)
                      |||||||+||++|.||+++|+ ++|||||++|++|+||++|+.|.+.|.+||+.|  ..|++++++.+|||..    ..|
T Consensus        20 ~e~yfs~~nl~~D~fl~~~~~~~~g~V~l~~i~sF~r~k~l~~d~~~I~~Al~~S~~~~lev~ed~~~vrR~~----~~p   95 (193)
T 2voo_A           20 IEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSP----SKP   95 (193)
T ss_dssp             HHHHTSTTTGGGCHHHHHHHHHTTTCEEHHHHTTSHHHHHHCCCHHHHHHHHHTCSSCCEEECTTSSEEEECT----TSC
T ss_pred             hheecchhhcccCHHHHHHhcccCCcEEeHHHhhhhHHHHhcCCHHHHHHHHhhcccceEEEecccceEEecc----cCC
Confidence            699999999999999999998 589999999999999999999999999999999  8999999999999863    333


Q ss_pred             ccccccccccccCccccccccCCCCcCchHHHHHHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCC
Q psy3930          78 ISMETEASDNVDKDLSDLQRKDGGGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLT  157 (299)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~k~r~r~~~~~~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~  157 (299)
                      .|..+++                                  +                                      
T Consensus        96 ~p~~~~~----------------------------------~--------------------------------------  103 (193)
T 2voo_A           96 LPEVTDE----------------------------------Y--------------------------------------  103 (193)
T ss_dssp             CCCCCHH----------------------------------H--------------------------------------
T ss_pred             Ccccchh----------------------------------h--------------------------------------
Confidence            3311100                                  0                                      


Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL  237 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~  237 (299)
                            ...                           ...++|||+|||+++++++|+++|++||.|..|+++++. +|.+
T Consensus       104 ------~~~---------------------------~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~  149 (193)
T 2voo_A          104 ------KND---------------------------VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAF  149 (193)
T ss_dssp             ------HHH---------------------------HHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCE
T ss_pred             ------hhc---------------------------cccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCc
Confidence                  000                           012689999999999999999999999999999999987 6999


Q ss_pred             ceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeecccCC
Q psy3930         238 KGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSFGI  281 (299)
Q Consensus       238 kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~~~~  281 (299)
                      +|||||+|.+.++|++|++. ++   ..++|+.|.|+.+..|..
T Consensus       150 kG~aFVeF~~~e~A~~A~~~-~~---~~~~Gr~l~V~~~~~y~~  189 (193)
T 2voo_A          150 KGSIFVVFDSIESAKKFVET-PG---QKYKETDLLILFKDDYFA  189 (193)
T ss_dssp             EEEEEEEESSHHHHHHHHHC-TT---CEETTEECEEEETTTC--
T ss_pred             ccEEEEEECCHHHHHHHHHh-CC---CeECCEEEEEEEhHHHHH
Confidence            99999999999999999986 54   478999999998877743

>2cqk_A C-MPL binding protein; LA domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.5.46

Probab=99.96  E-value=1.7e-30  Score=192.25  Aligned_cols=70  Identities=30%  Similarity=0.507  Sum_probs=68.9

Q ss_pred             CeeecCCCCcCcChHHHHhhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeeccc
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGNI   70 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr~~   70 (299)
                      |||||||+||++|.||+++|+.+|||||++|++||||++|++|++.|++||+.|+.|||++|+++|||+.
T Consensus        22 vEyYFSd~NL~~D~fL~~~md~~G~Vpl~~iasF~r~k~lt~d~~~i~~al~~S~~levsedg~kVRr~~   91 (101)
T 2cqk_A           22 LEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSPMVQVDEKGEKVRPSH   91 (101)
T ss_dssp             HHHHTSHHHHHHCHHHHHHSCTTSCEEHHHHHHCHHHHHHCCCHHHHHHHHHHSSSEEECSSSSEEEECC
T ss_pred             HHhhcchhhhccCHHHHHhhhcCCCEEhHHHhCChHHHHHcCCHHHHHHHHHhCCcEEEcCCCCeeeeCC
Confidence            6999999999999999999999999999999999999999999999999999999999999999999987

>1s29_A LA protein; winged helix-turn-helix, autoantigen, RNA-binding, RNA binding protein; 1.60A {Trypanosoma brucei} SCOP: a.4.5.46

Probab=99.95  E-value=3.7e-30  Score=188.10  Aligned_cols=70  Identities=30%  Similarity=0.513  Sum_probs=67.7

Q ss_pred             CeeecCCCCcCcChHHHHhh--ccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeeccc
Q psy3930           1 MEFYLSDSNLRKDRFFSQLL--QESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGNI   70 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~--~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr~~   70 (299)
                      |||||||+||++|.||+++|  +.+|||||++|++||||++||.|.+.|++||+.|+.|||++||++|||+.
T Consensus        18 vEyYFSd~NL~~D~fL~~~m~~~~~G~Vpl~~i~sF~r~k~lt~d~~~i~~al~~S~~lev~edg~~VRR~~   89 (92)
T 1s29_A           18 VEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVEAIRPSEKLVLSEDGLMVRRRD   89 (92)
T ss_dssp             HHHHTSHHHHTTCHHHHHHHTTSTTCCEEHHHHTTSHHHHTTCSCHHHHHHHHTTCSSEEECTTSSEEEESS
T ss_pred             HHhhcchhhhccCHHHHHHhccCCCCCEEhHHHhCChhHHHHcCCHHHHHHHHhhCCeEEEeCCCCEEeCCC
Confidence            69999999999999999999  67899999999999999999999999999999999999999999999974

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.82  E-value=1.1e-20  Score=153.68  Aligned_cols=114  Identities=17%  Similarity=0.274  Sum_probs=104.5

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLK  238 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~k  238 (299)
                      +.++|.+|+..+++..+.++.+++..+.+.........++|||+|||.++++++|+++|++||.|..+.++++..+|.++
T Consensus        50 ~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~  129 (166)
T 3md3_A           50 QSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSR  129 (166)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEECCCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEE
T ss_pred             CHHHHHHHHHHcCCCccCCCeeEEEEcCCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcc
Confidence            38999999999999999999999998876666667778999999999999999999999999999999999998899999


Q ss_pred             eEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         239 GFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       239 g~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      |||||+|.+.++|.+|+.. +||  ..++|+.|.|..
T Consensus       130 g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~i~v~~  163 (166)
T 3md3_A          130 GYGFVSFTSQDDAQNAMDS-MQG--QDLNGRPLRINW  163 (166)
T ss_dssp             EEEEEEESCHHHHHHHHHH-HTT--CEETTEECEEEE
T ss_pred             eEEEEEeCCHHHHHHHHHH-hCC--CccCCcEEEEEe
Confidence            9999999999999999999 898  678899987765

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.80  E-value=9e-20  Score=148.77  Aligned_cols=114  Identities=26%  Similarity=0.427  Sum_probs=100.0

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLK  238 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~k  238 (299)
                      +.++|.+|++.+++..+.++.+.+.++.+...  ....++|||+|||..+++++|+++|++||.|..+.++++..+|.++
T Consensus        54 ~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~--~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~  131 (168)
T 1b7f_A           54 SEMDSQRAIKVLNGITVRNKRLKVSYARPGGE--SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPR  131 (168)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEECCCCSS--TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEE
T ss_pred             CHHHHHHHHHhcCCCEeCCcEEEEEecCCCcc--cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcc
Confidence            48999999999999999999999988765443  4567899999999999999999999999999999999998899999


Q ss_pred             eEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         239 GFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       239 g~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      |||||+|.+.++|.+|++. +||..+...+++|.|..
T Consensus       132 g~afV~f~~~~~A~~A~~~-l~g~~~~g~~~~l~V~~  167 (168)
T 1b7f_A          132 GVAFVRYNKREEAQEAISA-LNNVIPEGGSQPLSVRL  167 (168)
T ss_dssp             EEEEEEESSHHHHHHHHHH-HTTCCCTTCSSCCEEEE
T ss_pred             eEEEEEECCHHHHHHHHHH-hcCCEecCCCeEEEEEe
Confidence            9999999999999999999 89844443448887764

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.79  E-value=1.1e-19  Score=154.43  Aligned_cols=140  Identities=22%  Similarity=0.333  Sum_probs=114.3

Q ss_pred             HHHHHhhhcCCCee-ee-------------eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccCC----
Q psy3930         130 RFFSQLLQESPEIE-VS-------------VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDK----  191 (299)
Q Consensus       130 ~fl~~~~~~~~~~~-l~-------------~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~----  191 (299)
                      .-|..++..++.+. +.             .|+.|.       +.++|.+|+..+++..+.++.++|.+.......    
T Consensus        43 ~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~-------~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~~~  115 (216)
T 2qfj_A           43 DTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYE-------VPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPII  115 (216)
T ss_dssp             HHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEES-------SHHHHHHHHHHHSSCCCC-CCCEEECCSCCGGGHHHH
T ss_pred             HHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeC-------CHHHHHHHHHHccCCeeCCeeEEEecCCCccccchhh
Confidence            56777777777521 22             344443       489999999999999999999999876533211    


Q ss_pred             -----CCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCC
Q psy3930         192 -----PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDY  266 (299)
Q Consensus       192 -----~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~  266 (299)
                           .....++|||+|||.++++++|+++|++||.|..|.++++..+|.++|||||+|.+.++|.+|++. +||  ..+
T Consensus       116 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-l~g--~~~  192 (216)
T 2qfj_A          116 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS-MNL--FDL  192 (216)
T ss_dssp             HHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTT--CBC
T ss_pred             hhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHH-ccC--CEe
Confidence                 134568999999999999999999999999999999999988999999999999999999999999 898  778


Q ss_pred             CCceEEEEeeccc
Q psy3930         267 QSSILTTTSRLSF  279 (299)
Q Consensus       267 ~g~~l~v~~k~~~  279 (299)
                      .|+.|.|......
T Consensus       193 ~g~~i~V~~a~~~  205 (216)
T 2qfj_A          193 GGQYLRVGKAVTP  205 (216)
T ss_dssp             SSSBCEEEECSSC
T ss_pred             CCcEEEEEEecCC
Confidence            9999988775544

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.79  E-value=1.3e-19  Score=151.62  Aligned_cols=116  Identities=21%  Similarity=0.328  Sum_probs=96.3

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccCC----CCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDK----PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKST  234 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~----~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~  234 (299)
                      +.++|.+|+.. ++..+.+..+.+.++.+....    .....++|||+|||.++++++|+++|++||.|..|.++++..+
T Consensus        64 ~~~~A~~A~~~-~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~  142 (196)
T 1l3k_A           64 TVEEVDAAMNA-RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS  142 (196)
T ss_dssp             SHHHHHHHHHT-CSCEETTEECEEEECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTT
T ss_pred             CHHHHHHHHhc-CCCEECCEEeeeecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCC
Confidence            38999999966 778899999998876544322    1344589999999999999999999999999999999999889


Q ss_pred             CCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeeccc
Q psy3930         235 GKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSF  279 (299)
Q Consensus       235 g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~~  279 (299)
                      |.++|||||+|.+.++|.+|+..  +|  ..++|+.|.|......
T Consensus       143 g~~~g~afV~F~~~~~A~~A~~~--~~--~~~~G~~i~v~~a~~k  183 (196)
T 1l3k_A          143 GKKRGFAFVTFDDHDSVDKIVIQ--KY--HTVNGHNCEVRKALSK  183 (196)
T ss_dssp             CCEEEEEEEEESSHHHHHHHHHC--SC--CEETTEECEEEECC--
T ss_pred             CCccceEEEEECCHHHHHHHHHh--CC--cEECCEEEEEEecCCh
Confidence            99999999999999999999986  46  7888999988776554

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.78  E-value=3.9e-20  Score=157.74  Aligned_cols=114  Identities=18%  Similarity=0.253  Sum_probs=98.7

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL  237 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~  237 (299)
                      .+.++|.+|++.+++..+.++.+++..+...........++|||+|||+++++++|+++|++||.|..|+++++.  +.+
T Consensus        65 ~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~  142 (213)
T 4f02_A           65 QQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGS  142 (213)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEEECCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEE
T ss_pred             CCHHHHHHHHHHhhhhhcCCcccccccccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCC
Confidence            348999999999999999999888877654433333456789999999999999999999999999999999884  457


Q ss_pred             ceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         238 KGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       238 kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      +|||||+|.+.++|++|++. |||  ..++|+.|.|...
T Consensus       143 ~g~~fV~f~~~~~a~~Ai~~-lng--~~~~g~~i~V~~a  178 (213)
T 4f02_A          143 KGYGFVHFETQEAAERAIEK-MNG--MLLNDRKVFVGRF  178 (213)
T ss_dssp             EEEEEEEESSHHHHHHHHHH-HTT--CEETTEECEEEEC
T ss_pred             ceEEEEEeCCHHHHHHHHHH-hCC--CEECCEEEEEEEc
Confidence            99999999999999999999 898  7889999998764

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.78  E-value=3.7e-18  Score=138.71  Aligned_cols=114  Identities=24%  Similarity=0.371  Sum_probs=99.3

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEE
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY  225 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~  225 (299)
                      .|+.|.+       .++|.+|++.+++..+.++.+++....+...  ....++|||+|||.++++++|+++|++||.|..
T Consensus        47 afV~f~~-------~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~--~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~  117 (167)
T 1fxl_A           47 GFVNYID-------PKDAEKAINTLNGLRLQTKTIKVSYARPSSA--SIRDANLYVSGLPKTMTQKELEQLFSQYGRIIT  117 (167)
T ss_dssp             EEEEESS-------HHHHHHHHHHHTTCEETTEECEEEECCCCCG--GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEE
T ss_pred             EEEEECC-------HHHHHHHHHHcCCCccCCceEEEEecCCCcc--cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeE
Confidence            4555554       8999999999999999999999987765433  445689999999999999999999999999999


Q ss_pred             EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         226 VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       226 v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      +.++++..+|.++|||||+|.+.++|.+|++. +||  ..+.|+.+
T Consensus       118 ~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~~  160 (167)
T 1fxl_A          118 SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG-LNG--QKPSGATE  160 (167)
T ss_dssp             EEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTT--CCCTTCSS
T ss_pred             EEEEecCCCCCccceEEEEeCCHHHHHHHHHH-hcC--CccCCCcc
Confidence            99999888999999999999999999999999 898  56667653

>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=99.77  E-value=1e-18  Score=131.02  Aligned_cols=80  Identities=28%  Similarity=0.422  Sum_probs=74.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..++++|||+|||+++|+++|+++|++||+|..|++++++.+|.++|||||+|.+.++|++|++. +||  ..+.|++|.
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~-lng--~~~~gr~l~   92 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT-LNG--LRLQSKTIK   92 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHH-hCC--CEECCEEEE
Confidence            45578999999999999999999999999999999999998999999999999999999999999 898  778899887


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |..
T Consensus        93 V~~   95 (99)
T 4fxv_A           93 VSY   95 (99)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            764

>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=99.76  E-value=2.7e-19  Score=146.54  Aligned_cols=117  Identities=21%  Similarity=0.305  Sum_probs=102.8

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEE
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY  225 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~  225 (299)
                      .|+.|.+       .++|.+|+ .+++..+.++.+++.++.+...  ....++|||+|||.++++++|+++|++||.|..
T Consensus        54 afV~f~~-------~~~A~~A~-~~~~~~~~g~~i~v~~~~~~~~--~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~  123 (172)
T 2g4b_A           54 AFLEFRS-------VDETTQAM-AFDGIIFQGQSLKIRRPHDYQP--LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKA  123 (172)
T ss_dssp             EEEEESS-------HHHHHHHG-GGTTCEETTEECEEECCSSCCC--CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEE
T ss_pred             EEEEeCC-------HHHHHHHH-HhCCcEecCceeeecCCcccCC--CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceE
Confidence            4556655       89999999 8999999999999987654332  345789999999999999999999999999999


Q ss_pred             EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         226 VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       226 v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      +.++++..+|.++|||||+|.+.++|.+|++. +||  ..++|+.|.|..
T Consensus       124 v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~V~~  170 (172)
T 2g4b_A          124 FNLVKDSATGLSKGYAFCEYVDINVTDQAIAG-LNG--MQLGDKKLLVQR  170 (172)
T ss_dssp             EEEEECTTTCSEEEEEEEEESSTTHHHHHHHH-HTT--CEETTEECEEEE
T ss_pred             EEEEecCCCCCcceEEEEEeCCHHHHHHHHHH-cCC--CEECCeEEEEEe
Confidence            99999988999999999999999999999999 898  778899998865

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=1.3e-17  Score=123.52  Aligned_cols=83  Identities=28%  Similarity=0.418  Sum_probs=76.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|++|.|
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~V   79 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ-LNG--FELAGRPMRV   79 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHH-HTT--CCSSSSCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHH-hCC--CeeCCcEEEE
Confidence            3468999999999999999999999999999999999988899999999999999999999999 898  7888999988


Q ss_pred             Eeeccc
Q psy3930         274 TSRLSF  279 (299)
Q Consensus       274 ~~k~~~  279 (299)
                      ......
T Consensus        80 ~~a~~~   85 (95)
T 2dnz_A           80 GHVTER   85 (95)
T ss_dssp             EESSCC
T ss_pred             EEcccc
Confidence            775443

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=6.2e-18  Score=125.59  Aligned_cols=87  Identities=21%  Similarity=0.371  Sum_probs=77.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEE-EeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYV-SLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v-~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ...++|||+|||+++++++|+++|++||.|..| .+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|++|.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~   79 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA-MNG--QYLCNRPIT   79 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHT-TTT--CEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHH-cCC--CEECCEEEE
Confidence            346899999999999999999999999999999 9999978999999999999999999999999 898  778899998


Q ss_pred             EEeecccCCCC
Q psy3930         273 TTSRLSFGITP  283 (299)
Q Consensus       273 v~~k~~~~~~~  283 (299)
                      |..........
T Consensus        80 v~~a~~~~~~~   90 (96)
T 1x5t_A           80 VSYAFKKDSKG   90 (96)
T ss_dssp             EEESCCCCCCC
T ss_pred             EEEecccCCCC
Confidence            88755543333

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.74  E-value=1.8e-18  Score=127.63  Aligned_cols=77  Identities=27%  Similarity=0.397  Sum_probs=70.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCC-ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G-~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .+|||+|||+++|+++|+++|++|| .|..|++++++.+|.++|||||+|.+.++|++|++.+.++  ..++|++|.|..
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~--~~~~gr~i~V~~   79 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHS--LNILGQKVSMHY   79 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTE--EEETTEEEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCC--eEECCEEEEEEE
Confidence            6899999999999999999999999 8999999999989999999999999999999999983455  678899887765

>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=99.74  E-value=2e-17  Score=123.57  Aligned_cols=85  Identities=27%  Similarity=0.369  Sum_probs=77.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.++++..+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   81 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE-VDG--QVFQGRMLH   81 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHH-TTT--EESSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHH-hCC--CEECCcEEE
Confidence            34568999999999999999999999999999999999988999999999999999999999999 998  778899998


Q ss_pred             EEeecccC
Q psy3930         273 TTSRLSFG  280 (299)
Q Consensus       273 v~~k~~~~  280 (299)
                      |.......
T Consensus        82 V~~a~~~~   89 (99)
T 1whw_A           82 VLPSTIKK   89 (99)
T ss_dssp             EEECCCCS
T ss_pred             EEEcCCCc
Confidence            88765543

>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=99.74  E-value=1.7e-17  Score=134.62  Aligned_cols=128  Identities=19%  Similarity=0.224  Sum_probs=97.0

Q ss_pred             eeeeeeecccccccCCCCHHHHHHHHHhcCccc-------cccccceeeeeecc----cCCCCCCCcEEEEecCCCCCCH
Q psy3930         142 IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLE-------VTEDGTKVRRTVVV----QDKPDVDECTIYVEKLPPEAEH  210 (299)
Q Consensus       142 ~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~-------~~~~~~~v~r~~~~----~~~~~~~~~~l~V~nLp~~~t~  210 (299)
                      ..+-.|+.|.+       .++|++|+..+++-.       +.+...........    ........++|||+|||+++++
T Consensus        12 ~~G~~fV~f~~-------~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~   84 (158)
T 2kn4_A           12 LKGETTTEAVD-------AATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSP   84 (158)
T ss_dssp             CEEEEEEECSS-------HHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCTTCCH
T ss_pred             ccchhHHHHHH-------HHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCH
Confidence            34455777766       788889987665321       12222221111111    1112355789999999999999


Q ss_pred             HHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeeccc
Q psy3930         211 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSF  279 (299)
Q Consensus       211 e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~~  279 (299)
                      ++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|++|.|......
T Consensus        85 ~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~v~~a~~~  150 (158)
T 2kn4_A           85 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA-MDG--AVLDGRELRVQMARYG  150 (158)
T ss_dssp             HHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHH-STT--EESSSSEEEEEEECCS
T ss_pred             HHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHH-hCC--CEECCeEEEEEECCCC
Confidence            99999999999999999999988999999999999999999999999 998  7788999988875443

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.74  E-value=6e-19  Score=143.81  Aligned_cols=111  Identities=17%  Similarity=0.325  Sum_probs=94.6

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL  237 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~  237 (299)
                      .+.++|.+|+..  +..+.+..+.+.+..+...  ....++|||+|||.++++++|+++|++||.|..+.++++..+|.+
T Consensus        53 ~~~~~a~~A~~~--~~~~~g~~i~v~~~~~~~~--~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~  128 (167)
T 2cjk_A           53 EKPSSVDEVVKT--QHILDGKVIDPKRAIPRDE--QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQS  128 (167)
T ss_dssp             SSTHHHHHHHHS--CCEETTEECCCEECCCHHH--HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTT
T ss_pred             ccHHHHHHHHhc--ccccCCeEcccccccchhh--ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCcc
Confidence            347899999975  4578888888877654432  234579999999999999999999999999999999999889999


Q ss_pred             ceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         238 KGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       238 kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      +|||||+|.+.++|.+|++  ++|  ..+.|+.|.|...
T Consensus       129 ~g~afV~f~~~~~a~~A~~--~~~--~~~~g~~i~V~~a  163 (167)
T 2cjk_A          129 RGFGFVTYDSADAVDRVCQ--NKF--IDFKDRKIEIKRA  163 (167)
T ss_dssp             SEEEEEEESSHHHHHHHHH--CSE--ECSSSSCEEEEEC
T ss_pred             ceEEEEEECCHHHHHHHHh--CCC--EEeCCeEEEEeec
Confidence            9999999999999999998  577  8888999987753

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.3e-17  Score=125.64  Aligned_cols=86  Identities=26%  Similarity=0.330  Sum_probs=78.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.++++..+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~   86 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA-MDG--AELDGRELR   86 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHH-HSS--CCBTTBCCE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHH-cCC--CEECCcEEE
Confidence            45578999999999999999999999999999999999988899999999999999999999999 888  778899998


Q ss_pred             EEeecccCC
Q psy3930         273 TTSRLSFGI  281 (299)
Q Consensus       273 v~~k~~~~~  281 (299)
                      |........
T Consensus        87 V~~a~~~~~   95 (103)
T 2dnm_A           87 VQVARYGRR   95 (103)
T ss_dssp             EEECSSCCS
T ss_pred             EEECCcCCC
Confidence            887654433

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.5e-17  Score=125.02  Aligned_cols=90  Identities=26%  Similarity=0.395  Sum_probs=79.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~   85 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA-MNG--KSVDGRQIR   85 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHH-HTT--CCTTSCCCE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHH-hCC--CEECCeEEE
Confidence            44578999999999999999999999999999999999988899999999999999999999999 888  778899999


Q ss_pred             EEeecccCCCCCC
Q psy3930         273 TTSRLSFGITPLG  285 (299)
Q Consensus       273 v~~k~~~~~~~r~  285 (299)
                      |.........+++
T Consensus        86 v~~a~~~~~~~~~   98 (102)
T 1x5s_A           86 VDQAGKSSDNRSG   98 (102)
T ss_dssp             EEEEECCCCCCCC
T ss_pred             EEECCCCCCCCCC
Confidence            9886655444443

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.73  E-value=1.1e-17  Score=127.68  Aligned_cols=80  Identities=19%  Similarity=0.275  Sum_probs=75.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      +..++|||+|||+++++++|+++|++||.|..|.++++..+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.|
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~-lng--~~~~gr~i~V   80 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN-LHL--TSVMGNIIHA   80 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTT--CEETTEECEE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHH-hCC--CEECCeEEEE
Confidence            3468999999999999999999999999999999999998999999999999999999999999 898  8888999998


Q ss_pred             Eee
Q psy3930         274 TSR  276 (299)
Q Consensus       274 ~~k  276 (299)
                      ...
T Consensus        81 ~~a   83 (110)
T 3s8s_A           81 QLD   83 (110)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            774

>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=99.73  E-value=1.2e-16  Score=130.79  Aligned_cols=114  Identities=16%  Similarity=0.265  Sum_probs=91.3

Q ss_pred             CHHHHHHHHHhcCcccccc---ccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCC
Q psy3930         159 DPDDVVKALRKSKLLEVTE---DGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG  235 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~---~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g  235 (299)
                      +.++|.+|++.+++..+.+   ..+.+....+... .....++|||+|||.++++++|+++|++||.|..+.++++. +|
T Consensus        56 ~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g  133 (175)
T 3nmr_A           56 TRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKN-NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DG  133 (175)
T ss_dssp             SHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGGCC-SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TS
T ss_pred             CHHHHHHHHHHhcCcEEccCCccceEEcccccccc-ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CC
Confidence            3899999999888877653   3344444433322 24467899999999999999999999999999999999986 79


Q ss_pred             CcceEEEEEecCHHHHHHHHHhcCCCCCCCC-CCceEEEEe
Q psy3930         236 KLKGFAFVEFSTKEEAAKALELGLNPCPPDY-QSSILTTTS  275 (299)
Q Consensus       236 ~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~-~g~~l~v~~  275 (299)
                      .++|||||+|.+.++|.+|++. +||..+.. .+++|.|..
T Consensus       134 ~~~g~afV~f~~~~~A~~A~~~-l~g~~~~~g~~~~l~V~~  173 (175)
T 3nmr_A          134 LSRGCAFVTFTTRAMAQTAIKA-MHQAQTMEGCSSPMVVKF  173 (175)
T ss_dssp             CEEEEEEEEESSHHHHHHHHHH-HTTSCCCTTCSSCCEEEE
T ss_pred             CEEEEEEEEECCHHHHHHHHHH-hcCCcccCCCCCCeEEEe
Confidence            9999999999999999999999 88843322 258887765

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=3e-17  Score=124.29  Aligned_cols=90  Identities=31%  Similarity=0.439  Sum_probs=79.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeecc-CCCCCcceEEEEEecCHHHHHHHHHhcC-CCCCCCCCCce
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKF-KSTGKLKGFAFVEFSTKEEAAKALELGL-NPCPPDYQSSI  270 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~-~~~g~~kg~~fV~F~~~~~A~~Al~~~l-ng~~~~~~g~~  270 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.++++ +.+|.++|||||+|.+.++|++|++. + ||  ..+.|+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~~~--~~~~g~~   88 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA-LCHS--THLYGRR   88 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHH-HHTC--CBSSSCB
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHH-hccC--CeECCCE
Confidence            556789999999999999999999999999999999998 77899999999999999999999999 7 88  7788999


Q ss_pred             EEEEeecccCCCCCC
Q psy3930         271 LTTTSRLSFGITPLG  285 (299)
Q Consensus       271 l~v~~k~~~~~~~r~  285 (299)
                      |.|...........+
T Consensus        89 l~v~~a~~~~~~~~~  103 (107)
T 2cph_A           89 LVLEWADSEVTVQSG  103 (107)
T ss_dssp             CEEEECCCCCCCCCS
T ss_pred             EEEEeCCCCCCCCCC
Confidence            988876554333333

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=1.5e-17  Score=124.05  Aligned_cols=92  Identities=24%  Similarity=0.305  Sum_probs=78.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCC---CCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCce
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKS---TGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSI  270 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~---~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~  270 (299)
                      ...++|||+|||.++++++|+++|++||.|..|.++++..   +|.++|||||+|.+.++|++|++. +||  ..+.|+.
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~   79 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ-LQG--HTVDGHK   79 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHH-STT--CEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHH-hCC--CeeCCeE
Confidence            3468999999999999999999999999999999998765   568999999999999999999999 998  7788999


Q ss_pred             EEEEeecccCCCCCCCCC
Q psy3930         271 LTTTSRLSFGITPLGFES  288 (299)
Q Consensus       271 l~v~~k~~~~~~~r~~~~  288 (299)
                      |.|........++.+..+
T Consensus        80 l~V~~a~~~~~~~~~~~s   97 (98)
T 2cpf_A           80 LEVRISERATKPASGPSS   97 (98)
T ss_dssp             CEEECSSCSSCCCCCCCC
T ss_pred             EEEEEccCCCCCCCCCCC
Confidence            988876655444444333

>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=99.73  E-value=3.9e-17  Score=123.28  Aligned_cols=84  Identities=23%  Similarity=0.404  Sum_probs=77.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.++++..+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   88 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI-MDM--IKLYGKPIR   88 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHH-SSS--CBCSSCBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHH-hCC--CeECCeEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999 898  778899998


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus        89 v~~a~~~   95 (105)
T 1x5u_A           89 VNKASAH   95 (105)
T ss_dssp             EEETTTT
T ss_pred             EEECCCC
Confidence            8875443

>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=99.73  E-value=2.2e-17  Score=124.89  Aligned_cols=85  Identities=22%  Similarity=0.377  Sum_probs=75.9

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCC---CC
Q psy3930         192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDY---QS  268 (299)
Q Consensus       192 ~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~---~g  268 (299)
                      .....++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+   .+
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~~~~g   85 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA-LHE--QKTLPGMN   85 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHH-HTT--TCCCTTCS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHH-hcC--CcccCCCC
Confidence            355678999999999999999999999999999999999988899999999999999999999999 887  444   78


Q ss_pred             ceEEEEeeccc
Q psy3930         269 SILTTTSRLSF  279 (299)
Q Consensus       269 ~~l~v~~k~~~  279 (299)
                      ++|.|......
T Consensus        86 ~~l~v~~a~~~   96 (106)
T 2dgp_A           86 RPIQVKPADSE   96 (106)
T ss_dssp             SCCEEEECCCC
T ss_pred             ceEEEEECCcc
Confidence            99888775544

>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=2.4e-17  Score=126.65  Aligned_cols=89  Identities=19%  Similarity=0.220  Sum_probs=79.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   98 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS-MNG--FQIGMKRLK   98 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHH-cCC--CEECCEEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999 888  778899998


Q ss_pred             EEeecccCCCCC
Q psy3930         273 TTSRLSFGITPL  284 (299)
Q Consensus       273 v~~k~~~~~~~r  284 (299)
                      |.........+.
T Consensus        99 V~~a~~~~~~~~  110 (115)
T 2cpz_A           99 VQLKRSKNDSKS  110 (115)
T ss_dssp             EECCCCSCCCCC
T ss_pred             EEEcCCCCcCCC
Confidence            887554433333

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=3.7e-17  Score=123.07  Aligned_cols=83  Identities=30%  Similarity=0.489  Sum_probs=76.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~   88 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG-VSG--FGYDHLILN   88 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHH-TTT--CEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHH-cCC--CeeCCcEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999 898  778899988


Q ss_pred             EEeecc
Q psy3930         273 TTSRLS  278 (299)
Q Consensus       273 v~~k~~  278 (299)
                      |.....
T Consensus        89 v~~a~~   94 (103)
T 2cq0_A           89 VEWAKP   94 (103)
T ss_dssp             EEESSC
T ss_pred             EEECCC
Confidence            876443

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.72  E-value=3e-17  Score=137.38  Aligned_cols=120  Identities=21%  Similarity=0.292  Sum_probs=103.3

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccCC------------------CCCCCcEEEEecCCCC
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDK------------------PDVDECTIYVEKLPPE  207 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~------------------~~~~~~~l~V~nLp~~  207 (299)
                      .|+.|.+       .++|.+|+ .+++..+.++.++|.++.+....                  .....++|||+|||.+
T Consensus        54 afV~F~~-------~~~A~~Al-~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~  125 (198)
T 2yh0_A           54 AFLEFRS-------VDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY  125 (198)
T ss_dssp             EEEEESC-------SHHHHHHG-GGTTEEETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTT
T ss_pred             EEEEeCC-------HHHHHHHH-HhcCCEEcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCC
Confidence            4666766       79999999 89999999999999876543111                  1245689999999999


Q ss_pred             CCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         208 AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       208 ~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      +++++|+++|++||.|..|.++++..+|.++|||||+|.+.++|.+|++. +||  ..+.|+.|.|...
T Consensus       126 ~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~v~~a  191 (198)
T 2yh0_A          126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG-LNG--MQLGDKKLLVQRA  191 (198)
T ss_dssp             CCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHH-HTT--CEETTEECEEEES
T ss_pred             CCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHH-cCC--CEECCEEEEEEEC
Confidence            99999999999999999999999988999999999999999999999999 898  7778998877663

>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=99.72  E-value=4.9e-17  Score=123.97  Aligned_cols=86  Identities=22%  Similarity=0.346  Sum_probs=77.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCC------CCCCCC
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLN------PCPPDY  266 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~ln------g~~~~~  266 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +|      |  ..+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~~~~--~~~   88 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA-ASLEAEGGG--LKL   88 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHH-HCTTTTTCC--EES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHH-hccccccCC--cEE
Confidence            44578999999999999999999999999999999999988999999999999999999999999 77      7  788


Q ss_pred             CCceEEEEeecccCC
Q psy3930         267 QSSILTTTSRLSFGI  281 (299)
Q Consensus       267 ~g~~l~v~~k~~~~~  281 (299)
                      .|+.|.|........
T Consensus        89 ~g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           89 DGRQLKVDLAVTRDE  103 (111)
T ss_dssp             SSCEEEEECCCCCCC
T ss_pred             cCEEEEEEECCCCcc
Confidence            899998877655433

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=2.1e-17  Score=123.43  Aligned_cols=88  Identities=20%  Similarity=0.362  Sum_probs=78.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceE-EEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVT-YVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~-~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ...++|||+|||+++++++|+++|++||.|. .|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.+.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~~~   83 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK-ING--KPLPGATPA   83 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHT-TTT--SEESSCSSC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHH-HcC--CccCCCCcc
Confidence            4568999999999999999999999999999 999999988999999999999999999999999 998  778888866


Q ss_pred             EEeecccCCCCC
Q psy3930         273 TTSRLSFGITPL  284 (299)
Q Consensus       273 v~~k~~~~~~~r  284 (299)
                      +.+++.|+.+.+
T Consensus        84 ~~l~v~~a~~~~   95 (99)
T 2div_A           84 KRFKLNYATYSG   95 (99)
T ss_dssp             EECCEEETTCCS
T ss_pred             eeEEEeecCCCC
Confidence            666777765544

>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=5.6e-17  Score=122.08  Aligned_cols=87  Identities=25%  Similarity=0.321  Sum_probs=77.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.++.+  +|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~   86 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE-MNG--RIVATKPLY   86 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHH-HTT--CBSSSSBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHH-hCC--CEeCCcEEE
Confidence            456789999999999999999999999999999999987  899999999999999999999999 888  778999999


Q ss_pred             EEeecccCCCCC
Q psy3930         273 TTSRLSFGITPL  284 (299)
Q Consensus       273 v~~k~~~~~~~r  284 (299)
                      |.........+.
T Consensus        87 V~~a~~~~~~~~   98 (103)
T 2d9p_A           87 VALAQRKEERQS   98 (103)
T ss_dssp             EEECSSCCCCCC
T ss_pred             EEEecccccCCC
Confidence            988655544333

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=2.8e-17  Score=125.83  Aligned_cols=85  Identities=29%  Similarity=0.360  Sum_probs=76.6

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhcCCceE--------EEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCC
Q psy3930         192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVT--------YVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCP  263 (299)
Q Consensus       192 ~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~--------~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~  263 (299)
                      .....++|||+|||.++++++|+++|++||.|.        .|.++.++.+|.++|||||+|.+.++|++|++. +||  
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~-l~g--   87 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEW-FDG--   87 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHH-HTT--
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHH-cCC--
Confidence            356679999999999999999999999999999        699999988999999999999999999999999 898  


Q ss_pred             CCCCCceEEEEeeccc
Q psy3930         264 PDYQSSILTTTSRLSF  279 (299)
Q Consensus       264 ~~~~g~~l~v~~k~~~  279 (299)
                      ..+.|+.|.|......
T Consensus        88 ~~~~g~~l~V~~a~~~  103 (113)
T 2cpe_A           88 KDFQGSKLKVSLARKK  103 (113)
T ss_dssp             CEETTEECEEECSSCC
T ss_pred             CccCCCEEEEEECCCC
Confidence            7788999988775444

>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=7.3e-17  Score=120.52  Aligned_cols=83  Identities=18%  Similarity=0.310  Sum_probs=75.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++  +||  ..+.|+.|.
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~--~~~--~~~~g~~l~   82 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN--MHF--HDIMGKKVE   82 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH--HCC--CBSSSCBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH--hCC--CEECCeEEE
Confidence            4557899999999999999999999999999999999998889999999999999999999997  477  778899998


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus        83 V~~a~~~   89 (99)
T 2dgs_A           83 VKRAEPR   89 (99)
T ss_dssp             EEECCCC
T ss_pred             EEECCCC
Confidence            8775544

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.71  E-value=6.3e-17  Score=128.46  Aligned_cols=86  Identities=20%  Similarity=0.266  Sum_probs=78.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|+.||.|..|.+++++.+|.++|||||+|.+.++|.+|++. +||  ..+.|+.|.
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~  115 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG-LNG--FNILNKRLK  115 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHH-TTT--EECSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHH-hCC--CEECCeEEE
Confidence            45568999999999999999999999999999999999988899999999999999999999999 998  778899999


Q ss_pred             EEeecccCC
Q psy3930         273 TTSRLSFGI  281 (299)
Q Consensus       273 v~~k~~~~~  281 (299)
                      |........
T Consensus       116 v~~a~~~~~  124 (139)
T 1u6f_A          116 VALAASGHQ  124 (139)
T ss_dssp             EEESSCCCC
T ss_pred             EEECCCCCC
Confidence            987655433

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.71  E-value=6.2e-17  Score=121.87  Aligned_cols=83  Identities=25%  Similarity=0.331  Sum_probs=75.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++|| |..|.+++++.+|.++|||||+|.+.++|++|+ . +||  ..+.|+.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~-l~g--~~~~g~~l~   86 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-T-YDG--ALLGDRSLR   86 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-G-GTT--CEETTEECE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-h-hCC--CeECCeEEE
Confidence            45578999999999999999999999997 999999999888999999999999999999999 7 898  788899998


Q ss_pred             EEeecccC
Q psy3930         273 TTSRLSFG  280 (299)
Q Consensus       273 v~~k~~~~  280 (299)
                      |.......
T Consensus        87 V~~a~~~~   94 (103)
T 2dng_A           87 VDIAEGRK   94 (103)
T ss_dssp             EEECCCCC
T ss_pred             EEEecCCC
Confidence            88755443

>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=2.1e-17  Score=124.14  Aligned_cols=84  Identities=26%  Similarity=0.451  Sum_probs=76.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~   85 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN-MNE--SELFGRTIR   85 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHH-HTT--EEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHH-hCC--CEECCcEEE
Confidence            34578999999999999999999999999999999999988999999999999999999999999 888  778899998


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus        86 V~~a~~~   92 (102)
T 2cqb_A           86 VNLAKPM   92 (102)
T ss_dssp             EEECCCC
T ss_pred             EEeCCCC
Confidence            8775444

>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=99.71  E-value=2.5e-18  Score=145.80  Aligned_cols=126  Identities=13%  Similarity=0.081  Sum_probs=97.2

Q ss_pred             HHHHHhhhcCCCe-eee--------eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeeccc--C--------
Q psy3930         130 RFFSQLLQESPEI-EVS--------VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ--D--------  190 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l~--------~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~--~--------  190 (299)
                      .-|..++..++.+ .+.        .|+.|       .+.++|..|++.+|+..+.++.++|..+....  +        
T Consensus        20 ~~L~~~F~~~G~v~~v~i~~~~~g~afV~f-------~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~~~p~~~~~~~~   92 (205)
T 3tyt_A           20 DRVFNVFCLYGNVEKVKFMKSKPGAAMVEM-------ADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLED   92 (205)
T ss_dssp             HHHHHHHTTTSCEEEEEECTTSTTCEEEEE-------SSHHHHHHHHHHHTTCEETTEECEEEECSCSCCCCCSCCBCTT
T ss_pred             HHHHHHHHhcCCeEEEEEecCCCCEEEEEE-------CCHHHHHHHHHHhCCCEECCceEEEEEccCCccCCCccccccc
Confidence            4577777777762 222        23333       45899999999999999999999988653110  0        


Q ss_pred             --------------C-----------CCCCCcEEEEecCCCCCCHHHHHHHhhcCCce--EEEEeeccCCCCCcceEEEE
Q psy3930         191 --------------K-----------PDVDECTIYVEKLPPEAEHDYIESVFSKYGKV--TYVSLPKFKSTGKLKGFAFV  243 (299)
Q Consensus       191 --------------~-----------~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i--~~v~i~~~~~~g~~kg~~fV  243 (299)
                                    +           .....++|||+|||+++++++|+++|++||.|  ..+++..+.  |..+|+|||
T Consensus        93 ~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV  170 (205)
T 3tyt_A           93 GSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLL  170 (205)
T ss_dssp             SCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEE
T ss_pred             CCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEE
Confidence                          0           01235689999999999999999999999998  899988764  556799999


Q ss_pred             EecCHHHHHHHHHhcCCCCCCC
Q psy3930         244 EFSTKEEAAKALELGLNPCPPD  265 (299)
Q Consensus       244 ~F~~~~~A~~Al~~~lng~~~~  265 (299)
                      +|.+.++|.+|+.. |||..+.
T Consensus       171 ~f~~~~~A~~Ai~~-lng~~~~  191 (205)
T 3tyt_A          171 EWDSKSDALETLGF-LNHYQMK  191 (205)
T ss_dssp             ECSSHHHHHHHHHH-HTTCEEC
T ss_pred             EeCCHHHHHHHHHH-hCCCCcc
Confidence            99999999999999 9984433

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=2.9e-17  Score=123.85  Aligned_cols=82  Identities=24%  Similarity=0.381  Sum_probs=75.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++|+++|+++|++||+|..|++++++. |.++|||||+|.+.++|++|+.  +||  ..++|+.|.
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~--~~~--~~~~gr~l~   82 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE--TPG--QKYKETDLL   82 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT--SSC--CCCTTTTCE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH--cCC--CEECCEEEE
Confidence            44568999999999999999999999999999999999985 9999999999999999999998  577  788999999


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |..+.++
T Consensus        83 V~~~~~~   89 (103)
T 1s79_A           83 ILFKDDY   89 (103)
T ss_dssp             EEEHHHH
T ss_pred             EEEchHH
Confidence            9987664

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.71  E-value=1.4e-16  Score=122.31  Aligned_cols=84  Identities=24%  Similarity=0.382  Sum_probs=77.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   88 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ-MGG--QWLGGRQIR   88 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-TTT--CEETTEECE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHH-hCC--CEECCEEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999 898  778899998


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus        89 V~~a~~~   95 (115)
T 2dgo_A           89 TNWATRK   95 (115)
T ss_dssp             EEESSCC
T ss_pred             EEEccCC
Confidence            8876544

>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=1e-17  Score=123.06  Aligned_cols=80  Identities=16%  Similarity=0.293  Sum_probs=70.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCC--ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G--~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      .+|||+|||.++++++|+++|++||  .|..|++++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.|.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~-l~g--~~~~gr~i~V~   78 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDL-LPK--RELHGQNPVVT   78 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHH-GGG--SCSSSCCCEEC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHH-cCC--CeeCCEEEEEE
Confidence            5799999999999999999999999  999999999988999999999999999999999999 898  78899999887


Q ss_pred             eeccc
Q psy3930         275 SRLSF  279 (299)
Q Consensus       275 ~k~~~  279 (299)
                      .....
T Consensus        79 ~~~~~   83 (90)
T 3p5t_L           79 PSNKL   83 (90)
T ss_dssp             CC---
T ss_pred             ECCCC
Confidence            65443

>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=99.71  E-value=6.1e-17  Score=122.11  Aligned_cols=84  Identities=23%  Similarity=0.341  Sum_probs=75.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCC-CCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKST-GKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~-g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ....++|||+|||.++++++|+++|++|| |..|.++++..+ |.++|||||+|.+.++|++|+ . +||  ..+.|+.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~-l~g--~~~~g~~l   86 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S-LNE--ESLGNKRI   86 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-G-GGT--CEETTEEC
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-h-cCC--CEeCCcEE
Confidence            34568999999999999999999999999 999999999877 999999999999999999999 7 888  77889999


Q ss_pred             EEEeecccCC
Q psy3930         272 TTTSRLSFGI  281 (299)
Q Consensus       272 ~v~~k~~~~~  281 (299)
                      .|........
T Consensus        87 ~V~~a~~~~~   96 (104)
T 1wi8_A           87 RVDVADQAQD   96 (104)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEccCCCC
Confidence            8887655433

>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=99.71  E-value=5.4e-17  Score=126.67  Aligned_cols=85  Identities=29%  Similarity=0.454  Sum_probs=78.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.++.+..+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   95 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG-LNG--QDLMGQPIS   95 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHH-HTT--CBSSSSBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHH-hCC--CeeCCeEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999 898  778999999


Q ss_pred             EEeecccC
Q psy3930         273 TTSRLSFG  280 (299)
Q Consensus       273 v~~k~~~~  280 (299)
                      |.......
T Consensus        96 v~~a~~~~  103 (126)
T 3ex7_B           96 VDWCFVRG  103 (126)
T ss_dssp             EEESEESS
T ss_pred             EEEecCCC
Confidence            98765543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.70  E-value=1.4e-17  Score=123.78  Aligned_cols=82  Identities=26%  Similarity=0.348  Sum_probs=72.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCc--eEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCC--CCCCCc
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGK--VTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCP--PDYQSS  269 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~--i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~--~~~~g~  269 (299)
                      ..-.||||+|||+++|+++|+++|++||.  +..|++++|+.+|.++|||||+|.+.++|++|++. +||..  +.++|+
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~-lng~~~~~~i~Gr   85 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQI-LQSLHPPLKIDGK   85 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHH-HHSSSSCEEETTE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHH-hcCCCCCceECCE
Confidence            34579999999999999999999999995  67899999998999999999999999999999999 88742  347899


Q ss_pred             eEEEEee
Q psy3930         270 ILTTTSR  276 (299)
Q Consensus       270 ~l~v~~k  276 (299)
                      +|.|...
T Consensus        86 ~i~V~~A   92 (95)
T 2lkz_A           86 TIGVDFA   92 (95)
T ss_dssp             EEEEEEC
T ss_pred             EEEEEEc
Confidence            9887653

>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=99.70  E-value=1.6e-16  Score=119.88  Aligned_cols=83  Identities=22%  Similarity=0.293  Sum_probs=74.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCC---c
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQS---S  269 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g---~  269 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.++++. +|.++|||||+|.+.++|++|++. +||  ..+.+   +
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~-l~g--~~~~gg~~~   87 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHA-LHG--SQTMPGASS   87 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHH-HSS--CCCCTTCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHH-HcC--CccCCCCCc
Confidence            4557899999999999999999999999999999999988 899999999999999999999999 888  56666   8


Q ss_pred             eEEEEeeccc
Q psy3930         270 ILTTTSRLSF  279 (299)
Q Consensus       270 ~l~v~~k~~~  279 (299)
                      .|.|......
T Consensus        88 ~l~V~~a~~~   97 (105)
T 2dnh_A           88 SLVVKFADTD   97 (105)
T ss_dssp             CCEEEESCSS
T ss_pred             cEEEEECccC
Confidence            8888764433

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.70  E-value=1.3e-17  Score=147.79  Aligned_cols=120  Identities=24%  Similarity=0.225  Sum_probs=104.9

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccCCC-CCCCcEEEEecCCCCC-CHHHHHHHhhcCCce
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP-DVDECTIYVEKLPPEA-EHDYIESVFSKYGKV  223 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~-~~~~~~l~V~nLp~~~-t~e~L~~~F~~~G~i  223 (299)
                      .|+.|.+       .++|.+|+..+++..+.++.+.|.++.+..... ....++|||+|||+++ ++++|+++|+.||.|
T Consensus       140 afV~f~~-------~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i  212 (284)
T 3smz_A          140 GFAEYMK-------KDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSP  212 (284)
T ss_dssp             EEEEESS-------HHHHHHHHHHHTTCEETTEECEEEECCGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCC
T ss_pred             EEEEECC-------HHHHHHHHHHhCCCEeCCcEEEEEECCCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCe
Confidence            4566655       899999999999999999999999877654332 4567899999999995 999999999999999


Q ss_pred             EEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         224 TYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       224 ~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      ..|.++++. +|.++|+|||+|.+.++|.+|+.. +||  ..+.|++|.|...
T Consensus       213 ~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~v~~a  261 (284)
T 3smz_A          213 TFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQ-ADG--LSLGGSHLRVSFC  261 (284)
T ss_dssp             SEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHH-HTT--CEETTEECEEEEC
T ss_pred             EEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHH-hCC--CccCCeEEEEEEe
Confidence            999999987 899999999999999999999999 898  7778998887764

>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=99.70  E-value=1.5e-16  Score=122.65  Aligned_cols=82  Identities=23%  Similarity=0.356  Sum_probs=75.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||.++++++|+++|++||.|..|.++.+. +|.++|||||+|.+.++|++|++. +||  ..+.|+.|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~-l~g--~~~~g~~l~V   80 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD-MNG--KSLHGKAIKV   80 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHH-CSS--CBCSSSBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHH-hCC--CEECCEEEEE
Confidence            346899999999999999999999999999999999998 999999999999999999999999 998  7789999999


Q ss_pred             Eeeccc
Q psy3930         274 TSRLSF  279 (299)
Q Consensus       274 ~~k~~~  279 (299)
                      ......
T Consensus        81 ~~a~~~   86 (116)
T 2fy1_A           81 EQAKKP   86 (116)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            876443

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=1.3e-16  Score=120.11  Aligned_cols=81  Identities=22%  Similarity=0.323  Sum_probs=73.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhc-CCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCC-CCCce
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSK-YGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPD-YQSSI  270 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~-~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~-~~g~~  270 (299)
                      ....++|||+|||+++++++|+++|++ ||.|..|.++++. +|.++|||||+|.+.++|.+|++. +||  .. +.|+.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~~g~~   81 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE-CQG--AVGLGSKP   81 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHH-TTT--CCSSSSSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHH-ccC--CcccCCEe
Confidence            345689999999999999999999999 9999999999998 999999999999999999999999 898  66 88998


Q ss_pred             EEEEeec
Q psy3930         271 LTTTSRL  277 (299)
Q Consensus       271 l~v~~k~  277 (299)
                      |.|....
T Consensus        82 l~v~~a~   88 (104)
T 2dhg_A           82 VRLSVAI   88 (104)
T ss_dssp             CCCCBCC
T ss_pred             EEEEEcc
Confidence            8766543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.70  E-value=2.4e-17  Score=123.67  Aligned_cols=79  Identities=29%  Similarity=0.367  Sum_probs=73.8

Q ss_pred             CCcEEEEecCCC------CCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCC
Q psy3930         195 DECTIYVEKLPP------EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQS  268 (299)
Q Consensus       195 ~~~~l~V~nLp~------~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g  268 (299)
                      .+++|||+|||.      ++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~-lng--~~~~g   81 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS-FHG--KRLDL   81 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHH-HTT--CBSSS
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHH-hCC--cccCC
Confidence            368999999999      999999999999999999999999998899999999999999999999999 899  77888


Q ss_pred             -ceEEEEee
Q psy3930         269 -SILTTTSR  276 (299)
Q Consensus       269 -~~l~v~~k  276 (299)
                       +.|.|...
T Consensus        82 ~r~l~V~~a   90 (100)
T 3ns6_A           82 KHRLFLYTM   90 (100)
T ss_dssp             SCBCEEEES
T ss_pred             CeEEEEEEC
Confidence             99988764

>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=99.70  E-value=3.9e-17  Score=131.47  Aligned_cols=108  Identities=21%  Similarity=0.285  Sum_probs=91.7

Q ss_pred             CHHHHHHHHHhc-Cccccccccceeeeeecc--------------cCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCce
Q psy3930         159 DPDDVVKALRKS-KLLEVTEDGTKVRRTVVV--------------QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKV  223 (299)
Q Consensus       159 ~~~~a~~Al~~~-~~~~~~~~~~~v~r~~~~--------------~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i  223 (299)
                      +.++|++|++.+ ++..+.+ .+.+..+.+.              ........++|||+|||+++++++|+++|++||.|
T Consensus        22 ~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i  100 (150)
T 2i2y_A           22 DAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPL  100 (150)
T ss_dssp             SHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCE
T ss_pred             CHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCE
Confidence            378999999998 8988988 7777654431              12224567899999999999999999999999999


Q ss_pred             EEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         224 TYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       224 ~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      ..|+++++     ++|||||+|.+.++|.+|+.. +||  ..+.|++|.|..
T Consensus       101 ~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~v~~  144 (150)
T 2i2y_A          101 RSVWVARN-----PPGFAFVEFEDPRDAADAVRE-LDG--RTLCGCRVRVEL  144 (150)
T ss_dssp             EEEEECSS-----SCSEEEEEESSHHHHHHHHHH-HSS--SCSSSSCCEEEE
T ss_pred             EEEEEeeC-----CCcEEEEEECCHHHHHHHHHH-cCC--CEECCeEEEEEE
Confidence            99999876     478999999999999999999 898  778899987765

>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=99.69  E-value=1e-16  Score=115.61  Aligned_cols=77  Identities=17%  Similarity=0.337  Sum_probs=71.9

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      ++|||+|||+++++++|+++|++||.|..+.++++..+|.++|||||+|.+.++|++|++. +||  ..+.|++|.|...
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~-l~g--~~~~g~~l~v~~a   78 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS-MQG--QDLNGRPLRINWA   78 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHH-HTT--CEETTEECEEEEC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHH-hcC--CeeCCcEEEEEec
Confidence            6899999999999999999999999999999999988999999999999999999999999 898  6778999877653

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1.3e-16  Score=120.64  Aligned_cols=83  Identities=29%  Similarity=0.452  Sum_probs=76.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ...+++|||+|||.++++++|+++|++||.|..|.++++..+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   96 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG-LNG--QDLMGQPIS   96 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHH-HTT--CBSSSSBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHH-hcC--CEECCcEEE
Confidence            45578999999999999999999999999999999999988999999999999999999999999 898  778899998


Q ss_pred             EEeecc
Q psy3930         273 TTSRLS  278 (299)
Q Consensus       273 v~~k~~  278 (299)
                      |.....
T Consensus        97 V~~a~~  102 (106)
T 1p27_B           97 VDWCFV  102 (106)
T ss_dssp             EEESEE
T ss_pred             EEeecC
Confidence            877443

>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=99.69  E-value=6.2e-17  Score=117.30  Aligned_cols=79  Identities=28%  Similarity=0.483  Sum_probs=73.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||+++++++|+++|++||.|..|.++++..+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.|
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~v   81 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN-MNE--SELFGRTIRV   81 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHH-HTT--CEETTEECEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHH-hCC--CEECCcEEEE
Confidence            4568999999999999999999999999999999999988999999999999999999999998 898  7788999887


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      ..
T Consensus        82 ~~   83 (85)
T 3mdf_A           82 NL   83 (85)
T ss_dssp             EE
T ss_pred             EE
Confidence            65

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.52  E-value=1.5e-18  Score=133.79  Aligned_cols=99  Identities=21%  Similarity=0.277  Sum_probs=83.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEE--------EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCC
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY--------VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPP  264 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~--------v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~  264 (299)
                      ....++|||+|||.++++++|+++|++||.|..        |.+++++.+|.++|||||+|.+.++|++|++. +||  .
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~-l~g--~   80 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDW-FDG--K   80 (116)
Confidence            345689999999999999999999999999998        89999877899999999999999999999999 898  7


Q ss_pred             CCCCceEEEEeecccCCCCCCCCCCCCccc
Q psy3930         265 DYQSSILTTTSRLSFGITPLGFESGGWWFK  294 (299)
Q Consensus       265 ~~~g~~l~v~~k~~~~~~~r~~~~g~~~~~  294 (299)
                      .+.|+.|.|..........++.+.|+..|.
T Consensus        81 ~~~g~~l~V~~a~~~~~~~~ggg~~~~~~~  110 (116)
T 2lcw_A           81 EFSGNPIKVSFATRRADFNRGGGNGRGGLE  110 (116)
Confidence            788999998876655454455444444443

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.69  E-value=1.2e-17  Score=148.54  Aligned_cols=120  Identities=14%  Similarity=0.266  Sum_probs=100.9

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccCC-----CCCCCcEEEEecCCCC-CCHHHHHHHhhc
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDK-----PDVDECTIYVEKLPPE-AEHDYIESVFSK  219 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~-----~~~~~~~l~V~nLp~~-~t~e~L~~~F~~  219 (299)
                      .|+.|.+       .++|.+|+..+++..+.+..+.|.++.+....     .....++|||+|||++ +++++|+++|++
T Consensus       162 afV~f~~-------~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~  234 (292)
T 2ghp_A          162 AYIDVTS-------KEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEG  234 (292)
T ss_dssp             EEEECSS-------HHHHHHHHHHHTTCEETTEECEEEECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGG
T ss_pred             EEEEECC-------HHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhc
Confidence            4666655       89999999999999999999999887654322     2346789999999999 999999999999


Q ss_pred             CCceEEEEeeccCC-CCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         220 YGKVTYVSLPKFKS-TGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       220 ~G~i~~v~i~~~~~-~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      ||.|..|+++++.. ||.++|||||+|.+.++|.+|+ . +||  ..+.|+.|.|...
T Consensus       235 ~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~-l~g--~~~~g~~i~V~~a  288 (292)
T 2ghp_A          235 FGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-Q-MNR--SLLGNREISVSLA  288 (292)
T ss_dssp             GSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-G-GTT--EEETTEEEEEEEC
T ss_pred             cCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-H-hcC--CEECCcEEEEEEe
Confidence            99999999999874 4999999999999999999999 8 998  7788999887663

>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=99.69  E-value=9.6e-17  Score=116.80  Aligned_cols=80  Identities=25%  Similarity=0.389  Sum_probs=73.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.|
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~v   80 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ-MGG--QWLGGRQIRT   80 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTT--CEETTEECEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHH-cCC--CEECCeEEEE
Confidence            3468999999999999999999999999999999999988999999999999999999999999 888  7788999888


Q ss_pred             Eee
Q psy3930         274 TSR  276 (299)
Q Consensus       274 ~~k  276 (299)
                      ...
T Consensus        81 ~~a   83 (87)
T 3bs9_A           81 NWA   83 (87)
T ss_dssp             EEE
T ss_pred             Eec
Confidence            764

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.69  E-value=8.8e-17  Score=132.06  Aligned_cols=115  Identities=22%  Similarity=0.282  Sum_probs=101.2

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceE
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVT  224 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~  224 (299)
                      -.|+.|.+       .++|.+|+ .+++..+.++.++|.++.+.........++|||+|||.++++++|+++|++||.|.
T Consensus        56 ~afV~f~~-------~~~a~~A~-~l~g~~~~g~~l~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~  127 (175)
T 1fje_B           56 FGYVDFES-------AEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR  127 (175)
T ss_dssp             EEEEEESS-------HHHHHHHH-HGGGEEETTEEEEEECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEE
T ss_pred             EEEEEECC-------HHHHHHHH-hcCCCEeCCeEEEEecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEE
Confidence            45788876       79999999 59999999999999988776666667789999999999999999999999999887


Q ss_pred             EEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         225 YVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       225 ~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .+     ..+|.++|||||+|.+.++|.+|++. +||  ..+.|+.|.|..
T Consensus       128 ~~-----~~~~~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~i~v~~  170 (175)
T 1fje_B          128 LV-----SQDGKSKGIAYIEFKSEADAEKNLEE-KQG--AEIDGRSVSLYY  170 (175)
T ss_dssp             EE-----CSSSSCCSEEEEECSSHHHHHHHHHH-HTE--EEETTEEEEEEE
T ss_pred             Ee-----cCCCCCceEEEEEECCHHHHHHHHHH-hCC--CEECCeEEEEEe
Confidence            76     34888999999999999999999999 898  778899887765

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.69  E-value=6.3e-17  Score=143.41  Aligned_cols=111  Identities=20%  Similarity=0.239  Sum_probs=99.4

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKL  237 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~  237 (299)
                      .+.++|.+|+..+++..+.++.+.+....        ..++|||+|||+++++++|+++|++||.|..+.++++..+|.+
T Consensus        65 ~~~~~A~~A~~~l~~~~~~g~~i~v~~~~--------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~  136 (284)
T 3smz_A           65 LNGEQAEAAINAFHQSRLRERELSVQLQP--------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQS  136 (284)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEEECC--------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCE
T ss_pred             CCHHHHHHHHHHcCCCeeCCeEEEEEecC--------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCcc
Confidence            45899999999999999999998887632        3579999999999999999999999999999999999889999


Q ss_pred             ceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeeccc
Q psy3930         238 KGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLSF  279 (299)
Q Consensus       238 kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~~  279 (299)
                      +|||||+|.+.++|.+|+.. +||  ..+.|+.|.|......
T Consensus       137 ~g~afV~f~~~~~a~~A~~~-l~~--~~~~g~~i~v~~a~~~  175 (284)
T 3smz_A          137 KGYGFAEYMKKDSAARAKSD-LLG--KPLGPRTLYVHWTDAG  175 (284)
T ss_dssp             EEEEEEEESSHHHHHHHHHH-HTT--CEETTEECEEEECCGG
T ss_pred             ceEEEEEECCHHHHHHHHHH-hCC--CEeCCcEEEEEECCCC
Confidence            99999999999999999998 888  7788999988765443

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.69  E-value=1.9e-17  Score=145.36  Aligned_cols=109  Identities=20%  Similarity=0.214  Sum_probs=94.1

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLK  238 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~k  238 (299)
                      +.++|..|+..+++..+.++.++|..+.        .+++|||+|||+.+++++|+++|+.||.|..|.++++. +|.++
T Consensus        67 ~~~~A~~A~~~l~g~~i~g~~l~v~~a~--------~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~  137 (261)
T 3sde_A           67 SRTLAEIAKAELDGTILKSRPLRIRFAT--------HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRAT  137 (261)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEECC--------CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TSCEE
T ss_pred             CHHHHHHHHHHcCCcEECCceeEeeecc--------cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC-CCCcC
Confidence            3899999999999999999999988764        25799999999999999999999999999999999995 99999


Q ss_pred             eEEEEEecCHHHHHHHHHhcC-CCCC-CCCCCceEEEEeec
Q psy3930         239 GFAFVEFSTKEEAAKALELGL-NPCP-PDYQSSILTTTSRL  277 (299)
Q Consensus       239 g~~fV~F~~~~~A~~Al~~~l-ng~~-~~~~g~~l~v~~k~  277 (299)
                      |||||+|.+.++|.+|+.. + +|.. ....++++.|....
T Consensus       138 g~afV~f~~~~~A~~A~~~-l~~~~~~~~~~~r~i~v~~~~  177 (261)
T 3sde_A          138 GKGFVEFAAKPPARKALER-CGDGAFLLTTTPRPVIVEPME  177 (261)
T ss_dssp             EEEEEEESSHHHHHHHHHH-HHHSCEESSSSCCBCEEEECC
T ss_pred             cEEEEEeCCHHHHHHHHHH-hcCCeEEecCCCceEEEeecc
Confidence            9999999999999999999 5 4421 22347888887643

>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=1.5e-16  Score=118.80  Aligned_cols=80  Identities=24%  Similarity=0.382  Sum_probs=74.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEE--------EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCC
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY--------VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPP  264 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~--------v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~  264 (299)
                      ....++|||+|||.++++++|+++|++||.|..        |++++++.+|.++|||||+|.+.++|++|++. +||  .
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~-l~g--~   86 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDW-FDG--K   86 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHH-HTT--C
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHH-hCC--C
Confidence            556789999999999999999999999999999        99999988999999999999999999999999 898  7


Q ss_pred             CCCCceEEEEe
Q psy3930         265 DYQSSILTTTS  275 (299)
Q Consensus       265 ~~~g~~l~v~~  275 (299)
                      .+.|+.|.|..
T Consensus        87 ~~~g~~l~V~~   97 (99)
T 2la6_A           87 EFSGNPIKVSF   97 (99)
T ss_dssp             BSSSSBCEEEE
T ss_pred             EeCCcEEEEEe
Confidence            78899998865

>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=99.68  E-value=1.9e-16  Score=120.41  Aligned_cols=85  Identities=33%  Similarity=0.429  Sum_probs=73.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.++.   ++.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~   92 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYG-RDG--YDYDGYRLR   92 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHH-cCC--CEECCeEEE
Confidence            45678999999999999999999999999999999965   455789999999999999999999 888  778899988


Q ss_pred             EEeecccCCCC
Q psy3930         273 TTSRLSFGITP  283 (299)
Q Consensus       273 v~~k~~~~~~~  283 (299)
                      |........++
T Consensus        93 V~~a~~~~~~~  103 (109)
T 1x4a_A           93 VEFPRSGRGTG  103 (109)
T ss_dssp             EECCCCCCCCC
T ss_pred             EEEcccCCCCC
Confidence            87755543333

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.68  E-value=6.4e-17  Score=128.03  Aligned_cols=114  Identities=20%  Similarity=0.239  Sum_probs=78.1

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLK  238 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~k  238 (299)
                      |...+..|+.++++-...+... .....  +.......++|||+|||.++++++|+++|++||.|..|.+++++.+|.++
T Consensus        13 ~~~~~~~a~~~~~g~~~~g~~~-~~~~~--~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~   89 (135)
T 2lea_A           13 GLVPRGSHMASMTGGQQMGRGS-MSYGR--PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESR   89 (135)
T ss_dssp             -----------------------CCSCC--SCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCC
T ss_pred             CCCchhhhhhhccCCCCCCCCC-CCcCC--CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccc
Confidence            4556677887777655444332 11212  22234557899999999999999999999999999999999998899999


Q ss_pred             eEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeecc
Q psy3930         239 GFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRLS  278 (299)
Q Consensus       239 g~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~~  278 (299)
                      |||||+|.+.++|++|++. +||  ..+.|+.|.|.....
T Consensus        90 G~afV~F~~~~~A~~Ai~~-l~g--~~i~g~~l~V~~a~~  126 (135)
T 2lea_A           90 GFAFVRFHDKRDAEDAMDA-MDG--AVLDGRELRVQMARY  126 (135)
T ss_dssp             SCCEEECSCHHHHHHHHTT-TTT--CCSSSSCCEEEECCC
T ss_pred             eEEEEEECCHHHHHHHHHH-cCC--CEECCEEEEEEECCC
Confidence            9999999999999999999 898  778899998877543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=2.6e-16  Score=117.76  Aligned_cols=80  Identities=20%  Similarity=0.410  Sum_probs=74.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.++.+. +|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   89 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMK-MDG--MTIKENIIK   89 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHH-HTT--EESSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHH-hCC--CEECCEEEE
Confidence            4567899999999999999999999999999999999998 999999999999999999999999 888  778899988


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus        90 v~~a   93 (100)
T 2do4_A           90 VAIS   93 (100)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            7663

>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=99.68  E-value=1.1e-16  Score=123.21  Aligned_cols=77  Identities=21%  Similarity=0.320  Sum_probs=70.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      ..+|||+|||+++++++|+++|++||.|..|+++++.  +.++|||||+|.+.++|++|++. +||  ..+.|+.|.|..
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~-l~~--~~~~g~~i~V~~   79 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK-MNG--MLLNDRKVFVGR   79 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHH-HTT--CEETTEECEEEE
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHH-cCC--CEECCEEEEEEE
Confidence            4689999999999999999999999999999999985  45799999999999999999999 898  788899998876


Q ss_pred             ec
Q psy3930         276 RL  277 (299)
Q Consensus       276 k~  277 (299)
                      ..
T Consensus        80 a~   81 (115)
T 4f25_A           80 FK   81 (115)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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=7.6e-17  Score=121.76  Aligned_cols=83  Identities=22%  Similarity=0.320  Sum_probs=74.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++.  ||  ..+.|+.|.
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~--~~--~~~~g~~l~   88 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS--RP--HTLDGRNID   88 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH--CS--EEETTEEEB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh--CC--CeECCEEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999997  76  778899887


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus        89 V~~a~~~   95 (105)
T 2dh8_A           89 PKPCTPR   95 (105)
T ss_dssp             CCCSCCS
T ss_pred             EEEccCC
Confidence            7654444

>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=99.68  E-value=1.8e-16  Score=120.74  Aligned_cols=83  Identities=28%  Similarity=0.437  Sum_probs=76.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.++.+..+|.++|||||+|.+.++|++|+.. +||  ..+.|+.|.
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~-l~g--~~~~g~~l~   99 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA-LNG--AEIMGQTIQ   99 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHH-cCC--CEECCcEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999 898  778899988


Q ss_pred             EEeecc
Q psy3930         273 TTSRLS  278 (299)
Q Consensus       273 v~~k~~  278 (299)
                      |.....
T Consensus       100 V~~a~~  105 (110)
T 1oo0_B          100 VDWCFV  105 (110)
T ss_dssp             EEESEE
T ss_pred             EEEccc
Confidence            876443

>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=99.68  E-value=1.3e-16  Score=130.56  Aligned_cols=84  Identities=27%  Similarity=0.419  Sum_probs=76.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+.+++++|+.+|++||.|..|.++.++.+|.++|||||+|.+.++|++|+.. +||  ..+.|++|.
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~-l~g--~~~~g~~l~  145 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA-LNG--AEIMGQTIQ  145 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHH-hCC--CEECCEEEE
Confidence            45568899999999999999999999999999999999988999999999999999999999999 898  778899998


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus       146 V~~a~~~  152 (165)
T 1rk8_A          146 VDWCFVK  152 (165)
T ss_dssp             EEESEEC
T ss_pred             EEEecCC
Confidence            8775544

>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=99.68  E-value=1.8e-16  Score=117.74  Aligned_cols=78  Identities=27%  Similarity=0.377  Sum_probs=73.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..++|+.|.|..
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~-l~g--~~~~g~~l~V~~   78 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN-LNG--YQLGSRFLKCGY   78 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHH-HTT--CEETTEECEEEE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHH-hCC--CeECCeEEEEEE
Confidence            57999999999999999999999999999999999988899999999999999999999999 898  778898887776


Q ss_pred             e
Q psy3930         276 R  276 (299)
Q Consensus       276 k  276 (299)
                      .
T Consensus        79 a   79 (96)
T 2x1f_A           79 S   79 (96)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.67  E-value=4.8e-16  Score=116.87  Aligned_cols=84  Identities=19%  Similarity=0.277  Sum_probs=74.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.++++..  .++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   86 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREK-LHG--TVVEGRKIE   86 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHH-hCC--CEECCEEEE
Confidence            45678999999999999999999999999999999998852  3899999999999999999999 888  778899998


Q ss_pred             EEeecccCC
Q psy3930         273 TTSRLSFGI  281 (299)
Q Consensus       273 v~~k~~~~~  281 (299)
                      |........
T Consensus        87 v~~a~~~~~   95 (103)
T 2cq3_A           87 VNNATARVM   95 (103)
T ss_dssp             EEECCSSCC
T ss_pred             EEEcccCCC
Confidence            887555433

>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=4.4e-16  Score=117.13  Aligned_cols=87  Identities=23%  Similarity=0.240  Sum_probs=76.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|+..   +  ..+.|+.|.
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~---~--~~~~g~~l~   86 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ---R--HMIDGRWCD   86 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS---C--EEETTEEEE
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc---C--CeeCCeEEE
Confidence            45578999999999999999999999999999999999988899999999999999999999985   3  467899998


Q ss_pred             EEeecccCCCCC
Q psy3930         273 TTSRLSFGITPL  284 (299)
Q Consensus       273 v~~k~~~~~~~r  284 (299)
                      |........+.+
T Consensus        87 v~~a~~~~~~~~   98 (103)
T 2cqg_A           87 CKLPNSKQSQDS   98 (103)
T ss_dssp             EECCCTTCCCCC
T ss_pred             EEecCCCCcCCC
Confidence            887665544443

>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=99.67  E-value=2.7e-16  Score=118.33  Aligned_cols=79  Identities=23%  Similarity=0.250  Sum_probs=70.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.+ .|.+++++ +|+++|||||+|.+.++|++|+ . +|+  ..+.++.|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~-~~~--~~~~gr~i~   85 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAM-A-KDK--ANMQHRYVE   85 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHH-T-TSS--CCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHH-H-hCC--CeECCcEEE
Confidence            3456899999999999999999999999954 99999998 9999999999999999999999 4 687  788899988


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus        86 V~~~~   90 (102)
T 1wez_A           86 LFLNS   90 (102)
T ss_dssp             EEEEC
T ss_pred             EEECC
Confidence            87644

>1s29_A LA protein; winged helix-turn-helix, autoantigen, RNA-binding, RNA binding protein; 1.60A {Trypanosoma brucei} SCOP: a.4.5.46

Probab=99.67  E-value=9.9e-18  Score=122.24  Aligned_cols=82  Identities=29%  Similarity=0.475  Sum_probs=76.8

Q ss_pred             HHHHHHHHHHhhhhcCCCCcchhHHHHHhhh--cCCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeee
Q psy3930         107 KQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQ--ESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       107 ~~~~~~i~~q~efyfsd~nL~~d~fl~~~~~--~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      +++...|++|+||||||+||++|.||+.+|.  ..||++++++++|++|+.++.+.+.+.+|++.+..+++++++.+|+|
T Consensus         8 ~~~~~~I~~QvEyYFSd~NL~~D~fL~~~m~~~~~G~Vpl~~i~sF~r~k~lt~d~~~i~~al~~S~~lev~edg~~VRR   87 (92)
T 1s29_A            8 SENKQKLQKQVEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVEAIRPSEKLVLSEDGLMVRR   87 (92)
T ss_dssp             HHHHHHHHHHHHHHTSHHHHTTCHHHHHHHTTSTTCCEEHHHHTTSHHHHTTCSCHHHHHHHHTTCSSEEECTTSSEEEE
T ss_pred             HHHHHHHHHHHHhhcchhhhccCHHHHHHhccCCCCCEEhHHHhCChhHHHHcCCHHHHHHHHhhCCeEEEeCCCCEEeC
Confidence            6778999999999999999999999999995  57899999999999999999999999999999999999999999999


Q ss_pred             eecc
Q psy3930         185 TVVV  188 (299)
Q Consensus       185 ~~~~  188 (299)
                      ..|.
T Consensus        88 ~~Pl   91 (92)
T 1s29_A           88 RDPL   91 (92)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            8764

>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=99.67  E-value=2.6e-16  Score=119.67  Aligned_cols=81  Identities=27%  Similarity=0.434  Sum_probs=75.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~-l~g--~~i~g~~l~   99 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ-LNG--FELAGRPMK   99 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHH-HTT--CCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHH-cCC--CEECCEEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999 898  788899998


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus       100 V~~a  103 (108)
T 2jrs_A          100 VGHV  103 (108)
T ss_dssp             EECS
T ss_pred             EEEc
Confidence            7653

>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=4.7e-16  Score=119.56  Aligned_cols=84  Identities=20%  Similarity=0.291  Sum_probs=76.4

Q ss_pred             CCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       192 ~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      .....++|||+|||.++++++|+++|++||.|..|++++++.+|.++|||||+|.+.++|++|++. +|+   .+.|+.|
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~---~~~g~~l   88 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD-PNP---IIDGRKA   88 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTC-SSC---EETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHh-CCC---cCCCEEE
Confidence            356679999999999999999999999999999999999988999999999999999999999998 785   4789999


Q ss_pred             EEEeeccc
Q psy3930         272 TTTSRLSF  279 (299)
Q Consensus       272 ~v~~k~~~  279 (299)
                      .|......
T Consensus        89 ~V~~a~~~   96 (116)
T 2cqd_A           89 NVNLAYLG   96 (116)
T ss_dssp             EEEESTTT
T ss_pred             EEEEcccC
Confidence            99886544

>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=99.67  E-value=1.1e-16  Score=141.69  Aligned_cols=73  Identities=19%  Similarity=0.314  Sum_probs=65.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCC-CceEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQ-SSILTT  273 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~-g~~l~v  273 (299)
                      ..++|||+|||.++++++|+++|++||.|..|+++.++     +|||||+|.+.++|.+|++. +||  ..+. |+.|.|
T Consensus       206 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~-l~g--~~~~~g~~l~v  277 (282)
T 3pgw_A          206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDA-LQG--FKITQNNAMKI  277 (282)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHH-cCC--cEeCCCCEEEE
Confidence            45789999999999999999999999999999998654     57999999999999999999 998  6676 888877


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      ..
T Consensus       278 ~~  279 (282)
T 3pgw_A          278 SF  279 (282)
T ss_pred             EE
Confidence            65

>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=8.8e-17  Score=120.77  Aligned_cols=82  Identities=11%  Similarity=0.125  Sum_probs=71.2

Q ss_pred             CCCcEEEEecCCC-CCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         194 VDECTIYVEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       194 ~~~~~l~V~nLp~-~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ...++|||+|||+ ++++++|+++|++||.|..|.++++      +|||||+|.+.++|.+|++. +||....+.|++|.
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~-l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDY-YTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHH-HHHSCCEETTEECE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHH-HcCCCceECCcEEE
Confidence            3568999999999 9999999999999999999999875      47999999999999999999 77755678999998


Q ss_pred             EEeecccCCC
Q psy3930         273 TTSRLSFGIT  282 (299)
Q Consensus       273 v~~k~~~~~~  282 (299)
                      |.....+...
T Consensus        86 V~~a~~~~~~   95 (102)
T 1x4d_A           86 VHLSQKYKRI   95 (102)
T ss_dssp             EEEECCCTTS
T ss_pred             EEECCCCCCC
Confidence            8876554333

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=2.3e-16  Score=116.54  Aligned_cols=80  Identities=31%  Similarity=0.465  Sum_probs=74.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|++|.
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~   89 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA-INN--KQLFGRVIK   89 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHH-TTT--EEETTEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHH-cCC--CeeCCcEEE
Confidence            45578999999999999999999999999999999999988899999999999999999999999 898  778899998


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |..
T Consensus        90 v~~   92 (94)
T 2e5h_A           90 ASI   92 (94)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            865

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.67  E-value=3.3e-16  Score=115.24  Aligned_cols=79  Identities=24%  Similarity=0.428  Sum_probs=71.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.++++  +|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~-l~g--~~~~g~~l~   79 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRM-MNG--MKLSGREID   79 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHH-HTT--CCBTTBCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHH-hCC--CEECCcEEE
Confidence            345789999999999999999999999999999999874  889999999999999999999999 888  778899886


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus        80 v~~a   83 (92)
T 2dgv_A           80 VRID   83 (92)
T ss_dssp             CEEC
T ss_pred             EEEc
Confidence            6553

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=3.9e-16  Score=117.42  Aligned_cols=84  Identities=21%  Similarity=0.253  Sum_probs=73.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.++++..  .++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   86 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAA-MNG--RKILGKEVK   86 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHH-HTT--EEETTEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHH-hCC--CCcCCCeEE
Confidence            45578999999999999999999999999999999998853  3689999999999999999999 888  778899998


Q ss_pred             EEeecccCC
Q psy3930         273 TTSRLSFGI  281 (299)
Q Consensus       273 v~~k~~~~~  281 (299)
                      |........
T Consensus        87 V~~a~~~~~   95 (103)
T 2cqi_A           87 VNWATTPSS   95 (103)
T ss_dssp             EEECCCTTC
T ss_pred             EEECCCCcc
Confidence            887655433

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=2.1e-16  Score=121.60  Aligned_cols=84  Identities=17%  Similarity=0.330  Sum_probs=75.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++.  ||  ..+.|+.|.|
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~--~~--~~~~g~~l~V  100 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA--RP--HSIDGRVVEP  100 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS--CS--EEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh--CC--cEECCEEEEE
Confidence            3458999999999999999999999999999999999988899999999999999999999986  66  7788999988


Q ss_pred             EeecccCC
Q psy3930         274 TSRLSFGI  281 (299)
Q Consensus       274 ~~k~~~~~  281 (299)
                      ........
T Consensus       101 ~~a~~~~~  108 (116)
T 1x4b_A          101 KRAVAREE  108 (116)
T ss_dssp             ECCSSCCC
T ss_pred             EECCCCcc
Confidence            77555433

>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=99.67  E-value=3.1e-16  Score=114.21  Aligned_cols=79  Identities=19%  Similarity=0.406  Sum_probs=71.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++.  +|  ..+.|+.|.
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~--~~~~g~~i~   83 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ--KE--HRLDGRVID   83 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS--SC--EEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh--CC--CEECCEEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999974  55  568899998


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |+.
T Consensus        84 v~~   86 (87)
T 3s7r_A           84 PKK   86 (87)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            864

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=2.3e-16  Score=116.68  Aligned_cols=80  Identities=26%  Similarity=0.359  Sum_probs=74.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|++|.
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~   88 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER-ANG--MELDGRRIR   88 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHH-HTT--EEETTEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHH-hCC--CEECCEEEE
Confidence            45568999999999999999999999999999999999988899999999999999999999999 888  778899988


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |..
T Consensus        89 v~~   91 (95)
T 2cqc_A           89 VSG   91 (95)
T ss_dssp             EEC
T ss_pred             EEe
Confidence            765

>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=99.67  E-value=4.6e-16  Score=125.98  Aligned_cols=84  Identities=26%  Similarity=0.407  Sum_probs=77.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.|+++..++.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~-l~g--~~~~g~~l~  112 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY-ING--TRLDDRIIR  112 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-TTT--SEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHH-hCC--CEECCeEEE
Confidence            45678999999999999999999999999999999999988899999999999999999999999 898  778899999


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |.....+
T Consensus       113 V~~a~~~  119 (156)
T 1h2v_Z          113 TDWDAGF  119 (156)
T ss_dssp             EEEESCC
T ss_pred             EEECCCC
Confidence            9887654

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.66  E-value=3.2e-16  Score=127.01  Aligned_cols=79  Identities=19%  Similarity=0.270  Sum_probs=73.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCC--ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G--~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..++|||+|||+++++++|+++|++||  .|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~-lng--~~~~Gr~l~  130 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLEL-LPG--KVLNGEKVD  130 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHH-STT--CEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHH-cCC--CEECCeEeE
Confidence            457999999999999999999999999  999999999988999999999999999999999999 999  788999999


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus       131 V~~a  134 (156)
T 3n9u_C          131 VRPA  134 (156)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            8764

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=2e-16  Score=119.16  Aligned_cols=77  Identities=25%  Similarity=0.289  Sum_probs=67.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|+++++      +|||||+|.+.++|++|++. +++....+.|++|.
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~-l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNY-YTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHH-HTTSCCEETTEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHH-hccCCceECCEEEE
Confidence            345789999999999999999999999999999999875      68999999999999999998 55434778898886


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus        86 V~~A   89 (105)
T 1sjq_A           86 IQFS   89 (105)
T ss_dssp             BCCC
T ss_pred             EEEc
Confidence            6553

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.66  E-value=1.8e-16  Score=113.98  Aligned_cols=73  Identities=26%  Similarity=0.498  Sum_probs=65.9

Q ss_pred             CcEEEEecCCCCC------CHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCc
Q psy3930         196 ECTIYVEKLPPEA------EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       196 ~~~l~V~nLp~~~------t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      +++|||+|||..+      ++++|+++|++||.|..|.+++  .+|.++|||||+|.+.++|++|++. +||  ..+.|+
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~--~~g~~~g~afV~f~~~~~A~~Ai~~-lng--~~~~g~   75 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKN-ADG--YKLDKQ   75 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCC--BTTBCCCEEEEEESSHHHHHHHHTT-SSS--CCCSSS
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecC--CCCcEeEEEEEEECCHHHHHHHHHH-hcC--cccCCc
Confidence            3689999999999      7899999999999999999984  4899999999999999999999999 999  777788


Q ss_pred             -eEEE
Q psy3930         270 -ILTT  273 (299)
Q Consensus       270 -~l~v  273 (299)
                       +|.|
T Consensus        76 ~~l~V   80 (81)
T 2krb_A           76 HTFRV   80 (81)
T ss_dssp             SCCCC
T ss_pred             eeEEe
Confidence             7654

>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=4.1e-16  Score=118.72  Aligned_cols=82  Identities=17%  Similarity=0.344  Sum_probs=72.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|++++++.+|.++|||||+|.+.++|++|++. + |  ..++|+.|.
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~-~-~--~~l~g~~l~   97 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-S-R--HELDSKTID   97 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHS-S-C--EEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHH-C-C--CcCCCEEEE
Confidence            45678999999999999999999999999999999999988899999999999999999999997 5 4  778899998


Q ss_pred             EEeecc
Q psy3930         273 TTSRLS  278 (299)
Q Consensus       273 v~~k~~  278 (299)
                      |.....
T Consensus        98 V~~a~~  103 (109)
T 2rs2_A           98 PKVAFP  103 (109)
T ss_dssp             EEECCC
T ss_pred             EEEccC
Confidence            876443

>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=99.65  E-value=3e-16  Score=114.32  Aligned_cols=79  Identities=28%  Similarity=0.493  Sum_probs=72.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCC-cceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGK-LKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~-~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ..++|||+|||.++++++|+++|++||.|..|.++.+..++. ++|||||+|.+.++|++|++. +||  ..+.|+.|.|
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~v   79 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH-MDG--GQIDGQEITA   79 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHH-HTT--CEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHH-cCC--CeECCeEEEE
Confidence            468999999999999999999999999999999999876665 899999999999999999999 898  7788999988


Q ss_pred             Eee
Q psy3930         274 TSR  276 (299)
Q Consensus       274 ~~k  276 (299)
                      ...
T Consensus        80 ~~a   82 (88)
T 4a8x_A           80 TAV   82 (88)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            764

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=2.7e-16  Score=120.10  Aligned_cols=82  Identities=20%  Similarity=0.256  Sum_probs=72.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHH---HHhhcCCceEEEEeeccCCCC---CcceEEEEEecCHHHHHHHHHhcCCCCCCCC
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIE---SVFSKYGKVTYVSLPKFKSTG---KLKGFAFVEFSTKEEAAKALELGLNPCPPDY  266 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~---~~F~~~G~i~~v~i~~~~~~g---~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~  266 (299)
                      ....++|||+|||+++++++|+   ++|++||+|..|.++++..++   .++|||||+|.+.++|++|++. |||  ..+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~-lng--~~~   88 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQC-VNN--VVV   88 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHH-HTT--EEE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHH-hCC--CEE
Confidence            3446899999999999999999   999999999999999887644   5669999999999999999999 898  778


Q ss_pred             CCceEEEEeec
Q psy3930         267 QSSILTTTSRL  277 (299)
Q Consensus       267 ~g~~l~v~~k~  277 (299)
                      .|+.|.|....
T Consensus        89 ~gr~l~V~~a~   99 (111)
T 2cpi_A           89 DGRTLKASLGT   99 (111)
T ss_dssp             TTEEEEEESCC
T ss_pred             CCEEEEEEecc
Confidence            89998776643

>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=99.65  E-value=3.8e-16  Score=114.07  Aligned_cols=78  Identities=29%  Similarity=0.451  Sum_probs=72.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      +.++|||+|||+++++++|+++|++||.|..+.++++..+|.++|||||+|.+.++|++|+ . +||  ..+.|+.|.|.
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~-~~g--~~~~g~~l~V~   80 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A-LDE--SLFRGRQIKVI   80 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-G-GTT--CEETTEECEEE
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-h-cCC--CEECCcEEEEE
Confidence            3579999999999999999999999999999999999889999999999999999999999 7 888  77889998887


Q ss_pred             ee
Q psy3930         275 SR  276 (299)
Q Consensus       275 ~k  276 (299)
                      ..
T Consensus        81 ~a   82 (89)
T 3ucg_A           81 PK   82 (89)
T ss_dssp             ET
T ss_pred             Ec
Confidence            64

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.65  E-value=3.3e-16  Score=120.76  Aligned_cols=80  Identities=24%  Similarity=0.352  Sum_probs=74.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~  113 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA-MNG--FQVGTKRLK  113 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHH-CCC--CEETTEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHH-cCC--CEECCEEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999 898  778899988


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |..
T Consensus       114 V~~  116 (118)
T 2khc_A          114 VQL  116 (118)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            765

>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=9.3e-16  Score=112.47  Aligned_cols=81  Identities=22%  Similarity=0.350  Sum_probs=70.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.++        +|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~   73 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN-LHH--YKLHGVNIN   73 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHH-HTT--CBCSSCBCE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHH-hcC--CccCCcEEE
Confidence            3456899999999999999999999999999999987        46999999999999999999 888  788899998


Q ss_pred             EEeecccCCCCC
Q psy3930         273 TTSRLSFGITPL  284 (299)
Q Consensus       273 v~~k~~~~~~~r  284 (299)
                      |........+++
T Consensus        74 v~~a~~~~~~~~   85 (90)
T 2dnq_A           74 VEASKNKSKASS   85 (90)
T ss_dssp             EECSSCCCCCCS
T ss_pred             EEECCCCCCCCC
Confidence            887655544333

>2cqk_A C-MPL binding protein; LA domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.5.46

Probab=99.65  E-value=2.7e-17  Score=121.50  Aligned_cols=84  Identities=27%  Similarity=0.428  Sum_probs=78.7

Q ss_pred             hHHHHHHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeee
Q psy3930         106 KKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       106 ~~~~~~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      .+++...|++|+||||||+||++|.||+.+|...+||+|+++++|++|+.++.+.+.+.+|++.+..+++++++.+|+|.
T Consensus        11 ~~~l~~~I~~QvEyYFSd~NL~~D~fL~~~md~~G~Vpl~~iasF~r~k~lt~d~~~i~~al~~S~~levsedg~kVRr~   90 (101)
T 2cqk_A           11 TEDLKECLKKQLEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSPMVQVDEKGEKVRPS   90 (101)
T ss_dssp             HHHHHHHHHHHHHHHTSHHHHHHCHHHHHHSCTTSCEEHHHHHHCHHHHHHCCCHHHHHHHHHHSSSEEECSSSSEEEEC
T ss_pred             HHHHHHHHHHHHHhhcchhhhccCHHHHHhhhcCCCEEhHHHhCChHHHHHcCCHHHHHHHHHhCCcEEEcCCCCeeeeC
Confidence            47788999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             eccc
Q psy3930         186 VVVQ  189 (299)
Q Consensus       186 ~~~~  189 (299)
                      .+..
T Consensus        91 ~~~~   94 (101)
T 2cqk_A           91 HKRC   94 (101)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            6543

>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=7.4e-16  Score=115.42  Aligned_cols=82  Identities=26%  Similarity=0.386  Sum_probs=71.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|   .++.+ .+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~   84 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNS-CNK--REIEGRAIR   84 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHH-TSS--EEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHH-hCC--CEeCCeEEE
Confidence            4567899999999999999999999999977   56666 4899999999999999999999999 898  778899998


Q ss_pred             EEeecccCC
Q psy3930         273 TTSRLSFGI  281 (299)
Q Consensus       273 v~~k~~~~~  281 (299)
                      |........
T Consensus        85 v~~a~~~~~   93 (101)
T 2fc9_A           85 LELQGPRGS   93 (101)
T ss_dssp             EEECSSCCC
T ss_pred             EEEcCCCCC
Confidence            887655433

>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=99.65  E-value=6.5e-16  Score=116.93  Aligned_cols=80  Identities=19%  Similarity=0.228  Sum_probs=74.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+.+++++|+++|++||.|..|.++++. +|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~  101 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ-YNG--VPLDGRPMN  101 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHH-hCC--CEeCCcEEE
Confidence            4557899999999999999999999999999999999998 999999999999999999999999 888  778899998


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus       102 V~~a  105 (107)
T 3ulh_A          102 IQLV  105 (107)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            8764

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=1.7e-15  Score=116.02  Aligned_cols=81  Identities=22%  Similarity=0.251  Sum_probs=74.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.++++. +|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   87 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISM-FNG--QLLFDRPMH   87 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHH-hCC--CEeCCCEEE
Confidence            3456899999999999999999999999999999999987 799999999999999999999999 888  778899999


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus        88 v~~a~   92 (114)
T 2do0_A           88 VKMDE   92 (114)
T ss_dssp             EEECS
T ss_pred             EEEcc
Confidence            87643

>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=99.64  E-value=5.1e-16  Score=114.87  Aligned_cols=79  Identities=25%  Similarity=0.386  Sum_probs=72.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.++++. +|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   88 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIAL-LNG--IRLYGRPIN   88 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHH-hCC--CEECCCEEE
Confidence            4556899999999999999999999999999999999987 599999999999999999999999 888  778899988


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |..
T Consensus        89 V~~   91 (95)
T 2ywk_A           89 VSG   91 (95)
T ss_dssp             EEC
T ss_pred             EEE
Confidence            765

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.64  E-value=7.9e-16  Score=119.66  Aligned_cols=80  Identities=19%  Similarity=0.414  Sum_probs=73.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|+ . +||  ..+.|+.|.|
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~-l~g--~~~~g~~l~V  109 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-A-MDE--TVFRGRTIKV  109 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-T-TTT--CEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-h-cCC--CeECCeEEEE
Confidence            34689999999999999999999999999999999999889999999999999999999999 7 898  7788999988


Q ss_pred             Eeec
Q psy3930         274 TSRL  277 (299)
Q Consensus       274 ~~k~  277 (299)
                      ....
T Consensus       110 ~~a~  113 (124)
T 2jwn_A          110 LPKR  113 (124)
T ss_dssp             EESS
T ss_pred             EECC
Confidence            7643

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=2.7e-16  Score=111.68  Aligned_cols=75  Identities=19%  Similarity=0.379  Sum_probs=69.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      ++|||+|||+++++++|+++|++||+|..|.+++++.+|.++|||||+|.+.++|++|++. ++   ..++|+.|.|+.
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~-~~---~~~~g~~l~v~~   75 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SR---HELDSKTIDPKV   75 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHT-TT---CCCSSCCCEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHh-CC---CccCCEEEEEEe
Confidence            5799999999999999999999999999999999988899999999999999999999998 66   677899888765

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=9.7e-17  Score=116.37  Aligned_cols=75  Identities=25%  Similarity=0.426  Sum_probs=68.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ...++|||+|||+++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~~   77 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA-LKA--SGVQAQMA   77 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHH-HHH--HTCCEESC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHH-hcC--CeEeeEEE
Confidence            3568999999999999999999999999999999999988999999999999999999999999 888  66666665

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.64  E-value=3.8e-16  Score=110.47  Aligned_cols=74  Identities=23%  Similarity=0.406  Sum_probs=68.6

Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      +|||+|||+++++++|+++|++||+|..|.+++++.+|.++|||||+|.+.++|++|++  +||  ..++|+.|.|+.
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~--~~~--~~~~g~~l~v~~   74 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE--IHF--HEINNKMVECKK   74 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS--SSC--CCSSSCCCEEEC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH--CCC--CEECCEEEEEEe
Confidence            48999999999999999999999999999999998889999999999999999999986  677  778899988764

>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=99.64  E-value=6.2e-16  Score=121.37  Aligned_cols=81  Identities=26%  Similarity=0.335  Sum_probs=74.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~-lng--~~i~g~~l~  119 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER-ANG--MELDGRRIR  119 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHH-HTT--CCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHH-hCC--CEECCEEEE
Confidence            45578999999999999999999999999999999999988999999999999999999999999 898  778899987


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus       120 V~~a  123 (129)
T 2kxn_B          120 VDFS  123 (129)
T ss_dssp             ESCC
T ss_pred             EEEe
Confidence            7653

>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=99.64  E-value=6.3e-16  Score=114.89  Aligned_cols=77  Identities=17%  Similarity=0.184  Sum_probs=70.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHH----HHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCc
Q psy3930         194 VDECTIYVEKLPPEAEHDYIE----SVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~----~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      ...++|||+|||+++++++|+    ++|++||.|..|.+++++.+   +|||||+|.+.++|++|++. +||  ..+.|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~-l~g--~~~~gr   80 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNS-LHR--YKIGSK   80 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHH-HTT--EEETTE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHH-hCC--CEECCe
Confidence            456899999999999999999    99999999999999988744   88999999999999999999 898  778899


Q ss_pred             eEEEEee
Q psy3930         270 ILTTTSR  276 (299)
Q Consensus       270 ~l~v~~k  276 (299)
                      .|.|...
T Consensus        81 ~l~V~~a   87 (96)
T 2dgx_A           81 KILVSLA   87 (96)
T ss_dssp             EEEEEEC
T ss_pred             EEEEEEc
Confidence            9988764

>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=99.64  E-value=7.6e-16  Score=115.58  Aligned_cols=80  Identities=21%  Similarity=0.257  Sum_probs=69.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.++++      +|||||+|.+.++|++|++. +++....+.|++|.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~-l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNY-YSAVTPHLRNQPIY   84 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHH-HHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHH-hccCCceECCcEEE
Confidence            345689999999999999999999999999999998864      68999999999999999998 55434778899998


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus        85 V~~a~~~   91 (101)
T 2cq1_A           85 IQYSNHK   91 (101)
T ss_dssp             EEECSCS
T ss_pred             EEEcCcc
Confidence            8775433

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=5.2e-16  Score=116.79  Aligned_cols=80  Identities=28%  Similarity=0.467  Sum_probs=74.2

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.|.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~v~   83 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN-LNG--REFSGRALRVD   83 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHH-SSS--BSCSSSCBEEE
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHH-hCC--CeeCCcEEEEE
Confidence            458999999999999999999999999999999999988999999999999999999999999 898  77889999887


Q ss_pred             eec
Q psy3930         275 SRL  277 (299)
Q Consensus       275 ~k~  277 (299)
                      ...
T Consensus        84 ~a~   86 (104)
T 1p1t_A           84 NAA   86 (104)
T ss_dssp             ETT
T ss_pred             eCC
Confidence            643

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.64  E-value=1.5e-16  Score=133.40  Aligned_cols=131  Identities=14%  Similarity=0.162  Sum_probs=101.5

Q ss_pred             HHHHHhhhcCCCe-e--------eeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC----------
Q psy3930         130 RFFSQLLQESPEI-E--------VSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD----------  190 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~--------l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~----------  190 (299)
                      .-|..++..++.+ .        .-.|+.|.+       .++|.+|+..+++..+.++.++|..+.+...          
T Consensus        19 ~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~-------~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~   91 (198)
T 1qm9_A           19 QSLFILFGVYGDVQRVKILFNKKENALVQMAD-------GNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQ   91 (198)
T ss_dssp             HHHHHHHHTTCCCSEEECSTTCSSCCEEECTT-------THHHHHHHHHHTTCCCSSCCCEEEECCCCSCCCSSSSSSSS
T ss_pred             HHHHHHHHhcCCEEEEEEEeCCCCEEEEEECC-------HHHHHHHHHHhCCCeecCeEEEEEEecCCCcCCCCcCCccc
Confidence            3456666666541 1        123555544       7999999999999999999999986543210          


Q ss_pred             -----------------------CCCCCCcEEEEecCCCCCCHHHHHHHhhcCC-ceEEEEeeccCCCCCcceEEEEEec
Q psy3930         191 -----------------------KPDVDECTIYVEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFS  246 (299)
Q Consensus       191 -----------------------~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G-~i~~v~i~~~~~~g~~kg~~fV~F~  246 (299)
                                             ...+..++|||+|||..+++++|+++|++|| .|..|++..+.     +|+|||+|.
T Consensus        92 ~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~  166 (198)
T 1qm9_A           92 GLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMG  166 (198)
T ss_dssp             SCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECS
T ss_pred             cccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeC
Confidence                                   0013378899999999999999999999999 99999996542     689999999


Q ss_pred             CHHHHHHHHHhcCCCCCCCCC-CceEEEEe
Q psy3930         247 TKEEAAKALELGLNPCPPDYQ-SSILTTTS  275 (299)
Q Consensus       247 ~~~~A~~Al~~~lng~~~~~~-g~~l~v~~  275 (299)
                      +.++|.+|+.. +||  ..+. |+.|.|..
T Consensus       167 ~~~~A~~A~~~-l~g--~~~~~g~~l~v~~  193 (198)
T 1qm9_A          167 SVEEAVQALID-LHN--HDLGENHHLRVSF  193 (198)
T ss_dssp             SHHHHHHHHHH-HTS--SCCSSCCSCCEEE
T ss_pred             CHHHHHHHHHH-hcC--CccCCCCeEEEEe
Confidence            99999999999 898  6667 88887665

>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=99.64  E-value=2.1e-15  Score=113.78  Aligned_cols=80  Identities=24%  Similarity=0.290  Sum_probs=71.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEE-EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~-v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ....++|||+|||+++++++|+++|++||.|.. |.|+.+ .+|+++|||||+|.+.++|++|++.  ||  ..++|+.|
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~--~~--~~~~gr~i   86 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK--HK--ERIGHRYI   86 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT--TT--CCSSSSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh--Cc--chhCCcEE
Confidence            345689999999999999999999999999987 899988 5999999999999999999999996  66  78889998


Q ss_pred             EEEeec
Q psy3930         272 TTTSRL  277 (299)
Q Consensus       272 ~v~~k~  277 (299)
                      .|....
T Consensus        87 ~v~~~~   92 (104)
T 1wg5_A           87 EIFKSS   92 (104)
T ss_dssp             EEEEEC
T ss_pred             EEEECC
Confidence            886643

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.3e-15  Score=115.64  Aligned_cols=85  Identities=21%  Similarity=0.251  Sum_probs=74.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCc-eEEEEee-ccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGK-VTYVSLP-KFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~-i~~v~i~-~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ...++|||+|||.++++++|+++|++||. |..|.++ .+..+|.++|||||+|.+.++|++|++. +|+....+.|+.|
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~~g~~~~~g~~l   84 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRK-LMPGRIQLWGHQI   84 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTT-TTTCCSCBTTBCC
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHH-hhCCCceecCCeE
Confidence            45689999999999999999999999998 9999998 7888899999999999999999999999 7511277889999


Q ss_pred             EEEeeccc
Q psy3930         272 TTTSRLSF  279 (299)
Q Consensus       272 ~v~~k~~~  279 (299)
                      .|......
T Consensus        85 ~V~~a~~~   92 (109)
T 2dis_A           85 AVDWAEPE   92 (109)
T ss_dssp             EEEESCSS
T ss_pred             EEEEcCCC
Confidence            88765443

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.64  E-value=2.6e-16  Score=123.84  Aligned_cols=83  Identities=28%  Similarity=0.372  Sum_probs=74.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEE--EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCC--CCCCCC
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTY--VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPC--PPDYQS  268 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~--v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~--~~~~~g  268 (299)
                      ....++|||+|||+++++++|+++|++||.|..  |++++++.+|.++|||||+|.+. +|.+|+.. +||.  .+.+.|
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~-l~g~~~~~~~~g   97 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQI-LQALHPPLTIDG   97 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHH-HTTCCCSCCGGG
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHH-hcCCCCCccCCC
Confidence            455789999999999999999999999999977  99999998999999999999999 99999999 8983  228889


Q ss_pred             ceEEEEeec
Q psy3930         269 SILTTTSRL  277 (299)
Q Consensus       269 ~~l~v~~k~  277 (299)
                      +.|.|....
T Consensus        98 r~l~V~~a~  106 (131)
T 2m2b_A           98 KTINVEFAK  106 (131)
T ss_dssp             CCCCCEECC
T ss_pred             EEEEEEECC
Confidence            999887643

>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=1.8e-16  Score=116.16  Aligned_cols=78  Identities=31%  Similarity=0.458  Sum_probs=71.4

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      ++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.+ |.+|+.. +||  ..+.|+.|.|...
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~-l~g--~~~~g~~l~V~~a   77 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK-LDN--TDFMGRTIRVTEA   77 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHT-SCS--SCCSSSSCSEEEC
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHH-hCC--CEECCeEEEEEEc
Confidence            58999999999999999999999999999999999888999999999999999 9999999 998  7788999988764


Q ss_pred             cc
Q psy3930         277 LS  278 (299)
Q Consensus       277 ~~  278 (299)
                      ..
T Consensus        78 ~~   79 (90)
T 2ki2_A           78 NP   79 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.63  E-value=7.6e-16  Score=116.41  Aligned_cols=81  Identities=25%  Similarity=0.416  Sum_probs=72.0

Q ss_pred             CCCCcEEEEecCCCCC------CHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCC
Q psy3930         193 DVDECTIYVEKLPPEA------EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDY  266 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~------t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~  266 (299)
                      ....++|||+|||..+      ++++|+++|++||.|..|.+++  .+|.++|||||+|.+.++|++|+.. +||  ..+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~--~~g~~~G~afV~f~~~~~A~~Ai~~-l~g--~~~   86 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKN-ADG--YKL   86 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCC--BTTBSCCEEEEEECSSSHHHHHHHH-CSS--EEC
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeC--CCCCeeeEEEEEECCHHHHHHHHHH-hCC--ccc
Confidence            3446899999999999      7899999999999999999984  4899999999999999999999999 999  778


Q ss_pred             CCc-eEEEEeecc
Q psy3930         267 QSS-ILTTTSRLS  278 (299)
Q Consensus       267 ~g~-~l~v~~k~~  278 (299)
                      .|+ +|.|.....
T Consensus        87 ~g~~~l~V~~a~~   99 (105)
T 2nlw_A           87 DKQHTFRVNLFTD   99 (105)
T ss_dssp             STTCEEEEECSCC
T ss_pred             CCCceEEEEEcch
Confidence            898 888876443

>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=99.63  E-value=2.8e-16  Score=120.55  Aligned_cols=89  Identities=22%  Similarity=0.294  Sum_probs=71.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..+.+..+..+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-l~g--~~~~g~~l~   98 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL-VNG--YKLYGKILV   98 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHH-STT--CBCSSCBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHH-hCC--CEeCCcEEE
Confidence            34578999999999999999999999999984332222222788899999999999999999999 998  777899998


Q ss_pred             EEeecccCCCCC
Q psy3930         273 TTSRLSFGITPL  284 (299)
Q Consensus       273 v~~k~~~~~~~r  284 (299)
                      |.........++
T Consensus        99 v~~a~~~~~~~~  110 (115)
T 2cpx_A           99 IEFGKNKKQRSS  110 (115)
T ss_dssp             EEECCCCSCCCC
T ss_pred             EEEccCCCCCCC
Confidence            887655544333

>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=99.63  E-value=2.9e-16  Score=135.10  Aligned_cols=115  Identities=15%  Similarity=0.169  Sum_probs=94.5

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC---------------------------------CC
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD---------------------------------KP  192 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~---------------------------------~~  192 (299)
                      .|+.|.+       .++|.+|++.+++..+.++.++|..+.+...                                 ..
T Consensus        75 afV~F~~-------~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (229)
T 2adc_A           75 ALVQMAD-------GNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI  147 (229)
T ss_dssp             EEEEESC-------HHHHHHHHHHHTTCBCSSSBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTC
T ss_pred             EEEEECC-------HHHHHHHHHHhCCCeECCeEEEEEEecCccccCccccccccccccccccCcccccCCccccccccC
Confidence            4666655       8999999999999999999999976543210                                 00


Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCC-ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCC-Cce
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQ-SSI  270 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G-~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~-g~~  270 (299)
                      ....++|||+|||.++++++|+++|++|| .|..|++..+     .+|||||+|.+.++|.+|++. +||  ..+. |+.
T Consensus       148 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~-l~g--~~~~~g~~  219 (229)
T 2adc_A          148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALID-LHN--HDLGENHH  219 (229)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHH-HTT--CBSSSSCB
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHH-HCC--CccCCCCe
Confidence            13368899999999999999999999999 9999999653     267999999999999999999 898  6677 888


Q ss_pred             EEEEe
Q psy3930         271 LTTTS  275 (299)
Q Consensus       271 l~v~~  275 (299)
                      |.|..
T Consensus       220 l~v~~  224 (229)
T 2adc_A          220 LRVSF  224 (229)
T ss_dssp             CEEEE
T ss_pred             EEEEE
Confidence            87765

>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=99.63  E-value=1.6e-16  Score=121.84  Aligned_cols=81  Identities=22%  Similarity=0.294  Sum_probs=74.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||.++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|+ . +||  ..+.|+.|.|
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~-l~g--~~~~g~~l~V   98 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-G-LTG--QRLLGVPIIV   98 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-H-HTT--EEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-H-cCC--CEeCCeEEEE
Confidence            44689999999999999999999999999999999999888999999999999999999999 7 888  7788999998


Q ss_pred             Eeecc
Q psy3930         274 TSRLS  278 (299)
Q Consensus       274 ~~k~~  278 (299)
                      .....
T Consensus        99 ~~a~~  103 (114)
T 2cq4_A           99 QASQA  103 (114)
T ss_dssp             EEHHH
T ss_pred             EecCC
Confidence            77543

>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=1.4e-15  Score=114.06  Aligned_cols=81  Identities=21%  Similarity=0.315  Sum_probs=70.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|+.|+   .|.++.+..+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~   85 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA-MED--GEIDGNKVT   85 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHH-hCC--CeECCeEEE
Confidence            45678999999999999999999999875   567777777899999999999999999999999 898  778899888


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus        86 V~~a~~~   92 (102)
T 2fc8_A           86 LDWAKPK   92 (102)
T ss_dssp             EEECCCC
T ss_pred             EEEecCC
Confidence            7775443

>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=99.63  E-value=4.4e-16  Score=115.96  Aligned_cols=81  Identities=23%  Similarity=0.238  Sum_probs=73.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-l~g--~~~~g~~l~   88 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID-LND--RPIGSRKVK   88 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHH-TTT--CEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHH-hCC--CeeCCeEEE
Confidence            34468999999999999999999999999998888888888999999999999999999999999 998  788899998


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus        89 V~~a   92 (98)
T 2cqp_A           89 LVLG   92 (98)
T ss_dssp             EEES
T ss_pred             EEEc
Confidence            8774

>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=99.63  E-value=6.1e-16  Score=117.97  Aligned_cols=80  Identities=19%  Similarity=0.224  Sum_probs=69.8

Q ss_pred             CCCCcEEEEecCCCC-CCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         193 DVDECTIYVEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~-~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ....++|||+|||++ +++++|+++|++||.|..|.+++.      +|||||+|.+.++|++|++. +|+....+.|++|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~-l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDH-CLKKALWFQGRCV   94 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHH-HHHSCCCSSSSCC
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHH-hccCCceECCEEE
Confidence            345789999999998 999999999999999999999753      68999999999999999998 7655577899999


Q ss_pred             EEEeeccc
Q psy3930         272 TTTSRLSF  279 (299)
Q Consensus       272 ~v~~k~~~  279 (299)
                      .|.....+
T Consensus        95 ~V~~a~~~  102 (112)
T 1x4f_A           95 KVDLSEKY  102 (112)
T ss_dssp             EEEEECSC
T ss_pred             EEEECccc
Confidence            98875544

>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=8.2e-16  Score=117.78  Aligned_cols=70  Identities=17%  Similarity=0.400  Sum_probs=65.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCC
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDY  266 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~  266 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.++++. +|.++|||||+|.+.++|++|++. +||  ..+
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~-l~g--~~~   91 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGH-FNG--KFI   91 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHH-HBT--CCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHH-hCC--CEE
Confidence            4567899999999999999999999999999999999998 999999999999999999999999 888  445

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.63  E-value=1.5e-16  Score=141.53  Aligned_cols=127  Identities=18%  Similarity=0.300  Sum_probs=100.2

Q ss_pred             HHHHHhhhcCCCe-e-----------eeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCc
Q psy3930         130 RFFSQLLQESPEI-E-----------VSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDEC  197 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~-----------l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~  197 (299)
                      .-|..++..++.+ .           +-.|+.|.+       .++|.+|+ .+++..+.++.+.+.+.         ..+
T Consensus        56 ~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~-------~~~A~~A~-~~~~~~~~g~~i~v~~~---------~~~  118 (292)
T 2ghp_A           56 NKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFAR-------YDGALAAI-TKTHKVVGQNEIIVSHL---------TEC  118 (292)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESS-------HHHHHHHH-TTTTCEETTEECEEEEC---------CSC
T ss_pred             HHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECC-------HHHHHHHH-HhCCcEeCCcEEEEEEC---------CCC
Confidence            4567777776652 1           123455544       89999999 58999999999888764         368


Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCC-ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G-~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      +|||+|||+++++++|+++|+.|| .|..|.++++. .|.++|||||+|.+.++|.+|+.. +||  ..+.|+.|.|...
T Consensus       119 ~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~v~~a  194 (292)
T 2ghp_A          119 TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDARYCVEK-LNG--LKIEGYTLVTKVS  194 (292)
T ss_dssp             EEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHH-HTT--CEETTEECEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CCCcceEEEEEECCHHHHHHHHHH-hCC--CEeCCcEEEEEEC
Confidence            999999999999999999999999 99999999887 588999999999999999999999 888  7778999888764


Q ss_pred             c
Q psy3930         277 L  277 (299)
Q Consensus       277 ~  277 (299)
                      .
T Consensus       195 ~  195 (292)
T 2ghp_A          195 N  195 (292)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.63  E-value=5.9e-16  Score=115.95  Aligned_cols=79  Identities=23%  Similarity=0.399  Sum_probs=69.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccC-CCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFK-STGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~-~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ....++|||+|||.++++++|+++|++|| |..|+++++. .+|.++|||||+|.+.++|.+|+ . +||  ..++|+.|
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~-l~g--~~~~g~~l   90 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S-LNE--ESLGNRRI   90 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-H-TTT--CCBTTBCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-h-cCC--CEECCeEE
Confidence            45679999999999999999999999999 9999999987 58999999999999999999999 7 898  77889988


Q ss_pred             EEEee
Q psy3930         272 TTTSR  276 (299)
Q Consensus       272 ~v~~k  276 (299)
                      .|...
T Consensus        91 ~V~~a   95 (100)
T 2j76_E           91 RVDVA   95 (100)
T ss_dssp             CCEEC
T ss_pred             EEEec
Confidence            76653

>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=99.62  E-value=3.1e-16  Score=116.09  Aligned_cols=79  Identities=24%  Similarity=0.269  Sum_probs=72.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.|.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-l~g--~~~~gr~l~v~   90 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID-LND--RPIGSRKVKLS   90 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHH-HTT--CEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHH-hCC--CeECCcEEEEE
Confidence            358999999999999999999999999999888888888999999999999999999999999 888  77889999887


Q ss_pred             ee
Q psy3930         275 SR  276 (299)
Q Consensus       275 ~k  276 (299)
                      ..
T Consensus        91 ~a   92 (95)
T 2ek1_A           91 GP   92 (95)
T ss_dssp             CC
T ss_pred             ec
Confidence            53

>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=99.62  E-value=1.1e-15  Score=117.78  Aligned_cols=80  Identities=24%  Similarity=0.252  Sum_probs=70.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.++++      +|||||+|.+.++|++|++. +++....+.|++|.
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~-l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNY-YTSVTPVLRGQPIY  100 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHH-HHHHCCCBTTBCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHH-hccCCceECCeEEE
Confidence            345789999999999999999999999999999999875      68999999999999999998 66444788999998


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus       101 V~~a~~k  107 (119)
T 2ad9_A          101 IQFSNHK  107 (119)
T ss_dssp             EEECSSS
T ss_pred             EEEccCC
Confidence            8875433

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.62  E-value=9e-16  Score=114.42  Aligned_cols=77  Identities=14%  Similarity=0.104  Sum_probs=68.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      .+.+++|||+|||+++++++|+++|++||.|..|.+++.      +|||||+|.+.++|.+|++. +||..+.+.|++|.
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~-ln~~~~~i~Gr~i~   90 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNY-AADNQIYIAGHPAF   90 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHH-HHHSCEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHH-hcCCCceeCCcEEE
Confidence            345789999999999999999999999999999999863      68999999999999999999 88855568899998


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus        91 V~~S   94 (100)
T 3r27_A           91 VNYS   94 (100)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            8764

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.62  E-value=2.2e-15  Score=117.24  Aligned_cols=83  Identities=17%  Similarity=0.209  Sum_probs=76.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.++++. +|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~-l~g--~~~~g~~l~  107 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQ-YKG--VPLDGRPMD  107 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHH-HTT--EESSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHH-cCC--CEECCcEEE
Confidence            4556899999999999999999999999999999999998 999999999999999999999999 888  778899998


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus       108 V~~a~~~  114 (124)
T 2kt5_A          108 IQLVASQ  114 (124)
T ss_dssp             EEEECCT
T ss_pred             EEEeCCC
Confidence            8875543

>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=99.61  E-value=3e-15  Score=112.97  Aligned_cols=79  Identities=19%  Similarity=0.199  Sum_probs=69.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.++++      +|||||+|.+.++|.+|++. ++|....+.|++|.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~-l~~~~~~i~Gr~l~   84 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTF-AADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHH-HHHSCCBSSSSBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHH-hccCCceECCEEEE
Confidence            345689999999999999999999999999999998864      68999999999999999998 77655778999998


Q ss_pred             EEeecc
Q psy3930         273 TTSRLS  278 (299)
Q Consensus       273 v~~k~~  278 (299)
                      |.....
T Consensus        85 V~~a~~   90 (104)
T 1wex_A           85 FNYSTS   90 (104)
T ss_dssp             EEECSS
T ss_pred             EEEccC
Confidence            877544

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.61  E-value=1.8e-15  Score=119.86  Aligned_cols=80  Identities=28%  Similarity=0.476  Sum_probs=74.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~  136 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN-MNE--SELFGRTIR  136 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHH-STE--EEETTEEEE
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHH-hCC--CEECCEEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999 898  778899998


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |..
T Consensus       137 v~~  139 (140)
T 2ku7_A          137 VNL  139 (140)
T ss_dssp             EEC
T ss_pred             EEe
Confidence            764

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=3.6e-15  Score=109.73  Aligned_cols=78  Identities=21%  Similarity=0.334  Sum_probs=68.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.+++        +||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   75 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRG-LDN--TEFQGKRMH   75 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHH-HTT--EEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHH-hCC--CeeCCcEEE
Confidence            45578999999999999999999999999999999974        3999999999999999999 898  778899998


Q ss_pred             EEeecccCC
Q psy3930         273 TTSRLSFGI  281 (299)
Q Consensus       273 v~~k~~~~~  281 (299)
                      |........
T Consensus        76 V~~a~~~~~   84 (92)
T 2dgt_A           76 VQLSTSRLR   84 (92)
T ss_dssp             EEESSCCCS
T ss_pred             EEEccCCCC
Confidence            887655433

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=2.5e-15  Score=114.17  Aligned_cols=78  Identities=23%  Similarity=0.408  Sum_probs=69.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.++++      +|||||+|.+.++|++|+.. +||  ..+.|+.|.
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   92 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS-VNG--TTIEGHVVK   92 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHH-cCC--CEECCcEEE
Confidence            456789999999999999999999999999999999875      68999999999999999999 898  778899988


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus        93 v~~a~~~   99 (109)
T 1x4g_A           93 CYWGKES   99 (109)
T ss_dssp             EECCCCC
T ss_pred             EEecCCC
Confidence            8765444

>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=99.61  E-value=3.4e-15  Score=111.40  Aligned_cols=78  Identities=26%  Similarity=0.367  Sum_probs=69.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.++++      +|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~-l~g--~~~~g~~l~   82 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE-LDN--MPLRGKQLR   82 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHH-HTT--CCBTTBCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHH-hCC--CEeCCceEE
Confidence            456789999999999999999999999999999999864      68999999999999999999 888  778899998


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus        83 v~~a~~~   89 (99)
T 2cpj_A           83 VRFACHS   89 (99)
T ss_dssp             EEESSCC
T ss_pred             EEEcCCC
Confidence            8775444

>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=99.61  E-value=5.7e-15  Score=112.09  Aligned_cols=76  Identities=22%  Similarity=0.340  Sum_probs=67.6

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCC-----
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQS-----  268 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g-----  268 (299)
                      ...++|||+|||+++++++|+++|++||.|..|.++.+       |||||+|.+.++|++|++. +||  ..+.|     
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~-l~g--~~~~g~~~~~   82 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK-LDN--TKFRSHEGET   82 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHH-SSS--EEEECTTSCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHH-HCc--CCccCCcCcc
Confidence            44689999999999999999999999999999999875       7999999999999999999 898  66777     


Q ss_pred             ceEEEEeeccc
Q psy3930         269 SILTTTSRLSF  279 (299)
Q Consensus       269 ~~l~v~~k~~~  279 (299)
                      +.|.|......
T Consensus        83 ~~i~V~~a~~~   93 (108)
T 1x4c_A           83 AYIRVKVDGPR   93 (108)
T ss_dssp             EEEEEEESSCC
T ss_pred             eEEEEEeCCCC
Confidence            88877765544

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.60  E-value=1.4e-15  Score=109.82  Aligned_cols=72  Identities=18%  Similarity=0.223  Sum_probs=66.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      +..|||+||++.+|+++|+++|.+||+|..+.+..      ++|||||+|.+.++|.+|++. |||  ..+.|+.|+|..
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~-Ln~--~~l~gr~I~V~~   77 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMA-LNN--CVLANTTIFAES   77 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHH-HTT--EEETTEEEEEEC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHH-hcC--CEECCcEEEEEE
Confidence            56899999999999999999999999999999875      479999999999999999999 898  888899999876


Q ss_pred             e
Q psy3930         276 R  276 (299)
Q Consensus       276 k  276 (299)
                      .
T Consensus        78 A   78 (89)
T 2wbr_A           78 P   78 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.60  E-value=1.5e-15  Score=115.89  Aligned_cols=77  Identities=21%  Similarity=0.330  Sum_probs=68.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCC-ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G-~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ...++|||+|||+++++++|+++|++|| .|..+.+...    .++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~-lng--~~l~Gr~i~   98 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALER-LNN--IEFRGSVIT   98 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHH-TTT--EEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHH-cCC--CEECCeEEE
Confidence            3468999999999999999999999999 8999998642    4689999999999999999999 999  888999998


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus        99 V~~a~  103 (111)
T 2jvr_A           99 VERDD  103 (111)
T ss_dssp             EEESC
T ss_pred             EEECC
Confidence            87754

>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=6.4e-16  Score=109.22  Aligned_cols=74  Identities=27%  Similarity=0.454  Sum_probs=68.1

Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      +|||+|||+++++++|+++|++||+|..|.+++++.+|.++|||||+|.+.++|++|++.  +|  ..+.|+.+.|+.
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~--~~--~~~~g~~l~v~~   74 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK--KY--HNVGLSKCEIKV   74 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT--SS--CCBTTBCCCEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh--CC--CeECCEEEEEEE
Confidence            589999999999999999999999999999999988899999999999999999999985  55  678898887764

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.60  E-value=2.3e-15  Score=111.77  Aligned_cols=82  Identities=16%  Similarity=0.299  Sum_probs=68.4

Q ss_pred             CCCCcEEEEecCCC-CCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         193 DVDECTIYVEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       193 ~~~~~~l~V~nLp~-~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ....++|||+|||+ ++++++|+++|++||.|..|.+.        +|||||+|.+.++|++|++. +||  ..+.|+.|
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l   75 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEC-ESQ--EMNFGKKL   75 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHH-HTC--SSCBTTTB
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHH-cCC--CeeCCcEE
Confidence            34578999999998 99999999999999999999984        57999999999999999999 898  77889999


Q ss_pred             EEEeecccCCCCCC
Q psy3930         272 TTTSRLSFGITPLG  285 (299)
Q Consensus       272 ~v~~k~~~~~~~r~  285 (299)
                      .|........+.++
T Consensus        76 ~V~~a~~~~~~~~~   89 (96)
T 2kvi_A           76 ILEVSSSNARPQFD   89 (96)
T ss_dssp             CEEEEECCCC----
T ss_pred             EEEEcCcCCCCCCC
Confidence            88886655444333

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.60  E-value=2.2e-15  Score=112.85  Aligned_cols=75  Identities=28%  Similarity=0.368  Sum_probs=68.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      ++|||+|||+++++++|+++|++||.|..|.++++     ++|||||+|.+.++|++|++. +||  ..+.|+.|.|...
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~V~~a   72 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG-LDG--KVICGSRVRVELS   72 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHH-HHH--SCSSSCCCEEEES
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHH-HCC--CeECCcEEEEEEc
Confidence            58999999999999999999999999999999876     578999999999999999999 888  6788999988875


Q ss_pred             ccc
Q psy3930         277 LSF  279 (299)
Q Consensus       277 ~~~  279 (299)
                      ...
T Consensus        73 ~~~   75 (101)
T 2hvz_A           73 TGM   75 (101)
T ss_dssp             SSC
T ss_pred             cCC
Confidence            544

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=2e-15  Score=114.92  Aligned_cols=79  Identities=20%  Similarity=0.312  Sum_probs=71.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.++++.  +.++|||||+|.+.++|++|++. +||  ..++|+.|.
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~-l~g--~~~~g~~l~  100 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREK-LHG--TVVEGRKIE  100 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHH-cCC--CEECCEEEE
Confidence            5667899999999999999999999999999999999885  44899999999999999999999 898  778899998


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus       101 V~~a  104 (109)
T 2err_A          101 VNNA  104 (109)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            8764

>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=3.3e-15  Score=113.71  Aligned_cols=75  Identities=25%  Similarity=0.375  Sum_probs=66.5

Q ss_pred             CCCCcEEEEecCCCC-CCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         193 DVDECTIYVEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~-~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ....++|||+|||++ +++++|+++|++||.|..|.+        ++|||||+|.+.++|++|++. +||  ..+.|+.|
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l   92 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLG-ENG--RVLAGQTL   92 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHH-HTT--CEETTEEC
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHH-cCC--CEECCeEE
Confidence            344689999999999 999999999999999999998        368999999999999999999 888  77889998


Q ss_pred             EEEeecc
Q psy3930         272 TTTSRLS  278 (299)
Q Consensus       272 ~v~~k~~  278 (299)
                      .|.....
T Consensus        93 ~V~~a~~   99 (110)
T 1wf1_A           93 DINMAGE   99 (110)
T ss_dssp             CEEESCC
T ss_pred             EEEECCC
Confidence            8877543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=8.7e-15  Score=109.17  Aligned_cols=78  Identities=27%  Similarity=0.348  Sum_probs=67.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcC--CceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCce
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKY--GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSI  270 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~--G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~  270 (299)
                      ....++|||+|||+++++++|+++|++|  |.|..|.++        +|||||+|.+.++|++|+.. +||  ..+.|+.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~   80 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKA-LNG--KVLDGSP   80 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHH-HSS--EEETTEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHH-hCC--CEeCCcE
Confidence            4557899999999999999999999999  899999875        46999999999999999999 898  7778999


Q ss_pred             EEEEeecccCC
Q psy3930         271 LTTTSRLSFGI  281 (299)
Q Consensus       271 l~v~~k~~~~~  281 (299)
                      |.|........
T Consensus        81 l~v~~a~~~~~   91 (99)
T 2cpd_A           81 IEVTLAKPVDK   91 (99)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCC
Confidence            88876544433

>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=99.59  E-value=2.1e-15  Score=115.71  Aligned_cols=80  Identities=13%  Similarity=0.091  Sum_probs=72.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCce-EEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKV-TYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i-~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ....++|||+|||+++++++|+++|+.||.| ..|.|+++. +|.++|||||+|.+.++|++|++.  ||  ..+.|+.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~--~~--~~~~gr~i   86 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL--HR--KKLNGREA   86 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG--CS--EEETTEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh--CC--CccCCeEE
Confidence            3456899999999999999999999999999 889999998 999999999999999999999985  76  88899999


Q ss_pred             EEEeec
Q psy3930         272 TTTSRL  277 (299)
Q Consensus       272 ~v~~k~  277 (299)
                      .|....
T Consensus        87 ~v~~a~   92 (114)
T 2cpy_A           87 FVHVVT   92 (114)
T ss_dssp             EEEEEC
T ss_pred             EEEECC
Confidence            997653

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.59  E-value=6.6e-15  Score=115.06  Aligned_cols=78  Identities=18%  Similarity=0.285  Sum_probs=68.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHH----HHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCC
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIE----SVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQS  268 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~----~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g  268 (299)
                      ....++|||+|||+.+++++|+    ++|++||.|..|.+.+   +|.++|||||+|.+.++|..|++. +||  ..+.|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~-lng--~~l~g   99 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEA-FQG--YPFQG   99 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHH-STT--CCCTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHH-HCC--CEeCC
Confidence            3457899999999999999876    6999999999998854   678899999999999999999999 999  78889


Q ss_pred             ceEEEEee
Q psy3930         269 SILTTTSR  276 (299)
Q Consensus       269 ~~l~v~~k  276 (299)
                      ++|.|...
T Consensus       100 r~l~V~~a  107 (127)
T 2a3j_A          100 NPLVITFS  107 (127)
T ss_dssp             SCCEEEEC
T ss_pred             CEEEEEEc
Confidence            99887653

>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=99.58  E-value=4.1e-15  Score=139.61  Aligned_cols=81  Identities=16%  Similarity=0.307  Sum_probs=75.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||+.+|+++|..+|++||.|..|.|+.+..+|.++|||||+|.+.++|.+||.. |||  ..+.|+.|.|
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  176 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH-ADG--KKIDGRRVLV  176 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHH-cCC--CEECCEEEEE
Confidence            4457999999999999999999999999999999999988999999999999999999999999 999  7889999999


Q ss_pred             Eeec
Q psy3930         274 TSRL  277 (299)
Q Consensus       274 ~~k~  277 (299)
                      .+..
T Consensus       177 ~~a~  180 (437)
T 3pgw_S          177 DVER  180 (437)
T ss_pred             EEeC
Confidence            8764

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=1.1e-14  Score=106.93  Aligned_cols=78  Identities=18%  Similarity=0.276  Sum_probs=71.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++| .|..|+++++ .+|.++|||||+|.+.++|++|++  +||  ..+.|+.|.
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~--~~g--~~~~gr~i~   80 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK--CNR--EYMGGRYIE   80 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH--SCS--EEETTEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH--hCC--ceeCCcEEE
Confidence            3456899999999999999999999999 8999999998 599999999999999999999999  677  778899988


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus        81 v~~a   84 (91)
T 2dgw_A           81 VFRE   84 (91)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            8764

>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=99.58  E-value=3.7e-15  Score=128.29  Aligned_cols=79  Identities=16%  Similarity=0.297  Sum_probs=73.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCC--ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYG--KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G--~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..++|||+|||+++++++|+++|++||  .|..|.|++++.+|.++|||||+|.+.++|++||+. +||  ..+.|+.|.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~-lng--~~~~Gr~l~  143 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDL-LPK--RELHGQNPV  143 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTT-STT--SCBTTBCCE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHH-cCC--CeECCEEeE
Confidence            467899999999999999999999999  999999999988999999999999999999999999 998  788899999


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus       144 V~~a  147 (229)
T 3q2s_C          144 VTPV  147 (229)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            9863

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.58  E-value=2.6e-15  Score=115.68  Aligned_cols=77  Identities=13%  Similarity=0.121  Sum_probs=69.1

Q ss_pred             cEEEEecC----CCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecC----HHH----HHHHHH--hcCCCC
Q psy3930         197 CTIYVEKL----PPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST----KEE----AAKALE--LGLNPC  262 (299)
Q Consensus       197 ~~l~V~nL----p~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~----~~~----A~~Al~--~~lng~  262 (299)
                      ..|||+||    |+.+++++|+++|+.||+|..|.++.|+.||.++|||||+|.+    +++    |.+|+.  . +|| 
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~-lng-   80 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHE-SSG-   80 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTT-TTC-
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhh-hcC-
Confidence            57999999    9999999999999999999999999999999999999999995    333    788888  5 788 


Q ss_pred             CCCCCCceEEEEee
Q psy3930         263 PPDYQSSILTTTSR  276 (299)
Q Consensus       263 ~~~~~g~~l~v~~k  276 (299)
                       ..+.|+.|+|.+.
T Consensus        81 -~~I~Gr~irV~ln   93 (136)
T 2j8a_A           81 -CFIMGFKFEVILN   93 (136)
T ss_dssp             -EEETTEEEEEEEC
T ss_pred             -CeecCcEEEEEEC
Confidence             8899999999874

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=1.2e-14  Score=106.47  Aligned_cols=76  Identities=18%  Similarity=0.312  Sum_probs=67.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.+++        +||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   74 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQ-LNG--KEVKGKRIN   74 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHH-hCC--CEECCcEEE
Confidence            44578999999999999999999999999999999974        3899999999999999999 888  778899998


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus        75 v~~a~~~   81 (90)
T 2dnp_A           75 VELSTKG   81 (90)
T ss_dssp             EEESCCC
T ss_pred             EEECCCC
Confidence            8775443

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.57  E-value=3.9e-15  Score=110.35  Aligned_cols=77  Identities=22%  Similarity=0.292  Sum_probs=67.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..+     ..+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   84 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEE-KQG--AEIDGRSVS   84 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHH-TTE--EEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHH-hCC--CEECCeEEE
Confidence            4567899999999999999999999999988766     23788999999999999999999999 898  778899987


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus        85 v~~a~   89 (96)
T 1fjc_A           85 LYYTG   89 (96)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            77643

>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=99.56  E-value=1.3e-14  Score=111.29  Aligned_cols=78  Identities=18%  Similarity=0.292  Sum_probs=70.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||.++++++|+++|++||.|..|.++++   +.++|||||+|.+.++|.+|+.. +||  ..+.|+.|.|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g~~l~v   79 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDH-LSG--FNVSNRYLVV   79 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHH-HTT--CBSSSCBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHH-cCC--CEECCeEEEE
Confidence            34689999999999999999999999999999999864   45689999999999999999999 898  7788999988


Q ss_pred             Eeec
Q psy3930         274 TSRL  277 (299)
Q Consensus       274 ~~k~  277 (299)
                      ....
T Consensus        80 ~~a~   83 (115)
T 3lqv_A           80 LYYN   83 (115)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            7653

>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=99.56  E-value=1.6e-14  Score=107.27  Aligned_cols=75  Identities=15%  Similarity=0.250  Sum_probs=66.2

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCC--Cce
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQ--SSI  270 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~--g~~  270 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.+.++      +|||||+|.+.++|++|++. +||  ..+.  |+.
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~-l~g--~~~~~~g~~   84 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK-MRG--FPLGGPDRR   84 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHH-HTT--CBCSSSSCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHH-HCC--CEeCCCCcE
Confidence            345689999999999999999999999999999998754      67999999999999999999 888  5666  888


Q ss_pred             EEEEee
Q psy3930         271 LTTTSR  276 (299)
Q Consensus       271 l~v~~k  276 (299)
                      |.|...
T Consensus        85 l~V~~a   90 (97)
T 1why_A           85 LRVDFA   90 (97)
T ss_dssp             CEEEEC
T ss_pred             EEEEEC
Confidence            877653

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.56  E-value=9.2e-15  Score=124.30  Aligned_cols=80  Identities=20%  Similarity=0.306  Sum_probs=72.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||+++++++|+++|++||+|..|++++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.+.+
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~-~~~--~~~~g~~i~~   89 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT-MNF--DVIKGKPVRI   89 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTT--CEETTEECEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHH-hhh--hhcCCccccc
Confidence            3468999999999999999999999999999999999998999999999999999999999999 888  7778888877


Q ss_pred             Eee
Q psy3930         274 TSR  276 (299)
Q Consensus       274 ~~k  276 (299)
                      ...
T Consensus        90 ~~~   92 (213)
T 4f02_A           90 MWS   92 (213)
T ss_dssp             EEC
T ss_pred             ccc
Confidence            654

>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=99.56  E-value=5.5e-15  Score=116.84  Aligned_cols=79  Identities=15%  Similarity=0.216  Sum_probs=72.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCc---eEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCc
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGK---VTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~---i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      ....++|||+|||+++|+++|+++|++||.   |..|++++++. |+++|||||+|.+.++|++|++  +||  ..++|+
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~--~~g--~~l~gr  115 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK--KDR--ESMGHR  115 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT--TTE--EESSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh--cCC--CEECCE
Confidence            445789999999999999999999999999   88999999985 9999999999999999999998  677  788899


Q ss_pred             eEEEEee
Q psy3930         270 ILTTTSR  276 (299)
Q Consensus       270 ~l~v~~k  276 (299)
                      .|.|...
T Consensus       116 ~i~V~~a  122 (136)
T 2hgl_A          116 YIEVFKS  122 (136)
T ss_dssp             EEEEEEC
T ss_pred             EEEEEEC
Confidence            9988764

>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=99.56  E-value=2e-15  Score=119.76  Aligned_cols=79  Identities=24%  Similarity=0.245  Sum_probs=69.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++|| +..|.|++++ +|+++|||||+|.+.++|++|+ . +|+  ..+.++.|.
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~-~g~srGfaFV~F~~~e~A~~Al-~-~~g--~~l~gR~i~  116 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEADVEFATHEEAVAAM-S-KDR--ANMQHRYIE  116 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSS-SSCSSCCCEEECSHHHHHHHHT-T-CCS--CSSSSCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECC-CCCCceEEEEEeCCHHHHHHHH-h-hCC--CEECCEEEE
Confidence            34568999999999999999999999999 7799999998 5999999999999999999999 6 788  788899887


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus       117 V~~a~  121 (139)
T 2hgn_A          117 LFLNS  121 (139)
T ss_dssp             CEECC
T ss_pred             EEECC
Confidence            76543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=7.7e-15  Score=111.60  Aligned_cols=77  Identities=21%  Similarity=0.249  Sum_probs=69.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||+++++++|+++|+.| .|..|+|++++ +|+++|||||+|.+.++|++|+ . +||  ..++|+.|.|
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~-~~~--~~~~gr~i~V   87 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-K-RNR--MLMIQRYVEV   87 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-H-TTT--EEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-h-cCC--CeECCeEEEE
Confidence            345799999999999999999999999 89999999987 5999999999999999999999 5 788  7788999988


Q ss_pred             Eee
Q psy3930         274 TSR  276 (299)
Q Consensus       274 ~~k  276 (299)
                      ...
T Consensus        88 ~~a   90 (109)
T 2dnn_A           88 SPA   90 (109)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            664

>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=99.55  E-value=4.2e-15  Score=115.67  Aligned_cols=80  Identities=23%  Similarity=0.287  Sum_probs=71.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|++||+  +||  ..+.|+.|.
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~--~~g--~~~~gr~i~   97 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC--RHK--QYMGNRFIQ   97 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT--SCS--BCSTTSCBE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH--hCC--CeECCcEEE
Confidence            4456899999999999999999999999999886566566699999999999999999999999  687  888899999


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus        98 V~~a  101 (124)
T 1wel_A           98 VHPI  101 (124)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            8764

>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=99.55  E-value=1.4e-14  Score=111.31  Aligned_cols=66  Identities=26%  Similarity=0.413  Sum_probs=60.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCce
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSI  270 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~  270 (299)
                      ..++|||+|||+++++++|+++|++||+|..|.++.+       |||||+|.+.++|++|++. |||  ..+.|+.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~-l~g--~~~~gr~   80 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK-LDN--TKFRSHE   80 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHH-HTT--CBCCCTT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHH-hCC--CEECCcE
Confidence            4689999999999999999999999999999999865       7999999999999999999 898  7788877

>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=99.55  E-value=5.6e-15  Score=111.98  Aligned_cols=79  Identities=19%  Similarity=0.172  Sum_probs=71.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCc---eEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCc
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGK---VTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~---i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      ....++|||+|||+++++++|+++|+.||.   |..|.+++++. |.++|||||+|.+.++|++|++  +||  ..++|+
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~--~~~--~~~~gr   82 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE--KHR--MYMGQR   82 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT--TTT--CCSSSS
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH--hCc--ceeCCe
Confidence            455789999999999999999999999998   89999999985 9999999999999999999999  577  778899


Q ss_pred             eEEEEee
Q psy3930         270 ILTTTSR  276 (299)
Q Consensus       270 ~l~v~~k  276 (299)
                      .|.|...
T Consensus        83 ~i~V~~a   89 (107)
T 2lmi_A           83 YVEVYEI   89 (107)
T ss_dssp             CCCCEEC
T ss_pred             EEEEEEC
Confidence            8877653

>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=99.55  E-value=2e-14  Score=108.05  Aligned_cols=75  Identities=24%  Similarity=0.410  Sum_probs=67.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||+++++++|+++|++||.|..|.+++        |||||+|.+.++|++|++. +||  ..+.|+.|.|
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~v   77 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEE-MNG--KDLEGENIEI   77 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHH-HTT--EEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHH-HCC--CccCCCEEEE
Confidence            4468999999999999999999999999999999873        4899999999999999999 888  6788999999


Q ss_pred             Eeeccc
Q psy3930         274 TSRLSF  279 (299)
Q Consensus       274 ~~k~~~  279 (299)
                      ......
T Consensus        78 ~~a~~~   83 (103)
T 2dgu_A           78 VFAKPP   83 (103)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            876544

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.55  E-value=1.7e-15  Score=113.45  Aligned_cols=80  Identities=18%  Similarity=0.208  Sum_probs=69.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|.. .++.+..+|.++|||||+|.+.++|++|++  +||  ..+.|+.|.
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~--l~g--~~~~g~~l~   88 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE--LTG--LKVFGNEIK   88 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH--GGG--CCBTTBCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh--cCC--cEECCcEEE
Confidence            345789999999999999999999999999887 666666689999999999999999999996  787  777899988


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus        89 V~~a~   93 (101)
T 1fj7_A           89 LEKPK   93 (101)
T ss_dssp             EECCS
T ss_pred             EEEcC
Confidence            77643

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=8.4e-15  Score=112.28  Aligned_cols=64  Identities=23%  Similarity=0.490  Sum_probs=59.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCC---CCcceEEEEEecCHHHHHHHHHhcC
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKST---GKLKGFAFVEFSTKEEAAKALELGL  259 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~---g~~kg~~fV~F~~~~~A~~Al~~~l  259 (299)
                      ...++|||+|||+++++++|+++|++||.|. +.++.+..+   |.++|||||+|.+.++|++|++. +
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~-~   72 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDA-C   72 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHH-S
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHh-h
Confidence            3468999999999999999999999999999 888887766   79999999999999999999998 5

>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=99.55  E-value=2.1e-14  Score=103.87  Aligned_cols=75  Identities=21%  Similarity=0.307  Sum_probs=66.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|.++++      +|||||+|.+.++|++|++.+.||  ..+.|++|.
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~--~~~~g~~l~   80 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNK--LIVNGRRLN   80 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTT--CEETTEECC
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCC--eeECCCEEE
Confidence            456789999999999999999999999999999999874      689999999999999999993388  778888887


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |..
T Consensus        81 v~~   83 (85)
T 2ytc_A           81 VKW   83 (85)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.55  E-value=8.4e-15  Score=113.05  Aligned_cols=79  Identities=16%  Similarity=0.225  Sum_probs=71.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCc---eEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCc
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGK---VTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~---i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      ....++|||+|||+++++++|+++|+.||.   |..|+++++. .|+++|||||+|.+.++|++|++  +||  ..+.|+
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~-~g~~~G~afV~F~~~~~a~~Al~--~~g--~~~~gr   88 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESEDDVKLALK--KDR--ESMGHR   88 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECS-SSCEEEEEEEEBSSHHHHHHHGG--GTT--EEETTE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECC-CCCCCeEEEEEECCHHHHHHHHh--cCC--CeECCe
Confidence            345689999999999999999999999998   8999999988 49999999999999999999999  477  788899


Q ss_pred             eEEEEee
Q psy3930         270 ILTTTSR  276 (299)
Q Consensus       270 ~l~v~~k  276 (299)
                      .|.|...
T Consensus        89 ~i~V~~a   95 (118)
T 2db1_A           89 YIEVFKS   95 (118)
T ss_dssp             EEEEEEE
T ss_pred             EEEEEEC
Confidence            9999764

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.55  E-value=5e-15  Score=111.05  Aligned_cols=78  Identities=24%  Similarity=0.430  Sum_probs=70.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||.++++++|+++|++||.|..|.++++. +|.++|||||+|.+.++|++|++   +|  ..++|+.|.|
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~---~~--~~~~g~~l~v   80 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE---SQ--INFHGKKLKL   80 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT---CC--CEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh---CC--CeECCEEEEE
Confidence            345899999999999999999999999999999999998 99999999999999999999987   55  6777888887


Q ss_pred             Eeec
Q psy3930         274 TSRL  277 (299)
Q Consensus       274 ~~k~  277 (299)
                      ....
T Consensus        81 ~~a~   84 (102)
T 2xs2_A           81 GPAI   84 (102)
T ss_dssp             EEEE
T ss_pred             EECC
Confidence            6544

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.55  E-value=1.1e-14  Score=110.68  Aligned_cols=74  Identities=26%  Similarity=0.514  Sum_probs=67.0

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|.++        +|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~-l~g--~~~~g~~l~   96 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEE-VHG--KSFANQPLE   96 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHH-cCC--CEECCeEEE
Confidence            5667899999999999999999999999999999987        57999999999999999999 898  777899987


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus        97 V~~a~  101 (108)
T 2jvo_A           97 VVYSK  101 (108)
T ss_dssp             EESCS
T ss_pred             EEEec
Confidence            76643

>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=99.54  E-value=7.4e-15  Score=108.99  Aligned_cols=78  Identities=22%  Similarity=0.400  Sum_probs=69.3

Q ss_pred             CCCCcEEEEecCCCCCCHHHHH----HHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCC
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIE----SVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQS  268 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~----~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g  268 (299)
                      ....++|||+|||.++++++|+    ++|++||.|..|.+++   +|.++|||||+|.+.++|++|++. +||  ..+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~-l~g--~~~~g   78 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRS-MQG--FPFYD   78 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHH-HTT--CEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHH-hCC--CEECC
Confidence            3456899999999999999999    9999999999999874   577889999999999999999999 898  77789


Q ss_pred             ceEEEEee
Q psy3930         269 SILTTTSR  276 (299)
Q Consensus       269 ~~l~v~~k  276 (299)
                      +.|.|...
T Consensus        79 ~~l~v~~a   86 (97)
T 1nu4_A           79 KPMRIQYA   86 (97)
T ss_dssp             EECEEEEC
T ss_pred             cEEEEEEc
Confidence            99887653

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.54  E-value=2e-14  Score=118.85  Aligned_cols=81  Identities=17%  Similarity=0.236  Sum_probs=75.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||+++++++|+++|++||.|..|.++.+. +|.++|||||+|.+.++|++|++. +||  ..+.|+.|.|
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  161 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQ-YKG--VPLDGRPMDI  161 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHH-STT--CBCSSSBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHH-hCC--CEECCEEEEE
Confidence            446899999999999999999999999999999999998 999999999999999999999999 998  7888999999


Q ss_pred             Eeecc
Q psy3930         274 TSRLS  278 (299)
Q Consensus       274 ~~k~~  278 (299)
                      .....
T Consensus       162 ~~a~~  166 (177)
T 2f3j_A          162 QLVAS  166 (177)
T ss_dssp             EEESS
T ss_pred             EEecC
Confidence            87543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=1.9e-14  Score=106.95  Aligned_cols=76  Identities=18%  Similarity=0.267  Sum_probs=66.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|. +.++.    +.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g~~l~   87 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSC-LQG--LRLGTDTLR   87 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHH-HTT--CCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHH-hCC--CEECCcEEE
Confidence            44568999999999999999999999999986 66664    35688999999999999999999 898  788899988


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus        88 V~~a   91 (97)
T 2e5j_A           88 VALA   91 (97)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            8764

>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=99.53  E-value=1.7e-14  Score=105.13  Aligned_cols=74  Identities=22%  Similarity=0.325  Sum_probs=60.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||.++++++|+++|++||.|..|+++++     ++|||||+|.+.++|++|     ++..+.+.++.|.|.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~-----~~~~~~~~g~~l~v~   73 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSL-----CGEDLIIKGISVHIS   73 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHT-----TTCEEEETTEEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHH-----hcCCceeCCEEEEEE
Confidence            4689999999999999999999999999999999865     578999999999999743     443355577777665


Q ss_pred             eecc
Q psy3930         275 SRLS  278 (299)
Q Consensus       275 ~k~~  278 (299)
                      ....
T Consensus        74 ~a~~   77 (88)
T 1wf0_A           74 NAEP   77 (88)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            5433

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.53  E-value=2.8e-14  Score=115.59  Aligned_cols=79  Identities=24%  Similarity=0.402  Sum_probs=73.2

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .++|||+|||+++++++|+++|+.||.|..+.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+++.+..
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~-l~~--~~~~g~~l~v~~   78 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT-LNG--LRLQTKTIKVSY   78 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTT--CEETTEECEEEE
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHH-cCC--CccCCceEEEEe
Confidence            47999999999999999999999999999999999988999999999999999999999999 888  778899988865


Q ss_pred             ec
Q psy3930         276 RL  277 (299)
Q Consensus       276 k~  277 (299)
                      ..
T Consensus        79 ~~   80 (167)
T 1fxl_A           79 AR   80 (167)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>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=99.53  E-value=3.3e-14  Score=108.48  Aligned_cols=74  Identities=27%  Similarity=0.292  Sum_probs=66.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||+++++++|+++|++||.|..|.+++      ++|||||+|.+.++|++|++. +||  ..+.|++|.|.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~-l~g--~~~~g~~l~V~   79 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRH-LAY--SKFHHVPLYLE   79 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHH-HTT--CBSSSSBCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHH-hCC--CEECCeEEEEE
Confidence            357999999999999999999999999999999875      367999999999999999999 898  77889999887


Q ss_pred             eec
Q psy3930         275 SRL  277 (299)
Q Consensus       275 ~k~  277 (299)
                      ...
T Consensus        80 ~a~   82 (111)
T 1whx_A           80 WAP   82 (111)
T ss_dssp             EEE
T ss_pred             ECC
Confidence            643

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.53  E-value=5.2e-14  Score=103.95  Aligned_cols=76  Identities=20%  Similarity=0.257  Sum_probs=65.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||.++++++|+++|++||.|..|  +.++.+|.   ||||+|.+.++|++|++  +||  ..+.|+.|.|.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~--l~g--~~~~g~~l~V~   77 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS--QSQ--HSLGGHRLRVR   77 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT--CSC--CEETTEECCCB
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh--cCC--eEECCEEEEEE
Confidence            45799999999999999999999999999987  44554665   99999999999999999  787  77889998887


Q ss_pred             eeccc
Q psy3930         275 SRLSF  279 (299)
Q Consensus       275 ~k~~~  279 (299)
                      .....
T Consensus        78 ~a~~~   82 (94)
T 2e5g_A           78 PREQK   82 (94)
T ss_dssp             CSCCS
T ss_pred             ECCcC
Confidence            55433

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.53  E-value=3e-14  Score=115.75  Aligned_cols=80  Identities=20%  Similarity=0.361  Sum_probs=73.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||+++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++. ++|  ..+.|+.|.+.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~-l~~--~~~~g~~l~v~   78 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV-LNG--ITVRNKRLKVS   78 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHH-HTT--CEETTEECEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHh-cCC--CEeCCcEEEEE
Confidence            358999999999999999999999999999999999988999999999999999999999998 888  77789998887


Q ss_pred             eec
Q psy3930         275 SRL  277 (299)
Q Consensus       275 ~k~  277 (299)
                      ...
T Consensus        79 ~~~   81 (168)
T 1b7f_A           79 YAR   81 (168)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=7.7e-14  Score=103.62  Aligned_cols=76  Identities=22%  Similarity=0.291  Sum_probs=65.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|+  ++++++|+++|++||.|..|.+.      .++|||||+|.+.++|++|+.. +||  ..+.|+.|.
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~-l~g--~~~~g~~l~   80 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAE-LNG--TQVESVQLK   80 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHH-TTT--EEETTEEEE
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHH-hCC--CeECCeEEE
Confidence            345689999996  89999999999999999999985      3468999999999999999999 998  677899988


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus        81 v~~a~~~   87 (97)
T 1x5p_A           81 VNIARKQ   87 (97)
T ss_dssp             EECCSSC
T ss_pred             EEECCCC
Confidence            8765443

>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=99.52  E-value=4.1e-14  Score=105.29  Aligned_cols=73  Identities=16%  Similarity=0.362  Sum_probs=66.1

Q ss_pred             CCCCcEEEEecCCC-CCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         193 DVDECTIYVEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       193 ~~~~~~l~V~nLp~-~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ....++|||+|||+ ++++++|+++|++||.|..|.+.        +|||||+|.+.++|++|++. +||  ..+.|+.|
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~-l~g--~~~~g~~l   87 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEX-ESQ--EMNFGKKL   87 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHH-HTT--SEETTEEC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHH-cCC--CEECCEEE
Confidence            56679999999998 99999999999999999999983        67999999999999999999 888  77789998


Q ss_pred             EEEee
Q psy3930         272 TTTSR  276 (299)
Q Consensus       272 ~v~~k  276 (299)
                      .|...
T Consensus        88 ~V~~a   92 (97)
T 2xnq_A           88 ILEVS   92 (97)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            87663

>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=99.52  E-value=1.8e-14  Score=106.15  Aligned_cols=77  Identities=21%  Similarity=0.344  Sum_probs=64.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCc-eEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGK-VTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~-i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ...++|||+|||+++++++|+++|++||. |..+.+.       ++|||||+|.+.++|++|++. +|| ...+.|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~-l~g-~~~~~g~~l~   76 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIET-LSG-KVELHGKIME   76 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHH-HTT-TCEETTEECE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHH-ccC-CeeECCEEEE
Confidence            45689999999999999999999999999 6555553       368999999999999999999 786 3456789888


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus        77 v~~a~~~   83 (93)
T 2cqh_A           77 VDYSVSK   83 (93)
T ss_dssp             EEECCCC
T ss_pred             EEEccCc
Confidence            8765443

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=1.3e-14  Score=112.62  Aligned_cols=78  Identities=18%  Similarity=0.231  Sum_probs=68.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCce----EEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCc
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKV----TYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i----~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      ...++|||+|||+++|+++|+++|++||.|    ..|.|+++. +|+++|||||+|.+.++|++|++.  |+  ..+.++
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~--~~--~~l~gR   95 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK--HK--DLLGKR   95 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT--TT--EESSSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh--CC--CeeCCe
Confidence            346899999999999999999999999975    689999885 899999999999999999999985  66  677899


Q ss_pred             eEEEEee
Q psy3930         270 ILTTTSR  276 (299)
Q Consensus       270 ~l~v~~k  276 (299)
                      .|.|...
T Consensus        96 ~i~V~~a  102 (123)
T 2dha_A           96 YIELFRS  102 (123)
T ss_dssp             EECCEEE
T ss_pred             EEEEEEC
Confidence            8877654

>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=99.51  E-value=2.6e-14  Score=111.37  Aligned_cols=78  Identities=24%  Similarity=0.345  Sum_probs=68.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceE--EEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCce
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVT--YVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSI  270 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~--~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~  270 (299)
                      ....++|||+|||+++++++|+++|++| .|.  .|+|++++. |+++|||||+|.+.++|++|++.  ++  ..+.|+.
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~--~~--~~l~gR~  112 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK--HK--ERIGHRY  112 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT--TT--CCBTTBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH--CC--CEECCEE
Confidence            3456899999999999999999999999 577  899999985 99999999999999999999985  55  7788998


Q ss_pred             EEEEee
Q psy3930         271 LTTTSR  276 (299)
Q Consensus       271 l~v~~k  276 (299)
                      |.|...
T Consensus       113 I~V~~a  118 (126)
T 2hgm_A          113 IEVFKS  118 (126)
T ss_dssp             CCCEEE
T ss_pred             EEEEEC
Confidence            877653

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.51  E-value=6.1e-14  Score=116.88  Aligned_cols=83  Identities=20%  Similarity=0.361  Sum_probs=74.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|+.||.|..|.+++++.+|.++|||||+|.+.++|.+|++.  +|  ..+.|+.|.
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~--~~--~~~~g~~l~   85 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA--RP--HKVDGRVVE   85 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT--CS--CEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc--CC--CEECCEEee
Confidence            45678999999999999999999999999999999999988999999999999999999999985  55  778899998


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      +......
T Consensus        86 v~~~~~~   92 (196)
T 1l3k_A           86 PKRAVSR   92 (196)
T ss_dssp             EEECCC-
T ss_pred             eecccCc
Confidence            8775443

>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=99.51  E-value=3.4e-14  Score=104.03  Aligned_cols=73  Identities=21%  Similarity=0.356  Sum_probs=59.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..|+++++     ++|||||+|.+.++|++     ++|..+.+.|+.+.
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~-----~~~~~~~~~g~~v~   77 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS-----LCGEDLIIKGISVH   77 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH-----HTTCEEEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH-----HcCCCcccCCEEEE
Confidence            345689999999999999999999999999999999874     58999999999999883     34444555677776


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |..
T Consensus        78 v~~   80 (89)
T 3d2w_A           78 ISN   80 (89)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            655

>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=99.51  E-value=4e-14  Score=103.29  Aligned_cols=73  Identities=19%  Similarity=0.372  Sum_probs=65.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||+++++++|+++|++| .|..+.+.      .++|||||+|.+.++|++|++. +||  ..+.|+.|.|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~-l~g--~~~~g~~l~V~   73 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQM-FHQ--YSFRGKDLIVQ   73 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHH-HTT--EEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHH-hCC--CeECCcEEEEE
Confidence            35789999999999999999999999 99999885      4588999999999999999999 898  77889999887


Q ss_pred             eec
Q psy3930         275 SRL  277 (299)
Q Consensus       275 ~k~  277 (299)
                      ...
T Consensus        74 ~a~   76 (88)
T 1wg1_A           74 LQP   76 (88)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            643

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.50  E-value=2.6e-14  Score=106.89  Aligned_cols=73  Identities=23%  Similarity=0.315  Sum_probs=64.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|++||.|..|++.+      ++|||||+|.+.++|.+|+.. +||  ..++|+.|.
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~-l~g--~~~~g~~l~   94 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVA-LAN--FPFQGRNLR   94 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHH-HTT--CEETTEECC
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHH-hCC--CeECCeEEE
Confidence            34568999999999999999999999999999999873      368999999999999999999 888  777788775


Q ss_pred             EE
Q psy3930         273 TT  274 (299)
Q Consensus       273 v~  274 (299)
                      |.
T Consensus        95 V~   96 (101)
T 2la4_A           95 TG   96 (101)
T ss_dssp             CC
T ss_pred             EE
Confidence            43

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.50  E-value=7e-14  Score=113.09  Aligned_cols=77  Identities=23%  Similarity=0.350  Sum_probs=70.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      ++|||+|||+++++++|+++|++||.|..|.+++++ +|.++|||||+|.+.++|.+|++. +||  ..+.|+.+.+...
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~-l~~--~~~~g~~i~v~~~   76 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQT-LNG--KQIENNIVKINWA   76 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHH-HTT--CEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHH-cCC--CccCCCeeEEEEc
Confidence            589999999999999999999999999999999987 688999999999999999999998 888  7778999888764


Q ss_pred             c
Q psy3930         277 L  277 (299)
Q Consensus       277 ~  277 (299)
                      .
T Consensus        77 ~   77 (166)
T 3md3_A           77 F   77 (166)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.49  E-value=7.2e-14  Score=106.61  Aligned_cols=82  Identities=22%  Similarity=0.232  Sum_probs=66.1

Q ss_pred             CCCcEEEE--ecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCC-C--CCC
Q psy3930         194 VDECTIYV--EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPP-D--YQS  268 (299)
Q Consensus       194 ~~~~~l~V--~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~-~--~~g  268 (299)
                      ...++|||  +|||.++++++|+++|++||.|..|.++.+      +|||||+|.+.++|++|++. |||..+ .  ..+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~-lnG~~~~~~lg~g   95 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVT-LNGKEVVDDLGQK   95 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHH-TTTCEEECTTSCE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHH-hCCCEEccccCCC
Confidence            34678999  779999999999999999999999988743      68999999999999999999 999433 1  146


Q ss_pred             ceEEEEee--cccCCC
Q psy3930         269 SILTTTSR--LSFGIT  282 (299)
Q Consensus       269 ~~l~v~~k--~~~~~~  282 (299)
                      ++|.+...  +.|..|
T Consensus        96 ~~l~v~~a~~~p~~~~  111 (114)
T 2cq2_A           96 ITLYLNFVEKVQWSGP  111 (114)
T ss_dssp             EECEEEEESCCCCSSC
T ss_pred             cEEEEEecccCcccCC
Confidence            77777553  344443

>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=99.48  E-value=4.5e-14  Score=112.47  Aligned_cols=82  Identities=22%  Similarity=0.320  Sum_probs=68.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEE--eecc---CCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCC
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVS--LPKF---KSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQ  267 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~--i~~~---~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~  267 (299)
                      ....++|||+|||+++++++|+++|++||.|..+.  ++.+   ..+|.++|||||+|.+.++|.+|+.. +||  ..+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~-lng--~~~~  118 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKE-ANG--YVLF  118 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHH-HTT--BEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHH-hCC--CEeC
Confidence            34568999999999999999999999999987641  1111   23788999999999999999999999 898  7788


Q ss_pred             CceEEEEeec
Q psy3930         268 SSILTTTSRL  277 (299)
Q Consensus       268 g~~l~v~~k~  277 (299)
                      |+.|.|....
T Consensus       119 g~~l~V~~a~  128 (143)
T 3egn_A          119 GKPMVVQFAR  128 (143)
T ss_dssp             TEECEEEECC
T ss_pred             CcEEEEEECC
Confidence            9999887653

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=1e-13  Score=102.58  Aligned_cols=77  Identities=21%  Similarity=0.314  Sum_probs=67.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEE-eeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVS-LPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~-i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ...++|||+|||+++++++|+++|++||.|..|+ ++.++.+|    .|||+|.+.++|++|+.. +||  ..+.|+.|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~-l~g--~~~~g~~l~   85 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDK-LNG--FQLENFTLK   85 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHH-HTT--CBCSSCBCE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHH-hCC--CEECCcEEE
Confidence            3468999999999999999999999999999995 88776443    399999999999999999 898  778899998


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus        86 V~~a~   90 (96)
T 2e44_A           86 VAYIP   90 (96)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            87643

>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=99.47  E-value=2.2e-13  Score=111.18  Aligned_cols=81  Identities=21%  Similarity=0.331  Sum_probs=69.2

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCC--CcceEEEEEecCHHHHHHHHHhcCCCCCC-CCCCceE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG--KLKGFAFVEFSTKEEAAKALELGLNPCPP-DYQSSIL  271 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g--~~kg~~fV~F~~~~~A~~Al~~~lng~~~-~~~g~~l  271 (299)
                      +.++|||+|||+++++++|+++|++||+|..|+++++..+|  .++|||||+|.+.++|++|++. +||..+ ...++++
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~-l~~~~~~~~~~~~~   80 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA-LHNMKVLPGMHHPI   80 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHH-HTTTCCCTTCSSCC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHH-hcCcEEccCCccce
Confidence            46899999999999999999999999999999999998666  8999999999999999999999 777332 2235666


Q ss_pred             EEEee
Q psy3930         272 TTTSR  276 (299)
Q Consensus       272 ~v~~k  276 (299)
                      .+...
T Consensus        81 ~~~~~   85 (175)
T 3nmr_A           81 QMKPA   85 (175)
T ss_dssp             EEEEC
T ss_pred             EEccc
Confidence            66553

>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=99.47  E-value=1e-13  Score=100.58  Aligned_cols=70  Identities=24%  Similarity=0.403  Sum_probs=64.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcC----C-------ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCC
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKY----G-------KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCP  263 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~----G-------~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~  263 (299)
                      ..++|||+|||+++++++|+++|++|    |       .|..+.+.++      +|||||+|.+.++|++|+ . +||  
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~-l~g--   74 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-A-FDG--   74 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-G-GTT--
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-h-cCC--
Confidence            46899999999999999999999999    8       8999998764      689999999999999999 7 898  


Q ss_pred             CCCCCceEEEE
Q psy3930         264 PDYQSSILTTT  274 (299)
Q Consensus       264 ~~~~g~~l~v~  274 (299)
                      ..+.|+.|.|.
T Consensus        75 ~~~~g~~l~V~   85 (87)
T 2hzc_A           75 IIFQGQSLKIR   85 (87)
T ss_dssp             CEETTEECEEE
T ss_pred             CEECCeEEEEe
Confidence            77889998875

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.46  E-value=1.5e-13  Score=116.27  Aligned_cols=79  Identities=28%  Similarity=0.348  Sum_probs=70.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||.++++++|+++|+.||.|..|.++++..+|.++|||||+|.+.++|.+|++. +||  ..+.|+.|.|
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-l~~--~~~~g~~l~v  102 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ-MNS--VMLGGRNIKV  102 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHH-HSS--CCCC-CCCEE
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHH-ccC--CeeCCeeEEE
Confidence            3468999999999999999999999999999999999988999999999999999999999998 888  7788999888


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      ..
T Consensus       103 ~~  104 (216)
T 2qfj_A          103 GR  104 (216)
T ss_dssp             EC
T ss_pred             ec
Confidence            54

>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=99.45  E-value=2.4e-13  Score=114.99  Aligned_cols=76  Identities=25%  Similarity=0.258  Sum_probs=68.8

Q ss_pred             CCCcEEEEecCC-CCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         194 VDECTIYVEKLP-PEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       194 ~~~~~l~V~nLp-~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..+++|||+||| ..+++++|+++|++||.|..|++++++     +|||||+|.+.++|++|++. |||  ..+.|++|.
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~-lng--~~~~g~~l~   73 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITH-LNN--NFMFGQKMN   73 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHH-hCC--CEECCceEE
Confidence            356899999999 799999999999999999999998753     68999999999999999999 999  888899999


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus        74 v~~s~   78 (205)
T 3tyt_A           74 VCVSK   78 (205)
T ss_dssp             EEECS
T ss_pred             EEEcc
Confidence            87643

>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=99.44  E-value=5.3e-13  Score=108.02  Aligned_cols=76  Identities=20%  Similarity=0.112  Sum_probs=64.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      ..+|||+|||+.+++++|+++|++||.|..|.+....    ++|||||+|.+.++|++|++. |||..+.-.++.|+|..
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~-LnG~~i~g~g~~L~V~~  120 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLS-LDGQNIYNACCTLRIDF  120 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHH-STTBCSSSSCSCEEEEE
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHH-hCCCEecCCCcEEEEEE
Confidence            3579999999999999999999999999999986432    478999999999999999999 99943333558888865


Q ss_pred             e
Q psy3930         276 R  276 (299)
Q Consensus       276 k  276 (299)
                      .
T Consensus       121 A  121 (164)
T 1sjr_A          121 S  121 (164)
T ss_dssp             C
T ss_pred             e
Confidence            4

>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=99.42  E-value=2.1e-13  Score=110.63  Aligned_cols=76  Identities=21%  Similarity=0.474  Sum_probs=67.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      +.++|||+|||+++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|++.   +  ..+.|+.+.+.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~---~--~~~~g~~i~v~   76 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT---Q--HILDGKVIDPK   76 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS---C--CEETTEECCCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc---c--cccCCeEcccc
Confidence            368999999999999999999999999999999999988999999999999999999999985   2  45567776654


Q ss_pred             e
Q psy3930         275 S  275 (299)
Q Consensus       275 ~  275 (299)
                      .
T Consensus        77 ~   77 (167)
T 2cjk_A           77 R   77 (167)
T ss_dssp             E
T ss_pred             c
Confidence            3

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.42  E-value=6.7e-13  Score=100.12  Aligned_cols=80  Identities=19%  Similarity=0.163  Sum_probs=69.1

Q ss_pred             CCCcEEEEecCCC-----CCCHHHHHHHhhcCCceEEEEeeccCC-CCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCC
Q psy3930         194 VDECTIYVEKLPP-----EAEHDYIESVFSKYGKVTYVSLPKFKS-TGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQ  267 (299)
Q Consensus       194 ~~~~~l~V~nLp~-----~~t~e~L~~~F~~~G~i~~v~i~~~~~-~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~  267 (299)
                      ...++|+|.|+..     +-++++|++.|++||.|..|.+++++. ++.++|||||+|.+.++|.+|++. |||  ..+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~-lnG--~~~~   82 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVD-LNG--RYFG   82 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHH-HTT--CEET
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHH-HCC--CEEC
Confidence            3467999999963     237899999999999999999998764 368899999999999999999999 999  8889


Q ss_pred             CceEEEEee
Q psy3930         268 SSILTTTSR  276 (299)
Q Consensus       268 g~~l~v~~k  276 (299)
                      |++|.+...
T Consensus        83 Gr~i~v~~a   91 (105)
T 2pe8_A           83 GRVVKACFY   91 (105)
T ss_dssp             TEECEEEEC
T ss_pred             CcEEEEEEc
Confidence            999988764

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.41  E-value=9.2e-13  Score=102.76  Aligned_cols=71  Identities=23%  Similarity=0.255  Sum_probs=61.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceE-EEEEecCHHHHHHHHHhcCCCCCCCCCC--ceEEE
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGF-AFVEFSTKEEAAKALELGLNPCPPDYQS--SILTT  273 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~-~fV~F~~~~~A~~Al~~~lng~~~~~~g--~~l~v  273 (299)
                      -.|||+||++.+|+++|+++|++||.|..|.+....     +|| |||+|.+.++|++|++. |||  ..+.|  +.|+|
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~-LnG--~~i~g~~~~LrI  100 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLS-LDG--QNIYNACCTLRI  100 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHH-HTT--CEEETTEEEEEE
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHH-cCC--CeecCCCcEEEE
Confidence            468999999999999999999999999999887642     577 99999999999999999 999  55555  66666


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      ..
T Consensus       101 ~~  102 (130)
T 3zzy_A          101 DF  102 (130)
T ss_dssp             EE
T ss_pred             Ee
Confidence            54

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=7.7e-13  Score=96.43  Aligned_cols=68  Identities=22%  Similarity=0.326  Sum_probs=59.5

Q ss_pred             CcE-EEEecCCCCCCHHH----HHHHhhcCC-ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCc
Q psy3930         196 ECT-IYVEKLPPEAEHDY----IESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       196 ~~~-l~V~nLp~~~t~e~----L~~~F~~~G-~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      ..| |||+|||..+++++    |+++|++|| +|..|       +|   |+|||+|.+.++|++|++. |||  ..+.|+
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~-l~G--~~l~gr   74 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKR-MEN--EDVFGN   74 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHH-HTT--CCSSSS
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHH-hcC--CccCCc
Confidence            445 99999999999888    558999995 99888       33   8999999999999999999 999  888899


Q ss_pred             eEEEEee
Q psy3930         270 ILTTTSR  276 (299)
Q Consensus       270 ~l~v~~k  276 (299)
                      +++|...
T Consensus        75 ~i~v~~A   81 (96)
T 2diu_A           75 RIIVSFT   81 (96)
T ss_dssp             CCEEESS
T ss_pred             eEEEEec
Confidence            9987653

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.39  E-value=3.2e-12  Score=99.10  Aligned_cols=69  Identities=26%  Similarity=0.270  Sum_probs=59.5

Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceE-EEEEecCHHHHHHHHHhcCCCCCCCCCC--ceEEEE
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGF-AFVEFSTKEEAAKALELGLNPCPPDYQS--SILTTT  274 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~-~fV~F~~~~~A~~Al~~~lng~~~~~~g--~~l~v~  274 (299)
                      .|||+|||+.+++++|+++|++||.|..|.+.. +     .|| |||+|.+.++|..|++. |||  ..+.|  +.|+|.
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~-LnG--~~i~g~~~~l~V~   97 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAA-LNG--ADIYAGCCTLKIE   97 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHH-HTT--CCCBTTBSEEEEE
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHH-hCC--CEecCCCeEEEEE
Confidence            478999999999999999999999999999864 2     276 99999999999999999 999  55544  677665


Q ss_pred             e
Q psy3930         275 S  275 (299)
Q Consensus       275 ~  275 (299)
                      .
T Consensus        98 ~   98 (124)
T 2e5i_A           98 Y   98 (124)
T ss_dssp             C
T ss_pred             E
Confidence            4

>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=99.36  E-value=3.1e-12  Score=112.92  Aligned_cols=78  Identities=22%  Similarity=0.395  Sum_probs=70.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHH----HHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCC
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIE----SVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQS  268 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~----~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g  268 (299)
                      ....++|||+|||.++++++|+    ++|++||.|..|.+.+   +|.++|||||+|.+.++|.+|++. +||  ..+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~g   79 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRS-MQG--FPFYD   79 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHH-hcC--CeeCC
Confidence            3457899999999999999977    8999999999999876   788999999999999999999999 898  88889


Q ss_pred             ceEEEEee
Q psy3930         269 SILTTTSR  276 (299)
Q Consensus       269 ~~l~v~~k  276 (299)
                      +.|.|...
T Consensus        80 ~~l~v~~a   87 (282)
T 3pgw_A           80 KPMRIQYA   87 (282)
T ss_pred             cEEEEEEe
Confidence            99998765

>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=99.34  E-value=3.7e-12  Score=109.28  Aligned_cols=77  Identities=22%  Similarity=0.265  Sum_probs=69.9

Q ss_pred             CCCCcEEEEecCCC-CCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         193 DVDECTIYVEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       193 ~~~~~~l~V~nLp~-~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ...+++|||+|||+ ++++++|+++|++||.|..|++++++     +|||||+|.+.++|++|++. +||  ..+.|+.|
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~-l~g--~~~~g~~l  102 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH-LNG--HKLHGKPI  102 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHH-HTT--CBCSSSBC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHH-hCC--CeECCeEE
Confidence            45679999999999 99999999999999999999998875     68999999999999999998 888  77889999


Q ss_pred             EEEeec
Q psy3930         272 TTTSRL  277 (299)
Q Consensus       272 ~v~~k~  277 (299)
                      .|....
T Consensus       103 ~v~~a~  108 (229)
T 2adc_A          103 RITLSK  108 (229)
T ss_dssp             EEECCS
T ss_pred             EEEEec
Confidence            887644

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.32  E-value=3.7e-12  Score=109.62  Aligned_cols=78  Identities=21%  Similarity=0.195  Sum_probs=67.4

Q ss_pred             CCCCcEEEEecCCCCC---------CHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCC
Q psy3930         193 DVDECTIYVEKLPPEA---------EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCP  263 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~---------t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~  263 (299)
                      ....++|||+|||..+         ++++|+.+|++||+|..|+++.+      +|||||+|.+.++|+.|+++ |+|..
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~a-m~g~~  203 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEA-MSNQT  203 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHH-HTTCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHH-hCCCE
Confidence            4567899999999998         79999999999999999999863      78999999999999999999 88844


Q ss_pred             CCC----------CCceEEEEeec
Q psy3930         264 PDY----------QSSILTTTSRL  277 (299)
Q Consensus       264 ~~~----------~g~~l~v~~k~  277 (299)
                      +.+          .|+.|.|....
T Consensus       204 l~~~~~~e~~~~~~gr~L~V~wA~  227 (240)
T 3u1l_A          204 LLLPSDKEWDDRREGTGLLVKWAN  227 (240)
T ss_dssp             CCCTTSTTGGGGGGSCCCEEEECC
T ss_pred             EeccccccccccCCCCEEEEEEcc
Confidence            421          78888887654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.31  E-value=4.8e-12  Score=105.78  Aligned_cols=75  Identities=23%  Similarity=0.271  Sum_probs=68.2

Q ss_pred             CCcEEEEecCCC-CCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         195 DECTIYVEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       195 ~~~~l~V~nLp~-~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      .+++|||+|||+ ++++++|+++|++||.|..|.+++++     +|||||+|.+.++|++|++. +||  ..+.|+.|.|
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~-l~~--~~~~g~~l~v   73 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH-LNG--HKLHGKPIRI   73 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHH-HTT--CCCSSCCCEE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHH-hCC--CeecCeEEEE
Confidence            468999999999 99999999999999999999998865     67999999999999999998 888  7788999988


Q ss_pred             Eeec
Q psy3930         274 TSRL  277 (299)
Q Consensus       274 ~~k~  277 (299)
                      ....
T Consensus        74 ~~a~   77 (198)
T 1qm9_A           74 TLSK   77 (198)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            7643

>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=99.29  E-value=1.7e-11  Score=93.38  Aligned_cols=77  Identities=18%  Similarity=0.230  Sum_probs=64.1

Q ss_pred             CCCcEEEEecCCCCCC-----------HHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCC
Q psy3930         194 VDECTIYVEKLPPEAE-----------HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPC  262 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t-----------~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~  262 (299)
                      ...++|+|.||.....           +++|+++|++||.|..|.| .++   .++|||||+|.+.++|++|+.. +|| 
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~-lng-   86 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQT-LDG-   86 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHH-STT-
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHH-cCC-
Confidence            4568999999944332           6899999999999999966 333   3789999999999999999999 999 


Q ss_pred             CCCCCCceEEEEeec
Q psy3930         263 PPDYQSSILTTTSRL  277 (299)
Q Consensus       263 ~~~~~g~~l~v~~k~  277 (299)
                       ..+.|++|.|....
T Consensus        87 -~~~~gr~l~v~~a~  100 (112)
T 2dit_A           87 -RWFGGRQITAQAWD  100 (112)
T ss_dssp             -CEETTEECEEEECC
T ss_pred             -CEECCcEEEEEEeC
Confidence             77889999887643

>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=99.28  E-value=2e-12  Score=108.26  Aligned_cols=79  Identities=37%  Similarity=0.649  Sum_probs=74.1

Q ss_pred             HHHHHHHHHHhhhhcCCCCcchhHHHHHhhh-cCCCeeeeeeecccccccCCCCHHHHHHHHHhc--Cccccccccceee
Q psy3930         107 KQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQ-ESPEIEVSVFLKCNKLARLTHDPDDVVKALRKS--KLLEVTEDGTKVR  183 (299)
Q Consensus       107 ~~~~~~i~~q~efyfsd~nL~~d~fl~~~~~-~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~--~~~~~~~~~~~v~  183 (299)
                      .++...|++|+||||||.||++|.||+.+|. ..+|++++++++|++|+.++.+.+.+..|+..+  ..+++++++.+++
T Consensus        10 ~~~~~~i~~q~e~yfs~~nl~~D~fl~~~~~~~~g~V~l~~i~sF~r~k~l~~d~~~I~~Al~~S~~~~lev~ed~~~vr   89 (193)
T 2voo_A           10 AALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIR   89 (193)
T ss_dssp             HHHHHHHHHHHHHHTSTTTGGGCHHHHHHHHHTTTCEEHHHHTTSHHHHHHCCCHHHHHHHHHTCSSCCEEECTTSSEEE
T ss_pred             HHHHHHHHHHhheecchhhcccCHHHHHHhcccCCcEEeHHHhhhhHHHHhcCCHHHHHHHHhhcccceEEEecccceEE
Confidence            6778999999999999999999999999998 588999999999999999999999999999999  8889999998888


Q ss_pred             ee
Q psy3930         184 RT  185 (299)
Q Consensus       184 r~  185 (299)
                      |.
T Consensus        90 R~   91 (193)
T 2voo_A           90 RS   91 (193)
T ss_dssp             EC
T ss_pred             ec
Confidence            76

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.28  E-value=6.5e-12  Score=109.94  Aligned_cols=77  Identities=22%  Similarity=0.413  Sum_probs=68.3

Q ss_pred             CCCCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCce
Q psy3930         191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSI  270 (299)
Q Consensus       191 ~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~  270 (299)
                      ......++|||+|||+++|+++|+++|++||.|..|.+.++      +|||||+|.+.++|.+|+.. +||  ..+.|+.
T Consensus        17 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~-l~g--~~i~g~~   87 (261)
T 3sde_A           17 KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAE-LDG--TILKSRP   87 (261)
T ss_dssp             CSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHH-HTT--CEETTEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHH-cCC--cEECCce
Confidence            33566789999999999999999999999999999999754      68999999999999999998 888  6778998


Q ss_pred             EEEEee
Q psy3930         271 LTTTSR  276 (299)
Q Consensus       271 l~v~~k  276 (299)
                      |.|...
T Consensus        88 l~v~~a   93 (261)
T 3sde_A           88 LRIRFA   93 (261)
T ss_dssp             CEEEEC
T ss_pred             eEeeec
Confidence            888653

>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=99.27  E-value=1.4e-12  Score=98.23  Aligned_cols=71  Identities=21%  Similarity=0.292  Sum_probs=61.6

Q ss_pred             EecCCCCCCHHHHHHHh------------hcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCC
Q psy3930         201 VEKLPPEAEHDYIESVF------------SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQS  268 (299)
Q Consensus       201 V~nLp~~~t~e~L~~~F------------~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g  268 (299)
                      +.|||..+++++|++.|            ++||.|..|.++++. +|.++|||||+|.+.++|++|++. +||  ..+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~-lng--~~~~G   95 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVID-LNN--RWFNG   95 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHH-HTT--CEETT
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHH-HCC--CEECC
Confidence            56778778887777666            999999999999886 588999999999999999999999 999  77889


Q ss_pred             ceEEEEe
Q psy3930         269 SILTTTS  275 (299)
Q Consensus       269 ~~l~v~~  275 (299)
                      ++|.|..
T Consensus        96 r~i~v~~  102 (104)
T 1jmt_A           96 QPIHAEL  102 (104)
T ss_dssp             EECCEEE
T ss_pred             EEEEEEE
Confidence            9987764

>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=99.27  E-value=1.1e-11  Score=93.32  Aligned_cols=79  Identities=22%  Similarity=0.286  Sum_probs=66.8

Q ss_pred             CCcEEEEecC--CCCC--------CHHHHHHHhhcCCceEEEEeeccCCC--CCcceEEEEEecCHHHHHHHHHhcCCCC
Q psy3930         195 DECTIYVEKL--PPEA--------EHDYIESVFSKYGKVTYVSLPKFKST--GKLKGFAFVEFSTKEEAAKALELGLNPC  262 (299)
Q Consensus       195 ~~~~l~V~nL--p~~~--------t~e~L~~~F~~~G~i~~v~i~~~~~~--g~~kg~~fV~F~~~~~A~~Al~~~lng~  262 (299)
                      +.+.|.+.|+  |.+.        .+++|++.|++||.|..|.++++..+  +.++|+|||+|.+.++|.+|++. ||| 
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~-lnG-   81 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQG-LTG-   81 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHH-HTT-
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHH-hCC-
Confidence            4578888887  3333        24799999999999999999988644  46899999999999999999999 999 


Q ss_pred             CCCCCCceEEEEee
Q psy3930         263 PPDYQSSILTTTSR  276 (299)
Q Consensus       263 ~~~~~g~~l~v~~k  276 (299)
                       ..+.|++|.+..-
T Consensus        82 -~~f~GR~i~v~~~   94 (105)
T 3v4m_A           82 -RKFANRVVVTKYC   94 (105)
T ss_dssp             -CEETTEECEEEEE
T ss_pred             -CEeCCCEEEEEEe
Confidence             8889999988763

>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=99.25  E-value=1.8e-12  Score=106.14  Aligned_cols=80  Identities=16%  Similarity=0.182  Sum_probs=67.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||.++++++|+++|..||.+.. .++++..+|.++|||||+|.+.++|++|+ . +||  ..+.|+.|.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~-l~g--~~~~g~~l~   84 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKAL-E-LTG--LKVFGNEIK   84 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHH-H-GGG--EEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHH-h-cCC--CEeCCeEEE
Confidence            455789999999999999999999999997765 23344457889999999999999999999 5 788  777899988


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus        85 v~~~~   89 (175)
T 1fje_B           85 LEKPK   89 (175)
T ss_dssp             EECCC
T ss_pred             EecCC
Confidence            86643

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.23  E-value=4.6e-11  Score=91.69  Aligned_cols=77  Identities=12%  Similarity=0.127  Sum_probs=68.4

Q ss_pred             CCCCCcEEEEecCCCC-CCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecC-HHHHHHHHHhcCCCCCCCCCCc
Q psy3930         192 PDVDECTIYVEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST-KEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       192 ~~~~~~~l~V~nLp~~-~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~-~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      ..+.++.|||+||+.+ +++++|+++|++||+|.+|.+.++..      .|||+|.+ +++|..|+.+ +|...+.++|.
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~-ln~~~~~i~g~   86 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKD-ANNGNLQLRNK   86 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHH-TTTSCBCTTSS
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHH-hhcCCcEEeCc
Confidence            3567899999999999 99999999999999999999988753      59999999 8999999999 76556888998


Q ss_pred             eEEEEe
Q psy3930         270 ILTTTS  275 (299)
Q Consensus       270 ~l~v~~  275 (299)
                      .+.+++
T Consensus        87 ~~~~ev   92 (121)
T 1owx_A           87 EVTWEV   92 (121)
T ss_dssp             SEEEEE
T ss_pred             EEEEEE
Confidence            888865

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.23  E-value=6.1e-11  Score=88.41  Aligned_cols=61  Identities=26%  Similarity=0.265  Sum_probs=52.8

Q ss_pred             CCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         205 PPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       205 p~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      +.++++++|+++|++||.|..|.++     +.++|||||+|.+.++|+.|++. ++|    +.+++|.|..
T Consensus        26 ~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~-~~~----~~g~~l~V~~   86 (100)
T 2d9o_A           26 KGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQN-EVG----LVDNPLKISW   86 (100)
T ss_dssp             CCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHT-CCB----CSSSBCEEEC
T ss_pred             CCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHh-cCC----CCCCeEEEEE
Confidence            3578999999999999999999997     35689999999999999999998 665    4588887765

>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=99.22  E-value=2.8e-11  Score=98.49  Aligned_cols=74  Identities=23%  Similarity=0.372  Sum_probs=63.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcC----C-------ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCC
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKY----G-------KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCP  263 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~----G-------~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~  263 (299)
                      +.++|||+|||+++++++|+++|++|    |       .|..+.+.+      ++|||||+|.+.++|++|+ . +||  
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~-~~~--   72 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-A-FDG--   72 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-G-GTT--
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-H-hCC--
Confidence            46899999999999999999999999    6       677777654      3689999999999999999 7 888  


Q ss_pred             CCCCCceEEEEeecc
Q psy3930         264 PDYQSSILTTTSRLS  278 (299)
Q Consensus       264 ~~~~g~~l~v~~k~~  278 (299)
                      ..+.|+.+.+.....
T Consensus        73 ~~~~g~~i~v~~~~~   87 (172)
T 2g4b_A           73 IIFQGQSLKIRRPHD   87 (172)
T ss_dssp             CEETTEECEEECCSS
T ss_pred             cEecCceeeecCCcc
Confidence            778899998876443

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.21  E-value=2.5e-11  Score=93.37  Aligned_cols=79  Identities=19%  Similarity=0.241  Sum_probs=67.6

Q ss_pred             CCcEEEEecCCC--C---CCHHHHHHHhhcCCceEEEEeeccCC----CCCcceEEEEEecCHHHHHHHHHhcCCCCCCC
Q psy3930         195 DECTIYVEKLPP--E---AEHDYIESVFSKYGKVTYVSLPKFKS----TGKLKGFAFVEFSTKEEAAKALELGLNPCPPD  265 (299)
Q Consensus       195 ~~~~l~V~nLp~--~---~t~e~L~~~F~~~G~i~~v~i~~~~~----~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~  265 (299)
                      ..++|++.|+-.  +   -.+++|++.|++||.|..|.|+++..    ++.++|++||+|.+.++|.+|++. |||  ..
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~-LnG--r~   95 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQA-LNG--RW   95 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHH-HTT--CE
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHH-HCC--CE
Confidence            357899999842  2   24689999999999999999998753    457789999999999999999999 999  88


Q ss_pred             CCCceEEEEee
Q psy3930         266 YQSSILTTTSR  276 (299)
Q Consensus       266 ~~g~~l~v~~k  276 (299)
                      +.|+.|.+..-
T Consensus        96 f~GR~i~v~~~  106 (118)
T 3ue2_A           96 FAGRKVVAEVY  106 (118)
T ss_dssp             ETTEECEEEEE
T ss_pred             ECCcEEEEEEc
Confidence            89999988764

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.18  E-value=6.3e-11  Score=98.57  Aligned_cols=75  Identities=23%  Similarity=0.374  Sum_probs=63.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcC----C-------ceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCC
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKY----G-------KVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCP  263 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~----G-------~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~  263 (299)
                      ..++|||+|||+++++++|+++|++|    |       .|..+.+.      .++|||||+|.+.++|++|+ . +||  
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~------~~~g~afV~F~~~~~A~~Al-~-l~g--   72 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-A-FDG--   72 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHG-G-GTT--
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHH-H-hcC--
Confidence            36899999999999999999999999    4       56666553      45789999999999999999 7 888  


Q ss_pred             CCCCCceEEEEeeccc
Q psy3930         264 PDYQSSILTTTSRLSF  279 (299)
Q Consensus       264 ~~~~g~~l~v~~k~~~  279 (299)
                      ..+.|+.|.|.....+
T Consensus        73 ~~~~g~~i~v~~~~~~   88 (198)
T 2yh0_A           73 IIFQGQSLKIRRPHDY   88 (198)
T ss_dssp             EEETTEEEEEECCCCC
T ss_pred             CEEcCceEEEeCCCCC
Confidence            7788999988765444

>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=99.10  E-value=1.4e-10  Score=104.91  Aligned_cols=70  Identities=23%  Similarity=0.295  Sum_probs=59.0

Q ss_pred             CCCCcEEEEec--CCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCC-CCCCc
Q psy3930         193 DVDECTIYVEK--LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPP-DYQSS  269 (299)
Q Consensus       193 ~~~~~~l~V~n--Lp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~-~~~g~  269 (299)
                      .....+|||+|  |+..+|+++|+++|++||+|..|.++.      ++|||||+|.+.++|++|++. |||..+ ...|+
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~-lnG~~~~~~~g~   87 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVT-LNGKEVVDDLGQ   87 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHH-TTTCEEECTTSC
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHH-hCCCccccccCC
Confidence            34567999998  578899999999999999999998864      368999999999999999999 999544 23345

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.93  E-value=9.8e-10  Score=83.83  Aligned_cols=75  Identities=15%  Similarity=0.136  Sum_probs=62.1

Q ss_pred             CCcEEEEecCCCCC----------CHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCC
Q psy3930         195 DECTIYVEKLPPEA----------EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPP  264 (299)
Q Consensus       195 ~~~~l~V~nLp~~~----------t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~  264 (299)
                      ..++|.+.|+=...          .+++|++.|++||.|..|.++++.    .+|+|||+|.+.++|.+|++. |||  .
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~-lnG--~   78 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNA-LHG--R   78 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHH-HTT--C
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHH-hCC--C
Confidence            34677777773221          246889999999999999997753    489999999999999999999 999  8


Q ss_pred             CCCCceEEEEee
Q psy3930         265 DYQSSILTTTSR  276 (299)
Q Consensus       265 ~~~g~~l~v~~k  276 (299)
                      .++|+.|.+..-
T Consensus        79 ~f~GR~i~v~~~   90 (114)
T 3s6e_A           79 WFAGKMITAAYV   90 (114)
T ss_dssp             EETTEECEEEEE
T ss_pred             EECCEEEEEEEE
Confidence            899999999764

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.83  E-value=1.1e-08  Score=73.72  Aligned_cols=76  Identities=20%  Similarity=0.229  Sum_probs=63.1

Q ss_pred             CCCCcEEEEecCCC----CC-C---HHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCC
Q psy3930         193 DVDECTIYVEKLPP----EA-E---HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPP  264 (299)
Q Consensus       193 ~~~~~~l~V~nLp~----~~-t---~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~  264 (299)
                      .+...||+|.-.|.    +. .   ..+|.+.|++||.|..++++.++        +||+|.+.++|.+|++  |||  .
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~--mnG--~   71 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS--LNG--K   71 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG--GTT--C
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh--cCC--e
Confidence            35567888887762    22 2   26789999999999999999874        9999999999999997  798  8


Q ss_pred             CCCCceEEEEeec-ccC
Q psy3930         265 DYQSSILTTTSRL-SFG  280 (299)
Q Consensus       265 ~~~g~~l~v~~k~-~~~  280 (299)
                      .+.|+.|+|..+. .|.
T Consensus        72 ~v~Gr~LkV~lkt~dW~   88 (91)
T 2dnr_A           72 ELLNRTITIALKSPSGP   88 (91)
T ss_dssp             EETTEEEEEEECCCSSC
T ss_pred             EeCCeEEEEEeCCCCcc
Confidence            8999999999976 563

>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=98.59  E-value=1.1e-07  Score=80.77  Aligned_cols=66  Identities=23%  Similarity=0.238  Sum_probs=58.4

Q ss_pred             CCHHHHHHHhhcCCceEEEEeeccC----CCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         208 AEHDYIESVFSKYGKVTYVSLPKFK----STGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       208 ~t~e~L~~~F~~~G~i~~v~i~~~~----~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      -.+++|.+.|++||.|..+.++++.    .+|.++|++||+|.+.++|.+|++. |||  ..++|+.|.+..-
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~-l~g--r~~~gr~i~~~~~  210 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQA-LNG--RWFAGRKVVAEVY  210 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHH-HTT--CBSSSSBCEEEEC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHH-hcC--ceECCeEEEEEEc
Confidence            3578999999999999999998553    3558999999999999999999999 999  8899999988763

>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=98.58  E-value=6.1e-08  Score=70.26  Aligned_cols=73  Identities=14%  Similarity=0.237  Sum_probs=62.3

Q ss_pred             CCCCcEEEEecCCCC------CC---HHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCC
Q psy3930         193 DVDECTIYVEKLPPE------AE---HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCP  263 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~------~t---~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~  263 (299)
                      .+...||+|.-++.+      ..   ..+|.+.|.+||.|..++++.++        +||+|.+.++|.+|++  +||  
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~--ldG--   79 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD--VDG--   79 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH--GGG--
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh--cCC--
Confidence            566789999988743      22   25689999999999999999874        9999999999999997  788  


Q ss_pred             CCCCCceEEEEeec
Q psy3930         264 PDYQSSILTTTSRL  277 (299)
Q Consensus       264 ~~~~g~~l~v~~k~  277 (299)
                      ..+.|+.|+|..|.
T Consensus        80 ~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           80 MKVKGRAVKISGPS   93 (95)
T ss_dssp             SEETTEEEEEECCC
T ss_pred             eeeCCeEEEEeccC
Confidence            99999999998764

>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=98.21  E-value=6.7e-08  Score=73.57  Aligned_cols=76  Identities=11%  Similarity=0.187  Sum_probs=39.1

Q ss_pred             HHHHHhhhcCCCe-eee-----------eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccCCC-----
Q psy3930         130 RFFSQLLQESPEI-EVS-----------VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP-----  192 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l~-----------~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~-----  192 (299)
                      .-|..++..++.+ .+.           .|+.|.       +.++|.+|++.+++..+.++.++|.++.+..+..     
T Consensus        20 ~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~-------~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~~~~~~~~   92 (115)
T 4f25_A           20 KALYDTFSAFGNILSCKVVCDENGSKGYGFVHFE-------TQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGA   92 (115)
T ss_dssp             HHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEES-------CHHHHHHHHHHHTTCEETTEECEEEESSCCCC-------
T ss_pred             HHHHHHHhccCCEEEEEEeecCCCCCceEEEEEC-------CHHHHHHHHHHcCCCEECCEEEEEEECCCcccccccccc
Confidence            4577777777752 222           244444       4899999999999999999999998876543322     


Q ss_pred             -CCCCcEEEEecCCCCCCHHH
Q psy3930         193 -DVDECTIYVEKLPPEAEHDY  212 (299)
Q Consensus       193 -~~~~~~l~V~nLp~~~t~e~  212 (299)
                       .....+|||+|||+++|++.
T Consensus        93 ~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           93 RAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             ---------------------
T ss_pred             ccCCCCceEeCCCCCCccccc
Confidence             23446799999999998864

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.80  E-value=4.8e-05  Score=56.28  Aligned_cols=71  Identities=20%  Similarity=0.181  Sum_probs=63.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcC-----CceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCc
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKY-----GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~-----G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      ..++|-+-|||..++...|+.+.+.+     |.+..|.+..|.      +-|+|+|.+...|-+|.-+ ++|  ..+.|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLa-L~G--~ef~gr   90 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMI-LNG--SQFQGK   90 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHH-HSS--EEETTE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhh-cCC--eeecCe
Confidence            35789999999999999999999999     999999998875      2499999999999999988 999  888899


Q ss_pred             eEEEE
Q psy3930         270 ILTTT  274 (299)
Q Consensus       270 ~l~v~  274 (299)
                      +|++-
T Consensus        91 ~Lr~g   95 (117)
T 2l9w_A           91 VIRSG   95 (117)
T ss_dssp             EEEEE
T ss_pred             EEEec
Confidence            99874

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.50  E-value=0.00093  Score=48.92  Aligned_cols=70  Identities=16%  Similarity=0.222  Sum_probs=57.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhc---C--CceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCc
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSK---Y--GKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~---~--G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      .+.+|.|.|||+++.++.|.-+|+.   -  |+|..+....        +-|+|+|.+.+.|++.++.    ..+.+.+.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k----~~H~L~~~   74 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ----ADHELHGA   74 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC----SCCBSSSS
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC----CcceecCe
Confidence            4578999999999999999999987   2  4788887643        2499999999999999986    34788889


Q ss_pred             eEEEEee
Q psy3930         270 ILTTTSR  276 (299)
Q Consensus       270 ~l~v~~k  276 (299)
                      .|.|..-
T Consensus        75 ~LsV~P~   81 (104)
T 2dhx_A           75 QLSLRPA   81 (104)
T ss_dssp             BCEEEEC
T ss_pred             EEEEEcC
Confidence            9988763

>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=97.27  E-value=9.1e-06  Score=61.33  Aligned_cols=54  Identities=17%  Similarity=0.133  Sum_probs=46.4

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcEEEEecCCCCCCHHHHHHHhhcCC
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYG  221 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~l~V~nLp~~~t~e~L~~~F~~~G  221 (299)
                      .+.++|.+|+..+++..+.++.++|..+.+....          .+++...++++|+++|++||
T Consensus        55 ~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~----------~~~~~~~~~~~l~~~~~~~g  108 (115)
T 3lqv_A           55 EDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRAF----------QKMDTKKKEEQLKLLKEKYG  108 (115)
T ss_dssp             SSHHHHHHHHHHHTTCBSSSCBCEEEECCHHHHT----------TTSCHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHcCCCEECCeEEEEEEecCChhh----------hhhhHhHhHHHHHHHHHHhC
Confidence            3489999999999999999999999988765542          46788889999999999998

>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=97.02  E-value=0.0022  Score=46.36  Aligned_cols=53  Identities=25%  Similarity=0.335  Sum_probs=43.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHh
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL  257 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~  257 (299)
                      .+.+++ ++|+++...||..+|+.||. ..|+.+-|.       .|||.|.+++.|..|+..
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~   68 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHh
Confidence            355666 99999999999999999994 344554453       599999999999999997

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.86  E-value=0.0037  Score=44.98  Aligned_cols=65  Identities=11%  Similarity=0.253  Sum_probs=54.0

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCC--cceEEEEEecCHHHHHHHHHhcCCCC
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGK--LKGFAFVEFSTKEEAAKALELGLNPC  262 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~--~kg~~fV~F~~~~~A~~Al~~~lng~  262 (299)
                      ++|.|++||+..|++++.+.++..+.+.+..++..+.+..  .-.-|||.|.+.+++....+. ++|+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~-~~g~   68 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDR-FDGY   68 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHH-HTTC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHH-hCCc
Confidence            4789999999999999999999999888888776553322  234589999999999999999 8884

>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=96.81  E-value=0.0026  Score=46.13  Aligned_cols=52  Identities=25%  Similarity=0.303  Sum_probs=44.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHh
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL  257 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~  257 (299)
                      +.+++ ++|+++...+|..+|+.|| -..|+.+-|.       .|||.|.+++.|..|+..
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~   58 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNT   58 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHh
Confidence            45566 9999999999999999999 4456666553       599999999999999997

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=96.80  E-value=4.9e-05  Score=55.78  Aligned_cols=69  Identities=12%  Similarity=0.097  Sum_probs=47.2

Q ss_pred             HHHHHhhhcCCCe-ee--------eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccCCC--------
Q psy3930         130 RFFSQLLQESPEI-EV--------SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKP--------  192 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l--------~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~--------  192 (299)
                      .-|..++..++.+ .+        -.|+.|.+       .++|.+|+..+++..+.+..++|..+.+.....        
T Consensus        15 ~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~-------~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~~~~~~~~~~   87 (101)
T 2hvz_A           15 GELERAFSYYGPLRTVWIARNPPGFAFVEFED-------PRDAEDAVRGLDGKVICGSRVRVELSTGMPRRSRFDRPPAR   87 (101)
T ss_dssp             HHHHHHHHHHCCCSEEEEESSSSSEEEEECSS-------HHHHHHHHHHHHHSCSSSCCCEEEESSSCCCSSCCCSCCCS
T ss_pred             HHHHHHHHhcCCeEEEEEeeCCCCEEEEEECC-------HHHHHHHHHHHCCCeECCcEEEEEEccCCCCcccCCCCCcc
Confidence            4466666666541 11        23555544       899999999999999999999998876543221        


Q ss_pred             CCCCcEEEEecCC
Q psy3930         193 DVDECTIYVEKLP  205 (299)
Q Consensus       193 ~~~~~~l~V~nLp  205 (299)
                      .....++|||||+
T Consensus        88 ~~~~~~ifvg~L~  100 (101)
T 2hvz_A           88 RKLLEVLFNGPLE  100 (101)
T ss_dssp             CCCCSCCCSCCCC
T ss_pred             ccCCCceecCCCC
Confidence            1225689999997

>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=96.78  E-value=0.0059  Score=46.00  Aligned_cols=72  Identities=19%  Similarity=0.345  Sum_probs=55.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCC-CceE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQ-SSIL  271 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~-g~~l  271 (299)
                      ....+.|.|-|+|+.. -..+-..|++||.|.....+.    +  ..+-.|.|.+..+|++||..  ||  ..+. +..|
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~----~--~NWihI~Y~s~~~A~rAL~k--NG--~ii~g~~mI   89 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN----T--GNWMHIRYQSKLQARKALSK--DG--RIFGESIMI   89 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS----S--SSEEEEEESSHHHHHHHHTT--TT--CEETTTEEC
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC----C--CCeEEEEeCCHHHHHHHHHh--CC--eEecCCEEE
Confidence            3446789999999885 667778899999999887632    1  23789999999999999995  77  5555 4667


Q ss_pred             EEEe
Q psy3930         272 TTTS  275 (299)
Q Consensus       272 ~v~~  275 (299)
                      .|+.
T Consensus        90 GV~p   93 (119)
T 1wwh_A           90 GVKP   93 (119)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7766

>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=96.47  E-value=0.00014  Score=53.33  Aligned_cols=30  Identities=17%  Similarity=0.123  Sum_probs=26.4

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .+.++|.+|++.+++..+.++.++|..+.|
T Consensus        69 ~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           69 VTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             CCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            348999999999999999999999988764

>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=96.12  E-value=0.029  Score=41.11  Aligned_cols=71  Identities=20%  Similarity=0.126  Sum_probs=55.5

Q ss_pred             CcEEEEecCCCCC-C----HHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCce
Q psy3930         196 ECTIYVEKLPPEA-E----HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSI  270 (299)
Q Consensus       196 ~~~l~V~nLp~~~-t----~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~  270 (299)
                      ..+|++.||+.++ .    .+.++.+|..|+++......+.-     + =..|.|.++++|.+|-.. ++|  ..+.|..
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF-----R-Rirv~F~~~~~A~~AR~~-Lh~--~~f~g~~   75 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF-----K-RVRINFSNPLSAADARLR-LHK--TEFLGKE   75 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT-----T-EEEEECSSTTHHHHHHHT-STT--SEETTEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc-----e-EEEEEeCChHHHHHHHHH-hcc--ceecCce
Confidence            3689999999875 3    25778999999987776655431     1 268999999999999998 888  8888998


Q ss_pred             EEEEe
Q psy3930         271 LTTTS  275 (299)
Q Consensus       271 l~v~~  275 (299)
                      +++=.
T Consensus        76 ~r~YF   80 (104)
T 1wey_A           76 MKLYF   80 (104)
T ss_dssp             CEEEC
T ss_pred             eEEEe
Confidence            77644

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.24  E-value=0.011  Score=55.19  Aligned_cols=58  Identities=19%  Similarity=0.250  Sum_probs=43.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHh
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL  257 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~  257 (299)
                      ...++|+|. .|...++.+|.++|++||+|..+-+-.+.  |   -|+.|+|.+.+++..++..
T Consensus        51 qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g---~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           51 QAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G---LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S---EEEEEECC---CCHHHHSS
T ss_pred             HhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C---eEEEEEeCCHHHHHHHHhc
Confidence            345899998 69999999999999999999999886543  3   5999999999999877664

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=95.16  E-value=0.001  Score=47.69  Aligned_cols=28  Identities=7%  Similarity=-0.057  Sum_probs=24.5

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      .+.++|.+|++.+|+..+.++.++|..+
T Consensus        51 ~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A           51 TTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             SSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            4589999999999999999999888644

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.13  E-value=0.033  Score=40.30  Aligned_cols=66  Identities=12%  Similarity=0.210  Sum_probs=49.6

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCC--cceEEEEEecCHHHHHHHHHhcCCCC
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGK--LKGFAFVEFSTKEEAAKALELGLNPC  262 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~--~kg~~fV~F~~~~~A~~Al~~~lng~  262 (299)
                      .-+|.|+.||+..|++++.+.++..-++.+..++..+.+..  .-.-|||.|.+.++.....+. .+|+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~-f~g~   76 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDR-FDGY   76 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHH-STTE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHH-cCCc
Confidence            45799999999999999998888766665555544332211  123489999999999999999 8883

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=95.01  E-value=0.00073  Score=49.44  Aligned_cols=30  Identities=10%  Similarity=-0.054  Sum_probs=26.2

Q ss_pred             CHHHHHHHHHhcCcccccc-ccceeeeeecc
Q psy3930         159 DPDDVVKALRKSKLLEVTE-DGTKVRRTVVV  188 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~-~~~~v~r~~~~  188 (299)
                      +.++|.+|++.+++..+.+ +.++|..+.+.
T Consensus        63 ~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~~   93 (100)
T 3ns6_A           63 SMNDAKKIIKSFHGKRLDLKHRLFLYTMKDV   93 (100)
T ss_dssp             SHHHHHHHHHHHTTCBSSSSCBCEEEESHHH
T ss_pred             CHHHHHHHHHHhCCcccCCCeEEEEEECchh
Confidence            4899999999999999999 99999887653

>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=95.01  E-value=0.0018  Score=46.24  Aligned_cols=32  Identities=9%  Similarity=0.010  Sum_probs=25.1

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|++.+++..+.++.++|..+.+...
T Consensus        54 ~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~~~   85 (90)
T 3p5t_L           54 SEASSKKLMDLLPKRELHGQNPVVTPSNKLEH   85 (90)
T ss_dssp             CHHHHHHHHHHGGGSCSSSCCCEECCC-----
T ss_pred             CHHHHHHHHHHcCCCeeCCEEEEEEECCCCcc
Confidence            48999999999999999999999988775543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=94.98  E-value=0.0023  Score=45.89  Aligned_cols=38  Identities=8%  Similarity=0.152  Sum_probs=29.5

Q ss_pred             eeecccccccCCCCHHHHHHHHHhc-CccccccccceeeeeecccC
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKS-KLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~-~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .|+.|.+       .++|.+|++.+ ++..+.|+.++|..+.+.+.
T Consensus        47 aFV~F~~-------~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~~   85 (91)
T 2lxi_A           47 AFVEFSH-------LQDATRWMEANQHSLNILGQKVSMHYSDPKPK   85 (91)
T ss_dssp             EEEECSS-------HHHHHHHHHTTTTEEEETTEEEEEECCCSCCC
T ss_pred             EEEEecC-------HHHHHHHHHhcCCCeEECCEEEEEEEcCCCCC
Confidence            4666655       89999999876 67789999999988776543

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.75  E-value=0.0028  Score=45.04  Aligned_cols=54  Identities=11%  Similarity=0.149  Sum_probs=39.1

Q ss_pred             HHHHHhhhcCCCe-eee-----eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         130 RFFSQLLQESPEI-EVS-----VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l~-----~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .-|..++..++.+ .+.     .|+.|.+       .++|.+|+..+++..+.++.++|.++.+...
T Consensus        23 ~~l~~~F~~~G~i~~v~~~~g~afV~f~~-------~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A           23 QEIRSLFEQYGKVLECDIIKNYGFVHIED-------KTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             HHHHHHHHTSSCEEEEEEETTEEEEEESS-------HHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             HHHHHHHHhCCCEEEEEEECCEEEEEECC-------HHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            4566777777652 222     3455544       8999999999999999999999998765543

>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=94.63  E-value=0.0058  Score=45.86  Aligned_cols=31  Identities=16%  Similarity=0.175  Sum_probs=27.0

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      +.++|.+|++.+++..+.++.++|..+.+..
T Consensus        57 ~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   87 (116)
T 2fy1_A           57 NPADAKNAAKDMNGKSLHGKAIKVEQAKKPS   87 (116)
T ss_dssp             SHHHHHHHHHHCSSCBCSSSBCEEEECCCSS
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            4899999999999999999999999876543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=94.54  E-value=0.0042  Score=45.30  Aligned_cols=32  Identities=9%  Similarity=-0.005  Sum_probs=27.4

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|+..+++..+.+..++|..+.+...
T Consensus        66 ~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   97 (103)
T 2cq0_A           66 RREDAARAIAGVSGFGYDHLILNVEWAKPSTN   97 (103)
T ss_dssp             SHHHHHHHHHHTTTCEETTEECEEEESSCCCC
T ss_pred             CHHHHHHHHHHcCCCeeCCcEEEEEECCCCCC
Confidence            38999999999999999999999988765443

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=94.40  E-value=0.0024  Score=47.60  Aligned_cols=50  Identities=12%  Similarity=0.197  Sum_probs=36.4

Q ss_pred             HHHHHhhhcCCCe-eee-------------eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeee
Q psy3930         130 RFFSQLLQESPEI-EVS-------------VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l~-------------~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      ..|+.++..++.+ .+.             .|+.|       .+.++|.+|++.+|+..+.++.++|..+.
T Consensus        21 ~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f-------~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A           21 TFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLF-------TSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             HHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEE-------SSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             HHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEE-------CCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            4577777777652 222             24444       34899999999999999999999987654

>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=94.39  E-value=0.0026  Score=44.72  Aligned_cols=30  Identities=7%  Similarity=-0.088  Sum_probs=25.2

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      +.++|.+|++.+++..+.++.++|..+.+.
T Consensus        57 ~~~~A~~A~~~l~g~~~~g~~l~v~~a~~k   86 (87)
T 3bs9_A           57 NKWDAENAIQQMGGQWLGGRQIRTNWATRK   86 (87)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEEEC--
T ss_pred             CHHHHHHHHHHcCCCEECCeEEEEEecCCC
Confidence            389999999999999999999999887643

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.34  E-value=0.0031  Score=44.87  Aligned_cols=54  Identities=19%  Similarity=0.195  Sum_probs=38.0

Q ss_pred             HHHHHhhhcCCCe-ee-----eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         130 RFFSQLLQESPEI-EV-----SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l-----~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .-|..++..++.+ .+     -.|++|.+       .++|.+|+..+++..+.++.++|..+.+...
T Consensus        24 ~~l~~~F~~~G~v~~~~~~~~~afV~f~~-------~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   83 (90)
T 2dnp_A           24 QELRSLFERRGRVIECDVVKDYAFVHMEK-------EADAKAAIAQLNGKEVKGKRINVELSTKGQK   83 (90)
T ss_dssp             HHHHHHHHHHSCEEEEEECSSCEEEEESC-------HHHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             HHHHHHHHcCCCEEEEEEECCEEEEEECC-------HHHHHHHHHHhCCCEECCcEEEEEECCCCCC
Confidence            3455666665541 11     23555544       8999999999999999999999998775543

>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=94.29  E-value=0.0046  Score=44.66  Aligned_cols=32  Identities=16%  Similarity=0.103  Sum_probs=27.9

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|+..+++..+.++.++|..+.+...
T Consensus        59 ~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   90 (99)
T 1whw_A           59 FPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKE   90 (99)
T ss_dssp             SHHHHHHHHHHTTTEESSSCEEEEEECCCCST
T ss_pred             CHHHHHHHHHHhCCCEECCcEEEEEEcCCCcc
Confidence            48999999999999999999999998776554

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=94.28  E-value=0.0057  Score=43.87  Aligned_cols=32  Identities=9%  Similarity=-0.074  Sum_probs=27.6

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|+..+++..+.++.++|..+.+...
T Consensus        57 ~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   88 (96)
T 1x5t_A           57 SFDASDAAIEAMNGQYLCNRPITVSYAFKKDS   88 (96)
T ss_dssp             SHHHHHHHHHTTTTCEETTEECEEEESCCCCC
T ss_pred             CHHHHHHHHHHcCCCEECCEEEEEEEecccCC
Confidence            38999999999999999999999998775543

>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=94.26  E-value=0.0058  Score=44.65  Aligned_cols=32  Identities=9%  Similarity=0.206  Sum_probs=27.5

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|+..+++..+.++.++|..+.+...
T Consensus        66 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   97 (105)
T 1x5u_A           66 SEEDADYAIKIMDMIKLYGKPIRVNKASAHNK   97 (105)
T ss_dssp             SHHHHHHHHHHSSSCBCSSCBCEEEETTTTSC
T ss_pred             CHHHHHHHHHHhCCCeECCeEEEEEECCCCCc
Confidence            48999999999999999999999998765543

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.17  E-value=0.074  Score=40.61  Aligned_cols=74  Identities=14%  Similarity=0.191  Sum_probs=51.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEE-EEeeccCC------------CC-CcceEEEEEecCHHHHHHHHHhcCCCC
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTY-VSLPKFKS------------TG-KLKGFAFVEFSTKEEAAKALELGLNPC  262 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~-v~i~~~~~------------~g-~~kg~~fV~F~~~~~A~~Al~~~lng~  262 (299)
                      ..|.|-|+|++.+. .+-..|++||.|.. +...++..            .+ ....+-.|+|.++.+|.+||..  || 
T Consensus         8 ~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~--NG-   83 (132)
T 3p3d_A            8 LAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE--NG-   83 (132)
T ss_dssp             CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT--TT-
T ss_pred             eEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh--CC-
Confidence            56788899877655 45567999999865 32221100            00 1245789999999999999995  88 


Q ss_pred             CCCCCCceEEEEe
Q psy3930         263 PPDYQSSILTTTS  275 (299)
Q Consensus       263 ~~~~~g~~l~v~~  275 (299)
                       ..++|..|.|.+
T Consensus        84 -~ii~G~mIGV~P   95 (132)
T 3p3d_A           84 -AVFNGVLLGVIP   95 (132)
T ss_dssp             -CEETTEECEEEE
T ss_pred             -eEeCcEEEEEEE
Confidence             777888888865

>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=94.17  E-value=0.0044  Score=44.71  Aligned_cols=53  Identities=9%  Similarity=0.085  Sum_probs=37.4

Q ss_pred             HHHHHhhhcCCCee-e-------eeeecccccccCCCCHHHHHHHHHhcCccccc--cccceeeeeeccc
Q psy3930         130 RFFSQLLQESPEIE-V-------SVFLKCNKLARLTHDPDDVVKALRKSKLLEVT--EDGTKVRRTVVVQ  189 (299)
Q Consensus       130 ~fl~~~~~~~~~~~-l-------~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~--~~~~~v~r~~~~~  189 (299)
                      .-|..++..++.+. +       -.|++|.       +.++|.+|++.+++..+.  ++.++|..+.+.+
T Consensus        32 ~~l~~~F~~~G~v~~v~~~~~~g~afV~f~-------~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~~   94 (97)
T 1why_A           32 AALAREFDRFGSIRTIDHVKGDSFAYIQYE-------SLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGP   94 (97)
T ss_dssp             HHHHHHHHTTSCEEEEEECSSSCCEEEEES-------SHHHHHHHHHHHTTCBCSSSSCBCEEEECCCCC
T ss_pred             HHHHHHHHhcCCeeEEEEeCCCCEEEEEEC-------CHHHHHHHHHHHCCCEeCCCCcEEEEEECCCCC
Confidence            45666666666521 1       2344444       489999999999999999  8899998876543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.17  E-value=0.004  Score=44.41  Aligned_cols=53  Identities=17%  Similarity=0.220  Sum_probs=37.9

Q ss_pred             HHHHHhhhcCCCe-ee-----eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         130 RFFSQLLQESPEI-EV-----SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l-----~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .-|..++..++.+ .+     -.|++|.+       .++|.+|+..+++..+.++.++|..+.+..
T Consensus        25 ~~l~~~F~~~G~v~~v~~~~~~afV~f~~-------~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   83 (92)
T 2dgt_A           25 QELRAKFEEYGPVIECDIVKDYAFVHMER-------AEDAVEAIRGLDNTEFQGKRMHVQLSTSRL   83 (92)
T ss_dssp             HHHHHHHHTTSCCCEEEECSSEEEEEESC-------HHHHHHHHHHHTTEEETTEEEEEEESSCCC
T ss_pred             HHHHHHHHhcCCeEEEEEECCEEEEEECC-------HHHHHHHHHHhCCCeeCCcEEEEEEccCCC
Confidence            3466666666541 11     23555554       899999999999999999999998876544

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=94.16  E-value=0.0059  Score=44.11  Aligned_cols=32  Identities=16%  Similarity=0.251  Sum_probs=26.9

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .+.++|.+|++ +++..+.++.++|.++.+...
T Consensus        60 ~~~~~a~~A~~-~~~~~~~g~~l~V~~a~~~~~   91 (99)
T 2dgs_A           60 EDEQSVDQAVN-MHFHDIMGKKVEVKRAEPRDS   91 (99)
T ss_dssp             SSHHHHHHHHH-HCCCBSSSCBCEEEECCCCCC
T ss_pred             CCHHHHHHHHH-hCCCEECCeEEEEEECCCCcc
Confidence            34899999997 899999999999998876544

>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=94.15  E-value=0.0031  Score=44.36  Aligned_cols=30  Identities=17%  Similarity=0.242  Sum_probs=26.3

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      +.++|.+|+..+++..+.++.++|..+.+.
T Consensus        56 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   85 (88)
T 4a8x_A           56 NPDEAEKALKHMDGGQIDGQEITATAVLAP   85 (88)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEEECCC
T ss_pred             cHHHHHHHHHHcCCCeECCeEEEEEECCCC
Confidence            489999999999999999999999887654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=94.11  E-value=0.0047  Score=45.26  Aligned_cols=38  Identities=8%  Similarity=0.024  Sum_probs=30.7

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      -.|+.|.+       .++|.+|+..+++..+.+..++|..+.+.+
T Consensus        67 ~afV~f~~-------~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~  104 (106)
T 1p27_B           67 YTLVEYET-------YKEAQAAMEGLNGQDLMGQPISVDWCFVRG  104 (106)
T ss_dssp             EEEEEESC-------HHHHHHHHHHHTTCBSSSSBCEEEESEESS
T ss_pred             EEEEEECC-------HHHHHHHHHHhcCCEECCcEEEEEeecCCC
Confidence            34566655       899999999999999999999998876543

>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=94.10  E-value=0.0029  Score=44.06  Aligned_cols=30  Identities=10%  Similarity=0.163  Sum_probs=26.1

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      +.++|.+|+..+++..+.++.++|..+.+.
T Consensus        52 ~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A           52 SQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             CHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            489999999999999999999999887643

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=94.09  E-value=0.0067  Score=44.06  Aligned_cols=32  Identities=19%  Similarity=0.123  Sum_probs=27.7

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|++.+++..+.++.++|.++.+...
T Consensus        63 ~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   94 (102)
T 1x5s_A           63 NIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   94 (102)
T ss_dssp             SHHHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             CHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            38999999999999999999999998876543

>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=94.05  E-value=0.0057  Score=46.92  Aligned_cols=30  Identities=17%  Similarity=0.238  Sum_probs=26.2

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      +.++|.+|+..+++..+.++.++|..+.+.
T Consensus        97 ~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~  126 (129)
T 2kxn_B           97 NVDDAKEAKERANGMELDGRRIRVDFSITK  126 (129)
T ss_dssp             CHHHHHHHHHHHTTCCSSSSCCEESCCSSS
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            489999999999999999999999877643

>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=93.91  E-value=0.0037  Score=43.72  Aligned_cols=27  Identities=15%  Similarity=0.112  Sum_probs=23.7

Q ss_pred             CHHHHHHHHHhcCccccccccceeeee
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      +.++|.+|++.+++..+.++.++|..+
T Consensus        58 ~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A           58 LAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            489999999999999999999888764

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=93.90  E-value=0.0056  Score=44.50  Aligned_cols=32  Identities=13%  Similarity=0.051  Sum_probs=27.5

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|++.+++..+.++.++|..+.+...
T Consensus        63 ~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2cqb_A           63 LAEDAAAAIDNMNESELFGRTIRVNLAKPMRI   94 (102)
T ss_dssp             SHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             CHHHHHHHHHHhCCCEECCcEEEEEeCCCCCC
Confidence            38999999999999999999999988775543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=93.90  E-value=0.0048  Score=44.72  Aligned_cols=37  Identities=14%  Similarity=0.149  Sum_probs=30.3

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .|+.|.+       .++|.+|+..+++..+.++.++|..+.+..
T Consensus        61 afV~f~~-------~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   97 (100)
T 2do4_A           61 AYVEYEN-------ESQASQAVMKMDGMTIKENIIKVAISNSGP   97 (100)
T ss_dssp             EEEEESS-------HHHHHHHHHHHTTEESSSCEEEEEECCCCS
T ss_pred             EEEEECC-------HHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            4555655       899999999999999999999998876544

>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=93.82  E-value=0.0046  Score=45.09  Aligned_cols=32  Identities=16%  Similarity=0.114  Sum_probs=27.5

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|+..+++..+.++.++|.++.+...
T Consensus        64 ~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2cqi_A           64 EHRDAAAALAAMNGRKILGKEVKVNWATTPSS   95 (103)
T ss_dssp             SHHHHHHHHHHHTTEEETTEEEEEEECCCTTC
T ss_pred             CHHHHHHHHHHhCCCCcCCCeEEEEECCCCcc
Confidence            48999999999999999999999998776443

>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=93.81  E-value=0.0039  Score=45.58  Aligned_cols=54  Identities=11%  Similarity=0.218  Sum_probs=38.0

Q ss_pred             HHHHHhhhcCCCe-ee-----eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         130 RFFSQLLQESPEI-EV-----SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l-----~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .-|..++..++.+ .+     -.|++|.+       .++|.+|+..+++..+.+..++|..+.+...
T Consensus        26 ~~l~~~F~~~G~i~~v~~~~~~afV~f~~-------~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   85 (103)
T 2dgu_A           26 EILEKAFSQFGKLERVKKLKDYAFIHFDE-------RDGAVKAMEEMNGKDLEGENIEIVFAKPPDQ   85 (103)
T ss_dssp             HHHHHHHHHHSCEEEEEECSSCEEEEESS-------HHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             HHHHHHHHhcCCEEEEEEECCEEEEEeCC-------HHHHHHHHHHHCCCccCCCEEEEEEcCCCcc
Confidence            4456666666542 11     23555544       8999999999999999999999988765543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=92.88  E-value=0.011  Score=44.09  Aligned_cols=33  Identities=21%  Similarity=0.121  Sum_probs=27.5

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .+.++|.+|+..+++..+.++.++|.++.+...
T Consensus        65 ~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           65 DDPPSAKAAIDWFDGKEFSGNPIKVSFATRRAD   97 (116)
Confidence            347889999999999999999999988775543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=93.76  E-value=0.0052  Score=43.97  Aligned_cols=33  Identities=18%  Similarity=0.178  Sum_probs=27.9

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .+.++|.+|+..+++..+.++.++|..+.+...
T Consensus        55 ~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   87 (95)
T 2dnz_A           55 SDSECARRALEQLNGFELAGRPMRVGHVTERLD   87 (95)
T ss_dssp             SCHHHHHHHHHHHTTCCSSSSCCEEEESSCCCC
T ss_pred             CCHHHHHHHHHHhCCCeeCCcEEEEEEcccccC
Confidence            348999999999999999999999998765543

>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=93.75  E-value=0.0063  Score=45.33  Aligned_cols=38  Identities=16%  Similarity=0.194  Sum_probs=31.3

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .|+.|.+       .++|.+|++.+++..+.++.++|..+.+...
T Consensus        70 afV~f~~-------~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~  107 (115)
T 2cpz_A           70 GFVSYDN-------PVSAQAAIQSMNGFQIGMKRLKVQLKRSKND  107 (115)
T ss_dssp             EEEECSS-------HHHHHHHHHHHTTCEETTEECEEECCCCSCC
T ss_pred             EEEEECC-------HHHHHHHHHHcCCCEECCEEEEEEEcCCCCc
Confidence            4666655       8999999999999999999999998775543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=93.73  E-value=0.0058  Score=44.53  Aligned_cols=31  Identities=16%  Similarity=0.034  Sum_probs=26.7

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      +.++|.+|+..+++..+.++.++|..+.+..
T Consensus        64 ~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   94 (103)
T 2dnm_A           64 DRRDAQDAEAAMDGAELDGRELRVQVARYGR   94 (103)
T ss_dssp             SSSHHHHHHHHHSSCCBTTBCCEEEECSSCC
T ss_pred             CHHHHHHHHHHcCCCEECCcEEEEEECCcCC
Confidence            3789999999999999999999999876543

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=93.70  E-value=0.0072  Score=43.51  Aligned_cols=53  Identities=9%  Similarity=0.060  Sum_probs=38.0

Q ss_pred             HHHHHhhhcCCC---eee---eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         130 RFFSQLLQESPE---IEV---SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       130 ~fl~~~~~~~~~---~~l---~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .-|..++..++.   +.+   -.|++|.+       .++|.+|+..+++..+.++.++|..+.+..
T Consensus        26 ~~l~~~F~~~G~v~~v~i~~g~afV~f~~-------~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A           26 EDLFRIFSPYGHIMQINIKNAFGFIQFDN-------PQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             HHHHHHHTTTCCCCEEEEETTEEEEEESC-------HHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             HHHHHHHHhcCCEEEEEEeCCEEEEEECC-------HHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            446666666664   111   23555554       899999999999999999999999876543

>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=93.69  E-value=0.0047  Score=45.76  Aligned_cols=37  Identities=19%  Similarity=0.150  Sum_probs=30.1

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      -.|+.|.+       .++|.+|++.+++..+.++.++|..+.+.
T Consensus        70 ~afV~F~~-------~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k  106 (108)
T 2jrs_A           70 YGFITFSD-------SECAKKALEQLNGFELAGRPMKVGHVTER  106 (108)
T ss_dssp             EEEEEESC-------HHHHHHHHHHHTTCCSSSSCCEEECSCSS
T ss_pred             EEEEEECC-------HHHHHHHHHHcCCCEECCEEEEEEEcccC
Confidence            34566655       89999999999999999999999877643

>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=93.60  E-value=0.0059  Score=45.45  Aligned_cols=51  Identities=10%  Similarity=0.085  Sum_probs=36.9

Q ss_pred             HHHHHhhhcCCCee-e-------eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         130 RFFSQLLQESPEIE-V-------SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       130 ~fl~~~~~~~~~~~-l-------~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .-|+.++..++.+. +       -.|+.|..       .++|.+|+..+++..+.++.++|.++..
T Consensus        25 ~~L~~~F~~~G~i~~v~i~~~~g~afV~f~~-------~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A           25 AEIQETFSRFGSLGRVLLPEGGITAIVEFLE-------PLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             HHHHHHHHTTSCEEEEECCSSSSCEEEEESC-------HHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             HHHHHHHHhcCCEEEEEEeCCCCEEEEEeCC-------HHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            45666666666521 1       23444544       8999999999999999999999988753

>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=93.51  E-value=0.0061  Score=44.08  Aligned_cols=31  Identities=10%  Similarity=-0.079  Sum_probs=26.6

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      +.++|.+|++.+++..+.++.++|+.+.+..
T Consensus        60 ~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpj_A           60 TRTLAEIAKVELDNMPLRGKQLRVRFACHSA   90 (99)
T ss_dssp             SSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             CHHHHHHHHHHhCCCEeCCceEEEEEcCCCC
Confidence            3789999999999999999999998876543

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=93.49  E-value=0.0068  Score=45.11  Aligned_cols=38  Identities=8%  Similarity=-0.074  Sum_probs=30.7

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .|+.|..       .++|.+|++.+++..+.++.++|..+.+...
T Consensus        60 afV~f~~-------~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   97 (115)
T 2dgo_A           60 GFVSFFN-------KWDAENAIQQMGGQWLGGRQIRTNWATRKPP   97 (115)
T ss_dssp             EEEEESS-------HHHHHHHHHHTTTCEETTEECEEEESSCCCC
T ss_pred             EEEEECC-------HHHHHHHHHHhCCCEECCEEEEEEEccCCCC
Confidence            4555554       8999999999999999999999998765443

>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=93.43  E-value=0.0074  Score=43.04  Aligned_cols=32  Identities=16%  Similarity=0.111  Sum_probs=27.4

Q ss_pred             CHHHHHHHHHhcCc-cccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKL-LEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~-~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|++.+++ ..+.+..++|.++.+...
T Consensus        53 ~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~~   85 (93)
T 2cqh_A           53 DQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   85 (93)
T ss_dssp             CHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             CHHHHHHHHHHccCCeeECCEEEEEEEccCccc
Confidence            48999999999999 999999999998776543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=93.38  E-value=0.0068  Score=44.88  Aligned_cols=28  Identities=18%  Similarity=0.071  Sum_probs=24.9

Q ss_pred             HHHHHHHHHhcCccccccccceeeeeec
Q psy3930         160 PDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       160 ~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .++|.+|+..+++..+.++.++|..+.+
T Consensus        79 ~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  106 (109)
T 2err_A           79 SADADRAREKLHGTVVEGRKIEVNNATA  106 (109)
T ss_dssp             SHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             HHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            7899999999999999999999987654

>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=93.35  E-value=0.0099  Score=42.77  Aligned_cols=36  Identities=8%  Similarity=0.004  Sum_probs=29.8

Q ss_pred             eeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeee
Q psy3930         144 VSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       144 l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      .-.|+.|..       .++|.+|++.+++..+.++.++|..+.
T Consensus        58 g~afV~f~~-------~~~a~~Ai~~l~g~~~~g~~l~V~~a~   93 (98)
T 2cqp_A           58 GEAMVAFES-------RDEATAAVIDLNDRPIGSRKVKLVLGS   93 (98)
T ss_dssp             EEEEEEESC-------HHHHHHHHHHTTTCEETTEECEEEESS
T ss_pred             eEEEEEECC-------HHHHHHHHHHhCCCeeCCeEEEEEEcC
Confidence            345666655       899999999999999999999998765

>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=93.35  E-value=0.04  Score=43.27  Aligned_cols=30  Identities=23%  Similarity=0.097  Sum_probs=24.8

Q ss_pred             EEeeccCCCCCcceEEEEEecCHHHHHHHHHh
Q psy3930         226 VSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL  257 (299)
Q Consensus       226 v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~  257 (299)
                      +.+..+.  +.++|||||+|.+.++|++|++.
T Consensus         3 ~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~   32 (158)
T 2kn4_A            3 YKLILNG--KTLKGETTTEAVDAATAEKVFKQ   32 (158)
T ss_dssp             EEEEEEC--SSCEEEEEEECSSHHHHHHHHHH
T ss_pred             EEEEecC--ccccchhHHHHHHHHhHHHHHHh
Confidence            4555553  36899999999999999999987

>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=93.34  E-value=0.009  Score=43.59  Aligned_cols=38  Identities=11%  Similarity=0.089  Sum_probs=30.2

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCcccccc---ccceeeeeecccC
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTE---DGTKVRRTVVVQD  190 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~---~~~~v~r~~~~~~  190 (299)
                      .|+.|.+       .++|.+|++.+++..+.+   ..++|.++.+...
T Consensus        59 afV~f~~-------~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~~   99 (105)
T 2dnh_A           59 AFVKFSS-------HTEAQAAIHALHGSQTMPGASSSLVVKFADTDKE   99 (105)
T ss_dssp             EEEEESS-------HHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSCC
T ss_pred             EEEEeCC-------HHHHHHHHHHHcCCccCCCCCccEEEEECccCcc
Confidence            4555555       899999999999999888   8899988776544

>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=93.32  E-value=0.0063  Score=44.92  Aligned_cols=37  Identities=11%  Similarity=0.080  Sum_probs=30.2

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .|+.|.+       .++|.+|+..+++..+.+..++|..+.+..
T Consensus        71 afV~f~~-------~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  107 (110)
T 1oo0_B           71 ALVEYET-------HKQALAAKEALNGAEIMGQTIQVDWCFVKG  107 (110)
T ss_dssp             EEEEESS-------HHHHHHHHHHHTTCEETTEECEEEESEESS
T ss_pred             EEEEECC-------HHHHHHHHHHcCCCEECCcEEEEEEcccCC
Confidence            4555554       899999999999999999999998876544

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=93.28  E-value=0.0045  Score=44.94  Aligned_cols=51  Identities=10%  Similarity=0.062  Sum_probs=35.7

Q ss_pred             HHHHHhhhcCCCe-ee-------eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         130 RFFSQLLQESPEI-EV-------SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l-------~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .-|..++..++.+ .+       -.|+.|.       +.++|.+|+..+++..+.++.++|.++.+
T Consensus        42 ~~l~~~f~~~G~i~~~~~~~~~g~afV~f~-------~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~  100 (101)
T 2la4_A           42 ADLIPLFQNFGFILDFKHYPEKGCCFIKYD-------THEQAAVCIVALANFPFQGRNLRTGWGKE  100 (101)
T ss_dssp             HHHHHHHHTTSCCSEEEEETTTTEEEEECS-------SHHHHHHHHHHHTTCEETTEECCCCBCCC
T ss_pred             HHHHHHHHhCCCEEEEEEecCCCEEEEEEC-------CHHHHHHHHHHhCCCeECCeEEEEEeccC
Confidence            4566666666642 11       1244444       48899999999999999999999887653

>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=93.28  E-value=0.0079  Score=44.33  Aligned_cols=31  Identities=16%  Similarity=0.077  Sum_probs=26.9

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      +.++|.+|++.+++..+.++.++|..+.+..
T Consensus        70 ~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~  100 (109)
T 1x4a_A           70 DPRDAEDAVYGRDGYDYDGYRLRVEFPRSGR  100 (109)
T ss_dssp             CHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             CHHHHHHHHHHcCCCEECCeEEEEEEcccCC
Confidence            4899999999999999999999998876543

>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=93.27  E-value=0.0051  Score=45.30  Aligned_cols=32  Identities=13%  Similarity=0.024  Sum_probs=25.1

Q ss_pred             CCHHHHHHHHHhcCc--cccccccceeeeeeccc
Q psy3930         158 HDPDDVVKALRKSKL--LEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~--~~~~~~~~~v~r~~~~~  189 (299)
                      .+.++|.+|++.+++  ..+.++.++|.++.+..
T Consensus        60 ~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~   93 (102)
T 1x4d_A           60 ATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK   93 (102)
T ss_dssp             SSHHHHHHHHHHHHHSCCEETTEECEEEEECCCT
T ss_pred             CCHHHHHHHHHHHcCCCceECCcEEEEEECCCCC
Confidence            348899999998765  56899999998877543

>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=93.27  E-value=0.0049  Score=44.33  Aligned_cols=30  Identities=13%  Similarity=0.028  Sum_probs=26.3

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      +.++|.+|++.+++..+.++.++|..+.+.
T Consensus        53 ~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   82 (96)
T 2x1f_A           53 DLESSASAVRNLNGYQLGSRFLKCGYSSNS   82 (96)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEECSCS
T ss_pred             CHHHHHHHHHHhCCCeECCeEEEEEEcCCC
Confidence            489999999999999999999999887654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=93.19  E-value=0.0074  Score=42.86  Aligned_cols=53  Identities=13%  Similarity=0.154  Sum_probs=37.8

Q ss_pred             HHHHHhhhcCCCee------------eeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         130 RFFSQLLQESPEIE------------VSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       130 ~fl~~~~~~~~~~~------------l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .-|..++..++.+.            .-.|+.|.+       .++|.+|+..+++..+.++.++|+.+.+..
T Consensus        23 ~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~-------~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   87 (92)
T 2dgv_A           23 KMLKDKFNECGHVLYADIKMENGKSKGCGVVKFES-------PEVAERACRMMNGMKLSGREIDVRIDRNAS   87 (92)
T ss_dssp             HHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESS-------HHHHHHHHHHHTTCCBTTBCCCCEECSCCS
T ss_pred             HHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECC-------HHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            44666666666421            223445544       899999999999999999999998876543

>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=93.16  E-value=0.013  Score=43.57  Aligned_cols=38  Identities=8%  Similarity=-0.032  Sum_probs=31.3

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .|+.|.+       .++|.+|+..+++..+.++.++|..+.+...
T Consensus        70 afV~f~~-------~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~  107 (115)
T 2cpx_A           70 AFITFPN-------KEIAWQALHLVNGYKLYGKILVIEFGKNKKQ  107 (115)
T ss_dssp             EEEECSS-------HHHHHHHHHHSTTCBCSSCBCEEEECCCCSC
T ss_pred             EEEEECC-------HHHHHHHHHHhCCCEeCCcEEEEEEccCCCC
Confidence            4666655       8999999999999999999999998776544

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=93.15  E-value=0.0052  Score=45.97  Aligned_cols=29  Identities=21%  Similarity=0.187  Sum_probs=25.7

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      +.++|.+|++.+++.++.++.++|..+..
T Consensus        76 ~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~  104 (111)
T 2jvr_A           76 SEEILVEALERLNNIEFRGSVITVERDDN  104 (111)
T ss_dssp             SHHHHHHHHHHTTTEEETTEEEEEEESCC
T ss_pred             CHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            48999999999999999999999987653

>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=93.14  E-value=0.0088  Score=44.10  Aligned_cols=32  Identities=19%  Similarity=0.185  Sum_probs=27.2

Q ss_pred             CHHHHHHHHHhcC------ccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSK------LLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~------~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|+..++      +..+.++.++|.++.+...
T Consensus        66 ~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           66 TQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE  103 (111)
T ss_dssp             SHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCC
T ss_pred             CHHHHHHHHHHhccccccCCcEEcCEEEEEEECCCCcc
Confidence            3899999999998      9999999999988776544

>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=93.09  E-value=0.0086  Score=43.58  Aligned_cols=36  Identities=14%  Similarity=0.174  Sum_probs=29.4

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .|+.|.+       .++|.+|++.+++..+.++.++|..+.+.
T Consensus        53 afV~f~~-------~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   88 (104)
T 1p1t_A           53 GFCEYQD-------QETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             EEEECSC-------HHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             EEEEECC-------HHHHHHHHHHhCCCeeCCcEEEEEeCCCc
Confidence            4555554       89999999999999999999999876543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=93.07  E-value=0.0043  Score=45.54  Aligned_cols=30  Identities=10%  Similarity=-0.003  Sum_probs=23.5

Q ss_pred             CCHHHHHHHHHhcCccc--cccccceeeeeec
Q psy3930         158 HDPDDVVKALRKSKLLE--VTEDGTKVRRTVV  187 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~--~~~~~~~v~r~~~  187 (299)
                      .+.++|.+|++.+++..  +.|+.++|..+.+
T Consensus        65 ~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~   96 (100)
T 3r27_A           65 EDVLGACNAVNYAADNQIYIAGHPAFVNYSTS   96 (100)
T ss_dssp             SSHHHHHHHHHHHHHSCEEETTEEEEEEECSC
T ss_pred             CCHHHHHHHHHHhcCCCceeCCcEEEEEeccc
Confidence            56899999999887654  7788888877653

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=93.04  E-value=0.0099  Score=45.82  Aligned_cols=32  Identities=9%  Similarity=0.043  Sum_probs=27.3

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|++.+++..+.++.++|..+.+...
T Consensus        93 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  124 (139)
T 1u6f_A           93 SGSSAQQAIAGLNGFNILNKRLKVALAASGHQ  124 (139)
T ss_dssp             SHHHHHHHHHHTTTEECSSCEEEEEESSCCCC
T ss_pred             CHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            38999999999999999999999988765543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=93.04  E-value=0.005  Score=45.61  Aligned_cols=32  Identities=0%  Similarity=-0.110  Sum_probs=25.2

Q ss_pred             CCHHHHHHHHHhcC--ccccccccceeeeeeccc
Q psy3930         158 HDPDDVVKALRKSK--LLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       158 ~~~~~a~~Al~~~~--~~~~~~~~~~v~r~~~~~  189 (299)
                      .+.++|.+|++.++  +..+.++.++|.++.+..
T Consensus        60 ~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~   93 (105)
T 1sjq_A           60 NTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE   93 (105)
T ss_dssp             SSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSS
T ss_pred             CCHHHHHHHHHHhccCCceECCEEEEEEEcCCCC
Confidence            34899999998764  478999999998876543

>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=93.01  E-value=0.0071  Score=44.63  Aligned_cols=52  Identities=12%  Similarity=0.096  Sum_probs=36.6

Q ss_pred             HHHHHhhhcCCCee-------eeeeecccccccCCCCHHHHHHHHHhcCcccccc-----ccceeeeeecc
Q psy3930         130 RFFSQLLQESPEIE-------VSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTE-----DGTKVRRTVVV  188 (299)
Q Consensus       130 ~fl~~~~~~~~~~~-------l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~-----~~~~v~r~~~~  188 (299)
                      .-|..++..++.+.       .-.|++|.+       .++|.+||+.+++..+.+     ..++|..+.+.
T Consensus        30 ~~l~~~F~~~G~i~~~~i~~~g~afV~f~~-------~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~   93 (108)
T 1x4c_A           30 QDLKDHMREAGDVCYADVYRDGTGVVEFVR-------KEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPR   93 (108)
T ss_dssp             HHHHHHHGGGSCEEEEEEETTTEEEEEESS-------HHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCC
T ss_pred             HHHHHHHHhcCCEeEEEEecCCEEEEEECC-------HHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCC
Confidence            34666666666421       123555554       899999999999999999     88888876654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=92.99  E-value=0.16  Score=36.25  Aligned_cols=30  Identities=17%  Similarity=0.080  Sum_probs=26.4

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      +.++|.+|++.+++..+.++.++|..+.+.
T Consensus        65 ~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           65 DSAAAQQAVSCLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             SHHHHHHHHHHHTTCCSSSSCCEEEECCCC
T ss_pred             CHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            489999999999999999999999887654

>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=92.99  E-value=0.0088  Score=42.74  Aligned_cols=35  Identities=9%  Similarity=0.076  Sum_probs=28.7

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeee
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      -.|+.|..       .++|.+|++.+++..+.++.++|..+.
T Consensus        59 ~afV~f~~-------~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           59 EAMVAFES-------RDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             EEEEEESS-------HHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             EEEEEECC-------HHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            45666655       899999999999999999999887654

>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=92.93  E-value=0.0089  Score=44.14  Aligned_cols=52  Identities=6%  Similarity=0.013  Sum_probs=36.7

Q ss_pred             HHHHHhhhcCCCe---ee---eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         130 RFFSQLLQESPEI---EV---SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       130 ~fl~~~~~~~~~~---~l---~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .-|..++..++.+   .+   -.|+.|..       .++|.+|+..+++..+.+..++|..+.+.
T Consensus        43 ~~l~~~F~~~G~v~~v~i~~g~afV~f~~-------~~~A~~A~~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           43 SDVETIFSKYGRVAGCSVHKGYAFVQYSN-------ERHARAAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             HHHHHHHGGGSCCSEEEEETTEEEEECSS-------SHHHHHHHHHHTTCEETTEECCEEESCCC
T ss_pred             HHHHHHHHhCCCeEEEEEeCCEEEEEECC-------HHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            3455555555541   11   23556655       78999999999999999999999887643

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=92.87  E-value=0.007  Score=44.82  Aligned_cols=52  Identities=12%  Similarity=0.157  Sum_probs=37.3

Q ss_pred             HHHHHhhhcCCCe-ee-----eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         130 RFFSQLLQESPEI-EV-----SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l-----~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .-|..++..++.+ .+     -.|+.|.+       .++|.+|+..+++..+.++.++|..+.+.
T Consensus        46 ~~L~~~F~~~G~i~~v~i~kg~afV~f~~-------~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           46 SELNEIFGPFGPMKEVKILNGFAFVEFEE-------AESAAKAIEEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             HHHHHHHTTTSCCCEEEEETTEEEEECSS-------HHHHHHHHHHHTTCEETTEECEEESCSCC
T ss_pred             HHHHHHHHhcCCEEEEEEECCEEEEEECC-------HHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            3466666666652 21     23555544       89999999999999999999999876644

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=92.86  E-value=0.0085  Score=42.72  Aligned_cols=28  Identities=14%  Similarity=0.024  Sum_probs=24.2

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      .+.++|.+|++.+++..+.++.++|..+
T Consensus        66 ~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           66 LDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             SCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            3489999999999999999998888764

>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=92.81  E-value=0.0096  Score=45.07  Aligned_cols=32  Identities=9%  Similarity=-0.016  Sum_probs=27.4

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|++.+++..+.+..+.|..+.+...
T Consensus        73 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  104 (126)
T 3ex7_B           73 TYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP  104 (126)
T ss_dssp             SHHHHHHHHHHHTTCBSSSSBCEEEESEESSS
T ss_pred             CHHHHHHHHHHhCCCeeCCeEEEEEEecCCCC
Confidence            48999999999999999999999998765443

>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=92.64  E-value=0.0083  Score=44.23  Aligned_cols=54  Identities=13%  Similarity=0.104  Sum_probs=37.7

Q ss_pred             HHHHHhhhcCCCe-e-------eeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         130 RFFSQLLQESPEI-E-------VSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~-------l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .-|..++..++.+ .       .-.|+.|..       .++|.+|+..+++..+.++.++|..+.+...
T Consensus        40 ~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~-------~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           40 QLMRQTFSPFGQIMEIRVFPEKGYSFVRFST-------HESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             HHHHHHHHHHSCEEEEEEETTTTEEEEEESS-------HHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             HHHHHHHHhcCCeEEEEEeCCCCEEEEEECC-------HHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence            3455666655542 1       123455544       8999999999999999999999988765443

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=92.61  E-value=0.0067  Score=43.33  Aligned_cols=28  Identities=18%  Similarity=0.238  Sum_probs=24.4

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeee
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      +.++|.+|+..+++..+.++.++|..+.
T Consensus        66 ~~~~A~~A~~~l~g~~~~g~~l~v~~a~   93 (95)
T 2cqc_A           66 NVDDAKEAKERANGMELDGRRIRVSGPS   93 (95)
T ss_dssp             SHHHHHHHHHHHTTEEETTEEEEEECCS
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEecC
Confidence            3899999999999999999999887654

>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=92.56  E-value=0.013  Score=44.42  Aligned_cols=53  Identities=6%  Similarity=-0.037  Sum_probs=35.2

Q ss_pred             HHHHHhhhcCCCe-eee-------eeecccccccCCCCHHHHHHHHHhcC--ccccccccceeeeeeccc
Q psy3930         130 RFFSQLLQESPEI-EVS-------VFLKCNKLARLTHDPDDVVKALRKSK--LLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l~-------~f~~F~~i~~~~~~~~~a~~Al~~~~--~~~~~~~~~~v~r~~~~~  189 (299)
                      .-|+.++..++.+ .+.       .|+.|..       .++|.+|++.++  +..+.++.++|..+.+..
T Consensus        46 ~dL~~lF~~fG~V~~v~i~~~kG~AFVeF~~-------~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~  108 (119)
T 2ad9_A           46 GEVISLGLPFGKVTNLLMLKGKNQAFIEMNT-------EEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE  108 (119)
T ss_dssp             HHHHHHHTTTSCCCEEEEEGGGTEEEEECSC-------HHHHHHHHHHHHHHCCCBTTBCCEEEECSSSS
T ss_pred             HHHHHHHHhcCCEEEEEEeCCCCEEEEEECC-------HHHHHHHHHHhccCCceECCeEEEEEEccCCC
Confidence            3456666666541 111       3455544       789999998776  468999999999876544

>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=92.48  E-value=0.29  Score=35.12  Aligned_cols=32  Identities=16%  Similarity=0.018  Sum_probs=27.5

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|+..+++..+.++.++|.++.+...
T Consensus        64 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   95 (103)
T 2cq3_A           64 NSADADRAREKLHGTVVEGRKIEVNNATARVM   95 (103)
T ss_dssp             CHHHHHHHHHHHTTCEETTEECEEEECCSSCC
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEEcccCCC
Confidence            38999999999999999999999998776543

>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=92.46  E-value=0.0088  Score=41.77  Aligned_cols=49  Identities=18%  Similarity=0.158  Sum_probs=34.1

Q ss_pred             HHHHHhhhcCCCee-e-------eeeecccccccCCCCHHHHHHHHHhc-Cccccccccceeeee
Q psy3930         130 RFFSQLLQESPEIE-V-------SVFLKCNKLARLTHDPDDVVKALRKS-KLLEVTEDGTKVRRT  185 (299)
Q Consensus       130 ~fl~~~~~~~~~~~-l-------~~f~~F~~i~~~~~~~~~a~~Al~~~-~~~~~~~~~~~v~r~  185 (299)
                      .-|..++..++.+. +       -.|++|.+       .++|.+|+..+ ++..+.++.++|+++
T Consensus        27 ~~l~~~f~~~G~i~~~~~~~~kg~afV~f~~-------~~~A~~a~~~l~~~~~~~g~~l~v~~a   84 (85)
T 2ytc_A           27 TDLRNHFYQFGEIRTITVVQRQQCAFIQFAT-------RQAAEVAAEKSFNKLIVNGRRLNVKWG   84 (85)
T ss_dssp             HHHHHHHHTTSCEEEEEEEGGGTEEEEEESS-------HHHHHHHHHTTTTTCEETTEECCEEEC
T ss_pred             HHHHHHHHhCCCEeEEEEECCCCEEEEEECC-------HHHHHHHHHHhcCCeeECCCEEEEEec
Confidence            34666666666521 1       23455544       89999999988 999999998888764

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=92.40  E-value=0.0098  Score=40.45  Aligned_cols=25  Identities=16%  Similarity=0.205  Sum_probs=21.2

Q ss_pred             CHHHHHHHHHhcCccccccccceeee
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      +.++|.+|++ +++..+.++.++|++
T Consensus        50 ~~~~a~~a~~-~~~~~~~g~~l~v~~   74 (75)
T 2mss_A           50 SEDIVEKVCE-IHFHEINNKMVECKK   74 (75)
T ss_dssp             CHHHHHHHHS-SSCCCSSSCCCEEEC
T ss_pred             CHHHHHHHHH-CCCCEECCEEEEEEe
Confidence            3788999996 899999999988865

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=92.40  E-value=0.0084  Score=44.06  Aligned_cols=29  Identities=7%  Similarity=-0.107  Sum_probs=24.3

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .+.++|.+|+. +++..+.++.+.|.++..
T Consensus        60 ~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           60 DSIESAKKFVE-TPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             SSHHHHHHHHT-SSCCCCTTTTCEEEEHHH
T ss_pred             CCHHHHHHHHH-cCCCEECCEEEEEEEchH
Confidence            34899999997 899999999999987653

>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=92.39  E-value=0.008  Score=42.52  Aligned_cols=29  Identities=14%  Similarity=0.090  Sum_probs=23.2

Q ss_pred             HHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         160 PDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       160 ~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .+ |.+|+..+++..+.++.++|.++.+..
T Consensus        53 ~~-a~~a~~~l~g~~~~g~~l~V~~a~~~~   81 (90)
T 2ki2_A           53 ES-VSEAIAKLDNTDFMGRTIRVTEANPKK   81 (90)
T ss_dssp             TH-HHHHHHTSCSSCCSSSSCSEEEC----
T ss_pred             HH-HHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            67 999999999999999999999876543

>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=92.37  E-value=0.0086  Score=43.32  Aligned_cols=51  Identities=10%  Similarity=0.072  Sum_probs=36.5

Q ss_pred             HHHHHhhhcCCCe---e---eeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         130 RFFSQLLQESPEI---E---VSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       130 ~fl~~~~~~~~~~---~---l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .-|..++..++.+   .   +-.|+.|..       .++|.+|+..+++..+.++.++|..+.+
T Consensus        38 ~~L~~~F~~~G~v~~v~i~~g~afV~f~~-------~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   94 (97)
T 2xnq_A           38 EDLFRIFSPYGHIMQINIKNAFGFIQFDN-------PQSVRDAIEXESQEMNFGKKLILEVSSS   94 (97)
T ss_dssp             HHHHHHHGGGSCEEEEEECSSEEEEEESS-------HHHHHHHHHHHTTSEETTEECEEEECCC
T ss_pred             HHHHHHHHhcCCEEEEEEeCCEEEEEECC-------HHHHHHHHHHcCCCEECCEEEEEEecCC
Confidence            3466666666652   1   123556655       8999999999999999999999887653

>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=92.36  E-value=0.012  Score=46.28  Aligned_cols=37  Identities=11%  Similarity=0.097  Sum_probs=30.5

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .|++|.+       .++|.+||..+++..+.+..++|..+.+..
T Consensus        84 afV~f~~-------~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  120 (156)
T 1h2v_Z           84 CFVEYYS-------RADAENAMRYINGTRLDDRIIRTDWDAGFK  120 (156)
T ss_dssp             EEEEESS-------HHHHHHHHHHTTTSEETTEECEEEEESCCC
T ss_pred             EEEEECC-------HHHHHHHHHHhCCCEECCeEEEEEECCCCC
Confidence            3555554       899999999999999999999999887544

>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=92.28  E-value=0.0082  Score=42.89  Aligned_cols=28  Identities=14%  Similarity=0.124  Sum_probs=24.1

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeee
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      +.++|.+|+..+++..+.++.++|..+.
T Consensus        66 ~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           66 HPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             STHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            3799999999999999999999887653

>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=92.27  E-value=0.0087  Score=43.84  Aligned_cols=28  Identities=11%  Similarity=0.186  Sum_probs=24.4

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeee
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      +.++|.+|++.+++..+.++.++|..+.
T Consensus        79 ~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           79 RKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            4899999999999999999999887653

>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=92.25  E-value=0.012  Score=46.05  Aligned_cols=30  Identities=20%  Similarity=0.157  Sum_probs=26.1

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      +.++|.+|+..+++..+.++.++|..+.+.
T Consensus       119 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A          119 DPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             SHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             CHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            489999999999999999999999877643

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=92.24  E-value=0.014  Score=39.82  Aligned_cols=26  Identities=23%  Similarity=0.263  Sum_probs=22.3

Q ss_pred             CHHHHHHHHHhcCccccccccceeeee
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      +.++|.+|+..++ ..+.++.++|+++
T Consensus        51 ~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A           51 DQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            4789999999999 8999999888764

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=92.19  E-value=0.014  Score=45.04  Aligned_cols=37  Identities=11%  Similarity=0.104  Sum_probs=30.4

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .|+.|.+       .++|.+|+..+++..+.++.++|.++.+..
T Consensus        92 afV~F~~-------~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~  128 (135)
T 2lea_A           92 AFVRFHD-------KRDAEDAMDAMDGAVLDGRELRVQMARYGR  128 (135)
T ss_dssp             CEEECSC-------HHHHHHHHTTTTTCCSSSSCCEEEECCCCC
T ss_pred             EEEEECC-------HHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            4555554       899999999999999999999999876543

>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=92.11  E-value=0.014  Score=43.61  Aligned_cols=32  Identities=13%  Similarity=0.060  Sum_probs=25.0

Q ss_pred             CCHHHHHHHHHhcC--ccccccccceeeeeeccc
Q psy3930         158 HDPDDVVKALRKSK--LLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       158 ~~~~~a~~Al~~~~--~~~~~~~~~~v~r~~~~~  189 (299)
                      .+.++|.+|++.++  ...+.++.++|.++.+..
T Consensus        70 ~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~  103 (112)
T 1x4f_A           70 ETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYK  103 (112)
T ss_dssp             SSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCS
T ss_pred             CCHHHHHHHHHHhccCCceECCEEEEEEECcccc
Confidence            44889999998764  467899999998876543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=92.03  E-value=0.012  Score=42.42  Aligned_cols=53  Identities=11%  Similarity=0.160  Sum_probs=38.0

Q ss_pred             HHHHHhhhcC--CCe---ee---eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         130 RFFSQLLQES--PEI---EV---SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       130 ~fl~~~~~~~--~~~---~l---~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .-|..++..+  +.+   .+   -.|+.|.+       .++|.+|+..+++..+.++.++|..+.+..
T Consensus        30 ~~l~~~F~~~g~g~v~~~~~~~g~afV~f~~-------~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpd_A           30 EMIEKEFNNIKPGAVERVKKIRDYAFVHFSN-------REDAVEAMKALNGKVLDGSPIEVTLAKPVD   90 (99)
T ss_dssp             HHHHHHHHTTSTTCEEEEEECSSEEEEEESS-------HHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             HHHHHHHHhcCCcceEEEEEeCCeEEEEeCC-------HHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence            3466666666  431   11   33666655       899999999999999999999998876544

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=92.01  E-value=0.011  Score=43.05  Aligned_cols=30  Identities=10%  Similarity=0.019  Sum_probs=25.7

Q ss_pred             HHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         160 PDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       160 ~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .++|.+|+.. ++..+.++.++|.++.+...
T Consensus        68 ~~~a~~a~~~-~~~~~~g~~l~V~~a~~~~~   97 (105)
T 2dh8_A           68 PNCVGTVLAS-RPHTLDGRNIDPKPCTPRGM   97 (105)
T ss_dssp             TTHHHHHHHH-CSEEETTEEEBCCCSCCSSC
T ss_pred             HHHHHHHHHh-CCCeECCEEEEEEEccCCCC
Confidence            7899999988 99999999999988776544

>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=92.00  E-value=0.014  Score=42.68  Aligned_cols=38  Identities=13%  Similarity=0.109  Sum_probs=29.6

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCcccc---ccccceeeeeecccC
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEV---TEDGTKVRRTVVVQD  190 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~---~~~~~~v~r~~~~~~  190 (299)
                      .|+.|..       .++|.+|++.+++..+   .+..++|.++.+...
T Consensus        58 afV~f~~-------~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~~   98 (106)
T 2dgp_A           58 AFLTYCE-------RESALKAQSALHEQKTLPGMNRPIQVKPADSESR   98 (106)
T ss_dssp             EEEEESS-------HHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCSC
T ss_pred             EEEEECC-------HHHHHHHHHHhcCCcccCCCCceEEEEECCcccc
Confidence            4566655       8999999999999887   788899988765443

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.96  E-value=0.46  Score=34.01  Aligned_cols=39  Identities=15%  Similarity=0.101  Sum_probs=31.8

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      -.|+.|..       .++|.+|+..+++..+.++.++|..+.+...
T Consensus        57 ~afV~f~~-------~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2d9p_A           57 FGFVCFSS-------PEEATKAVTEMNGRIVATKPLYVALAQRKEE   95 (103)
T ss_dssp             EEEEEESS-------HHHHHHHHHHHTTCBSSSSBCEEEECSSCCC
T ss_pred             EEEEEECC-------HHHHHHHHHHhCCCEeCCcEEEEEEeccccc
Confidence            34666655       8999999999999999999999998776544

>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=91.94  E-value=0.011  Score=43.80  Aligned_cols=31  Identities=13%  Similarity=0.099  Sum_probs=27.0

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      +.++|.+|++.+++..+.++.++|..+.+..
T Consensus        72 ~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           72 RSEDALRAIQCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             SHHHHHHHHHHHTTEEETTEEEEEESCCCCS
T ss_pred             cHHHHHHHHHHhCCCEECCEEEEEEeccccc
Confidence            4899999999999999999999998876544

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=91.85  E-value=0.013  Score=42.26  Aligned_cols=35  Identities=14%  Similarity=0.048  Sum_probs=28.1

Q ss_pred             eeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeee
Q psy3930         144 VSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       144 l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      +-.|+.|..       .++|.+|++.+++..+.++.++|..+
T Consensus        64 G~afV~f~~-------~~~a~~Ai~~l~g~~~~g~~l~V~~A   98 (99)
T 2la6_A           64 GEATVSFDD-------PPSAKAAIDWFDGKEFSGNPIKVSFA   98 (99)
T ss_dssp             EEEEEEBSS-------HHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             eEEEEEECC-------HHHHHHHHHHhCCCEeCCcEEEEEec
Confidence            344566655       89999999999999999999988764

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=91.79  E-value=0.019  Score=42.47  Aligned_cols=32  Identities=16%  Similarity=0.008  Sum_probs=27.4

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|+..+++..+.++.++|.++.+...
T Consensus        74 ~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           74 DPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP  105 (113)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEECSSCCCC
T ss_pred             CHHHHHHHHHHcCCCccCCCEEEEEECCCCCC
Confidence            38999999999999999999999988765543

>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=91.74  E-value=0.0092  Score=42.01  Aligned_cols=28  Identities=18%  Similarity=0.036  Sum_probs=24.4

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      +.++|.+|+ .+++..+.++.++|.++.+
T Consensus        57 ~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A           57 DKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             STHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            478999999 9999999999999987654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=91.71  E-value=0.0066  Score=42.46  Aligned_cols=28  Identities=21%  Similarity=0.158  Sum_probs=23.6

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      .+.++|.+|++.+++..+.++.+++.+.
T Consensus        55 ~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A           55 DSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             SCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            3489999999999999999988887654

>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=91.70  E-value=0.023  Score=41.16  Aligned_cols=30  Identities=17%  Similarity=0.128  Sum_probs=25.5

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .+.++|.+|+ .+++..+.++.++|..+.+.
T Consensus        69 ~~~~~a~~Ai-~l~g~~~~g~~l~V~~a~~~   98 (100)
T 2j76_E           69 EDLDSLLSAL-SLNEESLGNRRIRVDVADQA   98 (100)
T ss_dssp             CCHHHHHHHH-HTTTCCBTTBCCCCEECCCS
T ss_pred             CCHHHHHHHH-hcCCCEECCeEEEEEeccCC
Confidence            3489999999 89999999999999877643

>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=91.68  E-value=0.017  Score=43.09  Aligned_cols=45  Identities=11%  Similarity=0.149  Sum_probs=30.9

Q ss_pred             HHHHHhhhcCCCe-e------eeeeecccccccCCCCHHHHHHHHHhcCccccccccce
Q psy3930         130 RFFSQLLQESPEI-E------VSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTK  181 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~------l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~  181 (299)
                      .-|..++..++.+ .      .-.|++|.+       .++|.+||+.+++..+.+..++
T Consensus        31 ~~l~~~F~~~G~v~~~~i~~~g~afV~f~~-------~~~a~~Ai~~l~g~~~~gr~~~   82 (115)
T 3beg_B           31 QDLKDHMREAGDVCYADVYRDGTGVVEFVR-------KEDMTYAVRKLDNTKFRSHEGE   82 (115)
T ss_dssp             THHHHHHGGGSCEEEEEECTTSEEEEEESS-------HHHHHHHHHHHTTCBCCCTTSC
T ss_pred             HHHHHHHHhcCCeEEEEEecCCEEEEEECC-------HHHHHHHHHHhCCCEECCcEee
Confidence            3466666666642 1      123455544       8999999999999999998843

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.64  E-value=0.027  Score=40.64  Aligned_cols=38  Identities=13%  Similarity=0.132  Sum_probs=31.1

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      -.|+.|..       .++|.+|+..+++..+.++.++|..+.+..
T Consensus        55 ~afV~f~~-------~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (101)
T 2fc9_A           55 YAFIEFAS-------FEDAKEALNSCNKREIEGRAIRLELQGPRG   92 (101)
T ss_dssp             EEEEECSS-------HHHHHHHHHHTSSEEETTEEEEEEECSSCC
T ss_pred             EEEEEECC-------HHHHHHHHHHhCCCEeCCeEEEEEEcCCCC
Confidence            44666655       899999999999999999999998876543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=91.30  E-value=0.017  Score=42.00  Aligned_cols=31  Identities=10%  Similarity=0.067  Sum_probs=26.6

Q ss_pred             CHHHHHHHHHhcCccc-cccccceeeeeeccc
Q psy3930         159 DPDDVVKALRKSKLLE-VTEDGTKVRRTVVVQ  189 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~-~~~~~~~v~r~~~~~  189 (299)
                      +.++|.+|++.+++.. +.++.++|..+.+..
T Consensus        60 ~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~   91 (104)
T 2dhg_A           60 DELEQKRALTECQGAVGLGSKPVRLSVAIPKA   91 (104)
T ss_dssp             CHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCC
T ss_pred             CHHHHHHHHHHccCCcccCCEeEEEEEccCCC
Confidence            3899999999999999 999999998876544

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.28  E-value=0.12  Score=37.35  Aligned_cols=39  Identities=18%  Similarity=0.138  Sum_probs=32.1

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      -.|+.|..       .++|.+|++.+++..+.++.++|..+....+
T Consensus        48 ~AfV~F~~-------~esA~~A~~~l~G~~l~gr~i~v~~A~~~sd   86 (96)
T 2diu_A           48 SAILRFIN-------QDSAERAQKRMENEDVFGNRIIVSFTPKNRE   86 (96)
T ss_dssp             CEEEEESS-------HHHHHHHHHHHTTCCSSSSCCEEESSCCSCC
T ss_pred             EEEEEECC-------HHHHHHHHHHhcCCccCCceEEEEecCCCcc
Confidence            44666665       7999999999999999999999988765443

>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=91.22  E-value=0.021  Score=41.77  Aligned_cols=52  Identities=6%  Similarity=0.017  Sum_probs=34.6

Q ss_pred             HHHHhhhcCCCee-e-------eeeecccccccCCCCHHHHHHHHHhc--Cccccccccceeeeeeccc
Q psy3930         131 FFSQLLQESPEIE-V-------SVFLKCNKLARLTHDPDDVVKALRKS--KLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       131 fl~~~~~~~~~~~-l-------~~f~~F~~i~~~~~~~~~a~~Al~~~--~~~~~~~~~~~v~r~~~~~  189 (299)
                      -|..++..++.+. +       -.|+.|..       .++|.+|++.+  ++..+.++.++|..+.+..
T Consensus        31 ~L~~~F~~fG~v~~v~i~~~kg~aFVef~~-------~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~   92 (101)
T 2cq1_A           31 EVIALGLPFGKVTNILMLKGKNQAFLELAT-------EEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   92 (101)
T ss_dssp             HHHHTTTTTSCEEEEEEETTTTEEEEEESS-------HHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             HHHHHHHhcCCEEEEEEECCCCEEEEEECC-------HHHHHHHHHHhccCCceECCcEEEEEEcCccc
Confidence            4556666666521 1       13555544       78999999865  5678999999998876543

>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=91.22  E-value=0.026  Score=42.56  Aligned_cols=38  Identities=13%  Similarity=-0.002  Sum_probs=30.7

Q ss_pred             eeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         142 IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       142 ~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      -.+-.|+.|..       .++|.+||. +++..+.++.+.|.++.+
T Consensus        66 ~~G~afV~F~~-------~~~a~~Al~-~~g~~~~gr~i~V~~a~~  103 (124)
T 1wel_A           66 ATGEGFVEFRN-------EADYKAALC-RHKQYMGNRFIQVHPITK  103 (124)
T ss_dssp             EEEEEEEEBSS-------SHHHHHHHT-SCSBCSTTSCBEEEEECH
T ss_pred             CCeEEEEEECC-------HHHHHHHHH-hCCCeECCcEEEEEECCH
Confidence            34456777766       789999998 999999999999987654

>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=91.17  E-value=0.016  Score=46.17  Aligned_cols=31  Identities=13%  Similarity=0.035  Sum_probs=26.8

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      +.++|.+||..+++..+.+..+.|.++.+..
T Consensus       123 ~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  153 (165)
T 1rk8_A          123 THKQALAAKEALNGAEIMGQTIQVDWCFVKG  153 (165)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEESEECC
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEEecCCC
Confidence            4899999999999999999999998876544

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=91.11  E-value=0.016  Score=42.88  Aligned_cols=29  Identities=10%  Similarity=-0.010  Sum_probs=25.3

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      +.++|.+|+..+++..+.+..++|..+..
T Consensus        65 ~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   93 (114)
T 2do0_A           65 QSIEAVQAISMFNGQLLFDRPMHVKMDER   93 (114)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CHHHHHHHHHHhCCCEeCCCEEEEEEccc
Confidence            38999999999999999999999987653

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=90.98  E-value=0.011  Score=44.26  Aligned_cols=27  Identities=22%  Similarity=0.304  Sum_probs=23.6

Q ss_pred             CHHHHHHHHHhcCccccccccceeeee
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      +.++|.+|++.+++..+.++.++|+.+
T Consensus        91 ~~~~A~~A~~~l~g~~~~g~~l~V~~a  117 (118)
T 2khc_A           91 NPDSAQVAIKAMNGFQVGTKRLKVQLK  117 (118)
T ss_dssp             SSHHHHHHHHHCCCCEETTEECCEEEC
T ss_pred             CHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            378999999999999999999888764

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=90.97  E-value=0.015  Score=46.08  Aligned_cols=30  Identities=17%  Similarity=0.068  Sum_probs=26.4

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .+.++|.+||..+++..+.++.++|..+.+
T Consensus       107 ~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~  136 (156)
T 3n9u_C          107 ASENSVHKLLELLPGKVLNGEKVDVRPATR  136 (156)
T ss_dssp             SCHHHHHHHHHHSTTCEETTEECEEEECCH
T ss_pred             CCHHHHHHHHHHcCCCEECCeEeEEEEcCC
Confidence            458999999999999999999999987754

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=90.77  E-value=0.018  Score=41.58  Aligned_cols=37  Identities=19%  Similarity=0.193  Sum_probs=30.6

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      -.|+.|.+       .++|.+|++ +++..+.++.++|..+.+..
T Consensus        60 ~afV~f~~-------~~~a~~A~~-l~g~~~~g~~l~V~~a~~~~   96 (101)
T 1fj7_A           60 FGYVDFES-------AEDLEKALE-LTGLKVFGNEIKLEKPKGRD   96 (101)
T ss_dssp             EEEEEESS-------HHHHHHHHH-GGGCCBTTBCCEEECCSCCC
T ss_pred             EEEEEECC-------HHHHHHHHh-cCCcEECCcEEEEEEcCCCC
Confidence            35777766       799999998 99999999999998876544

>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=90.66  E-value=0.33  Score=34.49  Aligned_cols=31  Identities=10%  Similarity=0.080  Sum_probs=26.9

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      +.++|.+|++.+++..+.++.++|..+.+..
T Consensus        61 ~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~   91 (96)
T 2dgx_A           61 NLQDAIGAVNSLHRYKIGSKKILVSLATGAS   91 (96)
T ss_dssp             SHHHHHHHHHHHTTEEETTEEEEEEECCCSS
T ss_pred             CHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            3899999999999999999999998876543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=90.56  E-value=0.017  Score=41.75  Aligned_cols=28  Identities=14%  Similarity=0.081  Sum_probs=22.4

Q ss_pred             CHHHHHHHHHhcCcc----ccccccceeeeee
Q psy3930         159 DPDDVVKALRKSKLL----EVTEDGTKVRRTV  186 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~----~~~~~~~~v~r~~  186 (299)
                      +.++|.+|++.+++.    .++|+.+.|..+.
T Consensus        62 ~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Ak   93 (95)
T 2lkz_A           62 SAMDASQLLQILQSLHPPLKIDGKTIGVDFAK   93 (95)
T ss_dssp             SSHHHHHHHHHHHSSSSCEEETTEEEEEEECC
T ss_pred             CHHHHHHHHHHhcCCCCCceECCEEEEEEEcc
Confidence            378999999988875    4888888887764

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=90.56  E-value=0.023  Score=42.77  Aligned_cols=51  Identities=10%  Similarity=0.061  Sum_probs=37.1

Q ss_pred             HHHHHhhhcCCCee-e-------------eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         130 RFFSQLLQESPEIE-V-------------SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       130 ~fl~~~~~~~~~~~-l-------------~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .-|..++..++.+. +             -.|+.|.+       .++|.+|+ .+++..+.+..++|..+.+.
T Consensus        51 ~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~-------~~~a~~A~-~l~g~~~~g~~l~V~~a~~~  115 (124)
T 2jwn_A           51 QDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-------RNSVDAAV-AMDETVFRGRTIKVLPKRTN  115 (124)
T ss_dssp             HHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESS-------HHHHHHHH-TTTTCEETTEECEEEESSCC
T ss_pred             HHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECC-------HHHHHHHH-hcCCCeECCeEEEEEECCCC
Confidence            45777777777521 2             23445544       88999999 89999999999999877643

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=90.54  E-value=0.71  Score=33.16  Aligned_cols=39  Identities=10%  Similarity=-0.042  Sum_probs=31.6

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhc-CccccccccceeeeeecccC
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKS-KLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~-~~~~~~~~~~~v~r~~~~~~  190 (299)
                      -.|+.|.+       .++|.+|+..+ ++..+.+..++|.++.+...
T Consensus        60 ~afV~f~~-------~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~~   99 (107)
T 2cph_A           60 FGFVDFIT-------KQDAKKAFNALCHSTHLYGRRLVLEWADSEVT   99 (107)
T ss_dssp             EEEEEESS-------HHHHHHHHHHHHTCCBSSSCBCEEEECCCCCC
T ss_pred             eEEEEECC-------HHHHHHHHHHhccCCeECCCEEEEEeCCCCCC
Confidence            34666655       89999999999 89999999999998876544

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=90.48  E-value=0.019  Score=44.08  Aligned_cols=26  Identities=15%  Similarity=0.109  Sum_probs=22.8

Q ss_pred             CHHHHHHHHHhcCccccccccceeee
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      +.++|.+|++.+++..+.++.++|+.
T Consensus       114 ~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A          114 LAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            38999999999999999998888764

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=90.38  E-value=0.024  Score=42.74  Aligned_cols=31  Identities=13%  Similarity=0.142  Sum_probs=26.6

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      +.++|.+|+..+++..+.++.++|..+.+..
T Consensus        85 ~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  115 (124)
T 2kt5_A           85 RRADALKAMKQYKGVPLDGRPMDIQLVASQI  115 (124)
T ss_dssp             SHHHHHHHHHHHTTEESSSCEEEEEEECCTT
T ss_pred             CHHHHHHHHHHcCCCEECCcEEEEEEeCCCC
Confidence            3899999999999999999999998876543

>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=90.38  E-value=0.021  Score=41.98  Aligned_cols=52  Identities=8%  Similarity=0.016  Sum_probs=34.6

Q ss_pred             HHHHHhhhcCCCee-ee-------eeecccccccCCCCHHHHHHHHHhcCc--cccccccceeeeeecc
Q psy3930         130 RFFSQLLQESPEIE-VS-------VFLKCNKLARLTHDPDDVVKALRKSKL--LEVTEDGTKVRRTVVV  188 (299)
Q Consensus       130 ~fl~~~~~~~~~~~-l~-------~f~~F~~i~~~~~~~~~a~~Al~~~~~--~~~~~~~~~v~r~~~~  188 (299)
                      .-|+.++..++.+. +.       .|+.|..       .++|.+|++.+++  ..+.++.++|..+.+.
T Consensus        30 ~~L~~~F~~fG~V~~v~i~~~kg~aFVef~~-------~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~   91 (104)
T 1wex_A           30 ADLVEALEKFGTICYVMMMPFKRQALVEFEN-------IDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             HHHHHHHTTTSCEEEEEEETTTTEEEEEESS-------HHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             HHHHHHHHhCCCEEEEEEECCCCEEEEEECC-------HHHHHHHHHHhccCCceECCEEEEEEEccCc
Confidence            34666666666522 11       3455544       7899999987754  5689999999887643

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=90.32  E-value=0.092  Score=39.98  Aligned_cols=36  Identities=0%  Similarity=-0.051  Sum_probs=29.8

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .|+.|..       .++|..|+..+++..+.++.++|.++.+.
T Consensus        75 aFV~F~~-------~~~A~~Ai~~lng~~l~gr~l~V~~a~~~  110 (127)
T 2a3j_A           75 AYIVFAT-------QESAQAFVEAFQGYPFQGNPLVITFSETP  110 (127)
T ss_dssp             EEEEESS-------HHHHHHHHHHSTTCCCTTSCCEEEECCCC
T ss_pred             EEEEECC-------HHHHHHHHHHHCCCEeCCCEEEEEEccCc
Confidence            4555554       89999999999999999999999887643

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=90.30  E-value=0.37  Score=33.97  Aligned_cols=36  Identities=19%  Similarity=0.070  Sum_probs=30.5

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .|+.|..       .++|.+|+..+++..+.++.++|..+.+.
T Consensus        57 afV~f~~-------~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   92 (96)
T 2e44_A           57 VNVTYSS-------KDQARQALDKLNGFQLENFTLKVAYIPDE   92 (96)
T ss_dssp             EEEEESS-------HHHHHHHHHHHTTCBCSSCBCEEEECCCC
T ss_pred             EEEEECC-------HHHHHHHHHHhCCCEECCcEEEEEEcCcc
Confidence            5666665       78999999999999999999999887654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=90.21  E-value=0.12  Score=36.89  Aligned_cols=53  Identities=13%  Similarity=0.097  Sum_probs=37.3

Q ss_pred             HHHHhhhcCCCe-ee-------eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         131 FFSQLLQESPEI-EV-------SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       131 fl~~~~~~~~~~-~l-------~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      -|..++..++.+ .+       -.|+.|..       .++|.+|+..+++..+.++.++|.++.+...
T Consensus        29 ~l~~~F~~~G~i~~v~i~~~~g~afV~f~~-------~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~   89 (97)
T 1x5p_A           29 LLRGAFSPFGNIIDLSMDPPRNCAFVTYEK-------MESADQAVAELNGTQVESVQLKVNIARKQPM   89 (97)
T ss_dssp             HHHHHHTTTSCEEEEEEETTTTEEEEEESS-------HHHHHHHHHHTTTEEETTEEEEEECCSSCCC
T ss_pred             HHHHHHhhCCCEEEEEecCCCCEEEEEECC-------HHHHHHHHHHhCCCeECCeEEEEEECCCCCC
Confidence            456666666642 11       23455544       8999999999999999999999988765443

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=90.16  E-value=0.026  Score=41.97  Aligned_cols=31  Identities=13%  Similarity=0.169  Sum_probs=26.2

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+||.. ++..+.++.++|.++.+...
T Consensus        78 ~~~~a~~Ai~~-~~~~~~g~~l~V~~a~~~~~  108 (116)
T 1x4b_A           78 SMAEVDAAMAA-RPHSIDGRVVEPKRAVAREE  108 (116)
T ss_dssp             SHHHHHHHHTS-CSEEETTEEEEEECCSSCCC
T ss_pred             CHHHHHHHHHh-CCcEECCEEEEEEECCCCcc
Confidence            48999999987 99999999999988776544

>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=90.07  E-value=0.026  Score=43.64  Aligned_cols=32  Identities=13%  Similarity=0.069  Sum_probs=27.4

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .+.++|.+|+..+++..+.++.++|..+.+..
T Consensus       100 ~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~~  131 (143)
T 3egn_A          100 PNEKAAAKALKEANGYVLFGKPMVVQFARSAR  131 (143)
T ss_dssp             SSHHHHHHHHHHHTTBEETTEECEEEECCCSC
T ss_pred             CCHHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence            34899999999999999999999998876543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=89.91  E-value=0.037  Score=42.20  Aligned_cols=30  Identities=10%  Similarity=0.055  Sum_probs=25.7

Q ss_pred             CHHHHHHHHHhcCcc----ccccccceeeeeeccc
Q psy3930         159 DPDDVVKALRKSKLL----EVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~----~~~~~~~~v~r~~~~~  189 (299)
                      +. +|.+|+..+++.    .+.++.++|..+.+..
T Consensus        76 ~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~~  109 (131)
T 2m2b_A           76 TI-EAAQLLQILQALHPPLTIDGKTINVEFAKGSK  109 (131)
T ss_dssp             HH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCSC
T ss_pred             CH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCCC
Confidence            37 899999999999    9999999998876543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=89.89  E-value=0.56  Score=33.22  Aligned_cols=35  Identities=14%  Similarity=0.088  Sum_probs=28.3

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCcccccccc----ceeeeeec
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDG----TKVRRTVV  187 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~----~~v~r~~~  187 (299)
                      .|+.|..       .++|.+|+..+++..+.++.    ++|.++.+
T Consensus        55 afV~f~~-------~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~   93 (99)
T 2div_A           55 CFVEFAD-------LATAEKCLHKINGKPLPGATPAKRFKLNYATY   93 (99)
T ss_dssp             EEEECSC-------HHHHHHHHHTTTTSEESSCSSCEECCEEETTC
T ss_pred             EEEEeCC-------HHHHHHHHHHHcCCccCCCCcceeEEEeecCC
Confidence            4555654       89999999999999999998    88877654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=89.83  E-value=0.014  Score=42.74  Aligned_cols=35  Identities=17%  Similarity=0.307  Sum_probs=28.3

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccc-cceeeeeec
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTED-GTKVRRTVV  187 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~-~~~v~r~~~  187 (299)
                      .|+.|.+       .++|.+|+..+++..+.++ .++|..+..
T Consensus        64 afV~f~~-------~~~A~~Ai~~l~g~~~~g~~~l~V~~a~~   99 (105)
T 2nlw_A           64 IFLEYAS-------PAHAVDAVKNADGYKLDKQHTFRVNLFTD   99 (105)
T ss_dssp             EEEEECS-------SSHHHHHHHHCSSEECSTTCEEEEECSCC
T ss_pred             EEEEECC-------HHHHHHHHHHhCCcccCCCceEEEEEcch
Confidence            4555555       7899999999999999998 889887653

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=89.77  E-value=0.022  Score=40.70  Aligned_cols=38  Identities=13%  Similarity=0.096  Sum_probs=31.1

Q ss_pred             eeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         144 VSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       144 l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      +-.|+.|..       .++|.+|+..+++..+.++.++|..+.+.
T Consensus        54 g~afV~f~~-------~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   91 (96)
T 1fjc_A           54 GIAYIEFKS-------EADAEKNLEEKQGAEIDGRSVSLYYTGEK   91 (96)
T ss_dssp             EEEEEEESS-------HHHHHHHHHHTTEEEETTEEEEEEECSSS
T ss_pred             eEEEEEECC-------HHHHHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            345667766       89999999999999999999999877644

>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=89.53  E-value=0.028  Score=45.00  Aligned_cols=52  Identities=10%  Similarity=0.123  Sum_probs=36.9

Q ss_pred             HHHHHhhhcCCCe-eeee---------eecccccccCCCCHHHHHHHHHhcCcccccc--ccceeeeeecc
Q psy3930         130 RFFSQLLQESPEI-EVSV---------FLKCNKLARLTHDPDDVVKALRKSKLLEVTE--DGTKVRRTVVV  188 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l~~---------f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~--~~~~v~r~~~~  188 (299)
                      .-|..++..++.+ .+.+         |+.|       .+.++|.+|++.+++..+.+  ..++|..+.+.
T Consensus        61 d~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF-------~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~  124 (164)
T 1sjr_A           61 DVLHQIFSKFGTVLKIITFTKNNQFQALLQY-------ADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT  124 (164)
T ss_dssp             HHHHHHHHHHSCEEEEEEEESSSCEEEEEEE-------SCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSS
T ss_pred             HHHHHHHHhcCCEEEEEEEeCCCCCEEEEEE-------CCHHHHHHHHHHhCCCEecCCCcEEEEEEecCC
Confidence            4577777777762 2233         3333       45899999999999999966  78888877654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=89.43  E-value=0.031  Score=41.50  Aligned_cols=29  Identities=10%  Similarity=0.074  Sum_probs=24.7

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      +.++|.+|+..+++ .+.++.++|..+.+.
T Consensus        68 ~~~~a~~Ai~~~~~-~~~g~~l~V~~a~~~   96 (116)
T 2cqd_A           68 DRAAAERACKDPNP-IIDGRKANVNLAYLG   96 (116)
T ss_dssp             SHHHHHHHHTCSSC-EETTEECEEEESTTT
T ss_pred             CHHHHHHHHHhCCC-cCCCEEEEEEEcccC
Confidence            48999999999998 899999999887543

>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=89.18  E-value=0.027  Score=47.59  Aligned_cols=30  Identities=10%  Similarity=-0.065  Sum_probs=25.8

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .+.++|.+||+.+++..+.++.++|..+.+
T Consensus       120 ~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~  149 (229)
T 3q2s_C          120 GSEASSKKLMDLLPKRELHGQNPVVTPVNK  149 (229)
T ss_dssp             SCTTHHHHHHTTSTTSCBTTBCCEEEECCH
T ss_pred             CCHHHHHHHHHHcCCCeECCEEeEEEECCC
Confidence            347899999999999999999999987654

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=89.14  E-value=0.035  Score=40.27  Aligned_cols=38  Identities=11%  Similarity=0.096  Sum_probs=30.7

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      -.|+.|..       .++|.+|+ .+++..+.++.++|..+.+...
T Consensus        58 ~afV~f~~-------~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2dng_A           58 FCYVEFDE-------VDSLKEAL-TYDGALLGDRSLRVDIAEGRKQ   95 (103)
T ss_dssp             EEEEEESS-------HHHHHHHG-GGTTCEETTEECEEEECCCCCC
T ss_pred             EEEEEECC-------HHHHHHHH-hhCCCeECCeEEEEEEecCCCC
Confidence            45666655       89999999 8999999999999988775543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=89.09  E-value=0.03  Score=41.26  Aligned_cols=31  Identities=19%  Similarity=0.184  Sum_probs=24.7

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .+.++|.+|+..++ ..+.++.++|..+.+..
T Consensus        75 ~~~~~A~~Ai~~~~-~~l~g~~l~V~~a~~~~  105 (109)
T 2rs2_A           75 MDQAGVDKVLAQSR-HELDSKTIDPKVAFPRR  105 (109)
T ss_dssp             SSHHHHHHHHHSSC-EEETTEEEEEEECCCCC
T ss_pred             CCHHHHHHHHHHCC-CcCCCEEEEEEEccCCC
Confidence            34899999998765 88999999998876544

>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=89.07  E-value=0.053  Score=40.62  Aligned_cols=39  Identities=13%  Similarity=0.157  Sum_probs=25.8

Q ss_pred             HHHHHhhhcCCCeee-e-------eeecccccccCCCCHHHHHHHHHhcCcccc
Q psy3930         130 RFFSQLLQESPEIEV-S-------VFLKCNKLARLTHDPDDVVKALRKSKLLEV  175 (299)
Q Consensus       130 ~fl~~~~~~~~~~~l-~-------~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~  175 (299)
                      .-|+.++..++.+.- .       .|++|.       +.++|.+|++.+|+.++
T Consensus        42 ~~L~~~F~~fG~v~~v~i~~~rgfaFV~f~-------~~~~A~~Ai~~lnG~~~   88 (114)
T 2cq2_A           42 NQLLPVLEKCGLVDALLMPPNKPYSFARYR-------TTEESKRAYVTLNGKEV   88 (114)
T ss_dssp             HHHHHHHHHHSCEEEEECCTTCSCEEEEES-------SHHHHHHHHHHTTTCEE
T ss_pred             HHHHHHHHhcCCeEEEEEeCCCCEEEEEEC-------CHHHHHHHHHHhCCCEE
Confidence            446666666665221 1       244443       48999999999999887

>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=88.93  E-value=0.09  Score=48.83  Aligned_cols=31  Identities=10%  Similarity=-0.008  Sum_probs=26.9

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .+.++|.+||..+++..|.+..+.|..+.+.
T Consensus       152 ~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~  182 (437)
T 3pgw_S          152 EHERDMHSAYKHADGKKIDGRRVLVDVERGR  182 (437)
T ss_pred             ccHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            4588999999999999999999999887643

>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=88.82  E-value=0.028  Score=38.05  Aligned_cols=24  Identities=21%  Similarity=0.246  Sum_probs=20.0

Q ss_pred             HHHHHHHHHhcCccccccccceeee
Q psy3930         160 PDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       160 ~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      .++|.+|++. ++..+.++.+.|++
T Consensus        51 ~~~a~~Ai~~-~~~~~~g~~l~v~~   74 (75)
T 1iqt_A           51 EEPVKKIMEK-KYHNVGLSKCEIKV   74 (75)
T ss_dssp             SHHHHHHHTT-SSCCBTTBCCCEEE
T ss_pred             HHHHHHHHHh-CCCeECCEEEEEEE
Confidence            7899999975 77889999888765

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=88.75  E-value=0.046  Score=44.20  Aligned_cols=30  Identities=13%  Similarity=0.168  Sum_probs=26.3

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      +.++|.+|++.+++..+.+..++|..+.+.
T Consensus       138 ~~~~A~~Ai~~lng~~l~Gr~l~V~~a~~~  167 (177)
T 2f3j_A          138 RRADALKAMKQYKGVPLDGRPMDIQLVASQ  167 (177)
T ss_dssp             CHHHHHHHHHHSTTCBCSSSBCEEEEESSG
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            489999999999999999999999887644

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=88.46  E-value=0.028  Score=43.21  Aligned_cols=51  Identities=10%  Similarity=0.126  Sum_probs=36.8

Q ss_pred             HHHHHhhhcCCCe-eee---------eeecccccccCCCCHHHHHHHHHhcCcccccc--ccceeeeeec
Q psy3930         130 RFFSQLLQESPEI-EVS---------VFLKCNKLARLTHDPDDVVKALRKSKLLEVTE--DGTKVRRTVV  187 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l~---------~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~--~~~~v~r~~~  187 (299)
                      .-|..++..++.+ .+.         .|+.|       .+.++|.+|++.+++..+.+  ..++|..+++
T Consensus        43 ~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef-------~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~  105 (130)
T 3zzy_A           43 DVLHQIFSKFGTVLKIITFTKNNQFQALLQY-------ADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL  105 (130)
T ss_dssp             HHHHHHHTTSSCEEEEEEEEETTEEEEEEEE-------SCHHHHHHHHHHHTTCEEETTEEEEEEEECSC
T ss_pred             HHHHHHHhCcCCEEEEEEEcCCCCcEEEEEE-------CCHHHHHHHHHHcCCCeecCCCcEEEEEecCC
Confidence            4578888888862 223         23333       45899999999999999988  6677777654

>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=88.38  E-value=0.042  Score=40.57  Aligned_cols=21  Identities=0%  Similarity=-0.118  Sum_probs=17.0

Q ss_pred             CHHHHHHHHHhcCcccccccc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDG  179 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~  179 (299)
                      +.++|.+|+..+++..+.+..
T Consensus        75 ~~~~a~~A~~~l~g~~~~~~~   95 (114)
T 1x5o_A           75 STEKCEAVIGHFNGKFIKTPP   95 (114)
T ss_dssp             CHHHHHHHHHHHBTCCCCCCT
T ss_pred             CHHHHHHHHHHhCCCEEcCCc
Confidence            389999999999998885433

>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=88.33  E-value=0.017  Score=42.89  Aligned_cols=29  Identities=10%  Similarity=-0.083  Sum_probs=24.8

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      +.++|.+|+ .+++..+.++.++|..+.+.
T Consensus        76 ~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~  104 (114)
T 2cq4_A           76 EIQSVPLAI-GLTGQRLLGVPIIVQASQAE  104 (114)
T ss_dssp             CGGGHHHHH-HHTTEEETTEEEEEEEHHHH
T ss_pred             cHHHHHHHH-HcCCCEeCCeEEEEEecCCC
Confidence            478999999 99999999999999876543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=88.25  E-value=1.1  Score=31.62  Aligned_cols=31  Identities=23%  Similarity=0.242  Sum_probs=26.8

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      +.++|.+|+..+++..+.++.++|.++.+..
T Consensus        59 ~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   89 (98)
T 2cpf_A           59 KPEQAQKALKQLQGHTVDGHKLEVRISERAT   89 (98)
T ss_dssp             SHHHHHHHHHHSTTCEETTEECEEECSSCSS
T ss_pred             CHHHHHHHHHHhCCCeeCCeEEEEEEccCCC
Confidence            3899999999999999999999998876544

>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=88.10  E-value=0.038  Score=40.13  Aligned_cols=38  Identities=16%  Similarity=0.125  Sum_probs=30.4

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      -.|+.|..       .++|.+|+ .+++..+.++.++|..+.+...
T Consensus        59 ~afV~f~~-------~~~a~~A~-~l~g~~~~g~~l~V~~a~~~~~   96 (104)
T 1wi8_A           59 FGYAEFED-------LDSLLSAL-SLNEESLGNKRIRVDVADQAQD   96 (104)
T ss_dssp             CEEEEESS-------HHHHHHHH-GGGTCEETTEECEEEECCCCCC
T ss_pred             EEEEEECC-------HHHHHHHH-hcCCCEeCCcEEEEEEccCCCC
Confidence            34556655       89999999 9999999999999998776544

>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=88.06  E-value=0.042  Score=40.20  Aligned_cols=32  Identities=16%  Similarity=-0.000  Sum_probs=26.5

Q ss_pred             CHHHHHHHHHhcC--ccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSK--LLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~--~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|+..++  +..+.++.++|..+.+...
T Consensus        61 ~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~~   94 (109)
T 2dis_A           61 SHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID   94 (109)
T ss_dssp             SHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCS
T ss_pred             CHHHHHHHHHHhhCCCceecCCeEEEEEcCCCCC
Confidence            3899999999885  5899999999998876543

>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=88.01  E-value=0.22  Score=36.60  Aligned_cols=38  Identities=3%  Similarity=-0.116  Sum_probs=31.0

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      -.|+.|..       .++|.+|+..+++..+.++.++|..+.+..
T Consensus        66 ~afV~f~~-------~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           66 VASVSFRD-------PEEADYCIQTLDGRWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             EEEEECSC-------HHHHHHHHHHSTTCEETTEECEEEECCSCC
T ss_pred             EEEEEECC-------HHHHHHHHHHcCCCEECCcEEEEEEeCCCC
Confidence            34666655       899999999999999999999998876543

>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=87.91  E-value=0.16  Score=35.98  Aligned_cols=36  Identities=11%  Similarity=0.161  Sum_probs=29.6

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .|+.|.+       .++|.+|+..+++..+.++.++|..+.+.
T Consensus        54 afV~f~~-------~~~A~~A~~~l~g~~~~g~~l~v~~a~~~   89 (97)
T 1nu4_A           54 AFVIFKE-------VSSATNALRSMQGFPFYDKPMRIQYAKTD   89 (97)
T ss_dssp             EEEEESS-------HHHHHHHHHHHTTCEETTEECEEEECSSC
T ss_pred             EEEEeCC-------HHHHHHHHHHhCCCEECCcEEEEEEccCC
Confidence            4566655       89999999999999999999999887654

>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=87.69  E-value=0.032  Score=38.97  Aligned_cols=25  Identities=20%  Similarity=0.202  Sum_probs=19.6

Q ss_pred             CHHHHHHHHHhcCccccccccceeee
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      +.++|.+|++. ++..+.++.+.|++
T Consensus        62 ~~~~a~~A~~~-~~~~~~g~~i~v~~   86 (87)
T 3s7r_A           62 DAASVEKVLDQ-KEHRLDGRVIDPKK   86 (87)
T ss_dssp             STHHHHHHHHS-SCEEETTEEEEEEE
T ss_pred             CHHHHHHHHHh-CCCEECCEEEEEEe
Confidence            37899999955 66678888888765

>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=87.66  E-value=0.04  Score=38.74  Aligned_cols=28  Identities=7%  Similarity=0.032  Sum_probs=24.8

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeee
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      +.++|.+|++.+++..+.++.++|..+.
T Consensus        49 ~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A           49 NGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            3899999999999999999999998764

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.65  E-value=0.6  Score=33.25  Aligned_cols=34  Identities=6%  Similarity=0.036  Sum_probs=28.8

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .|++|..       .++|.+|++ +++..+.++.++|+.+.+
T Consensus        52 ~fVtF~d-------~~sAlaAi~-mnG~~v~Gr~LkV~lkt~   85 (91)
T 2dnr_A           52 MWVTFLE-------GSSALNVLS-LNGKELLNRTITIALKSP   85 (91)
T ss_dssp             EEEEESS-------HHHHHHGGG-GTTCEETTEEEEEEECCC
T ss_pred             EEEEECC-------hHHHHHHHh-cCCeEeCCeEEEEEeCCC
Confidence            5777766       789999996 999999999999987654

>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=87.42  E-value=0.025  Score=39.45  Aligned_cols=31  Identities=23%  Similarity=0.348  Sum_probs=25.8

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeee
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      .|+.|.+       .++|.+|+ .+++..+.++.++|+|
T Consensus        56 afV~f~~-------~~~a~~A~-~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           56 AFLEFRS-------VDETTQAM-AFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             EEEEESS-------HHHHHHHG-GGTTCEETTEECEEEC
T ss_pred             EEEEcCC-------HHHHHHHH-hcCCCEECCeEEEEeC
Confidence            3556655       89999999 9999999999998875

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=86.52  E-value=0.18  Score=34.51  Aligned_cols=31  Identities=19%  Similarity=0.401  Sum_probs=25.0

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccc-ccee
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTED-GTKV  182 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~-~~~v  182 (299)
                      -.|+.|..       .++|.+|++.+++..+.++ .++|
T Consensus        49 ~afV~f~~-------~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A           49 YIFLEYAS-------PAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             EEEEEESS-------HHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             EEEEEECC-------HHHHHHHHHHhcCcccCCceeEEe
Confidence            34566655       8999999999999999998 7765

>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=86.10  E-value=0.21  Score=35.83  Aligned_cols=33  Identities=9%  Similarity=0.186  Sum_probs=28.7

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeee
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      .|++|..       .++|.+||+ +++.++.++.++|+.+.
T Consensus        61 ~fVtF~d-------~~sAl~AI~-ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           61 MLVTFAD-------SHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             EEEECSC-------SHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             EEEEEcC-------hHHHHHHHh-cCCeeeCCeEEEEeccC
Confidence            6888876       789999997 99999999999998654

>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=85.76  E-value=0.08  Score=38.70  Aligned_cols=35  Identities=17%  Similarity=0.177  Sum_probs=28.0

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      -.|+.|.+       .++|.+||. +++..+.++.++|.++.+
T Consensus        57 ~afV~F~~-------~~~a~~Al~-~~~~~~~gr~i~V~~a~~   91 (107)
T 2lmi_A           57 DALIEMES-------EQDVQKALE-KHRMYMGQRYVEVYEINN   91 (107)
T ss_dssp             EEEEEBSS-------HHHHHHHHT-TTTCCSSSSCCCCEECCH
T ss_pred             EEEEEECC-------HHHHHHHHH-hCcceeCCeEEEEEECCH
Confidence            45666655       899999998 899999999998877654

>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=85.44  E-value=0.064  Score=41.43  Aligned_cols=35  Identities=20%  Similarity=0.190  Sum_probs=27.9

Q ss_pred             eeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeee
Q psy3930         144 VSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       144 l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      +-.|+.|.+       .++|.+||+ +++..+.++.++|.++.
T Consensus        89 G~aFV~F~~-------~e~a~~Al~-~~g~~l~gr~i~V~~a~  123 (136)
T 2hgl_A           89 GEAFVELGS-------EDDVKMALK-KDRESMGHRYIEVFKSH  123 (136)
T ss_dssp             EEEEEECSS-------HHHHHHHHT-TTEEESSSSEEEEEECC
T ss_pred             eEEEEEECC-------HHHHHHHHh-cCCCEECCEEEEEEECC
Confidence            345666655       899999998 99999999998887654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=85.42  E-value=2.1  Score=29.87  Aligned_cols=28  Identities=11%  Similarity=-0.031  Sum_probs=24.4

Q ss_pred             HHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         160 PDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       160 ~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .++|.+|+. +++..+.++.+.|..+.+.
T Consensus        55 ~~~a~~ai~-l~g~~~~g~~l~V~~a~~~   82 (94)
T 2e5g_A           55 VGAREAVLS-QSQHSLGGHRLRVRPREQK   82 (94)
T ss_dssp             HHHHHHHHT-CSCCEETTEECCCBCSCCS
T ss_pred             HHHHHHHHh-cCCeEECCEEEEEEECCcC
Confidence            889999998 9999999999999876543

>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=85.32  E-value=0.33  Score=36.09  Aligned_cols=36  Identities=11%  Similarity=0.052  Sum_probs=30.4

Q ss_pred             eeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeee
Q psy3930         144 VSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       144 l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      +-.|+.|..       .++|.+|++.+|+..+.|+.+.+....
T Consensus        56 G~~fV~f~~-------~e~A~~Ai~~lnG~~f~GR~i~v~~~~   91 (114)
T 3s6e_A           56 GNVYVKCPS-------IAAAIAAVNALHGRWFAGKMITAAYVP   91 (114)
T ss_dssp             CCEEEECSS-------HHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEEEECC-------HHHHHHHHHHhCCCEECCEEEEEEEEc
Confidence            456777766       799999999999999999999887654

>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=84.90  E-value=0.094  Score=37.83  Aligned_cols=36  Identities=11%  Similarity=0.084  Sum_probs=26.8

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .|+.|.+       .++|.+|+..  +..+.++.+.|..+.+...
T Consensus        60 afV~f~~-------~~~a~~A~~~--~~~~~g~~l~v~~a~~~~~   95 (103)
T 2cqg_A           60 GFVRFTE-------YETQVKVMSQ--RHMIDGRWCDCKLPNSKQS   95 (103)
T ss_dssp             EEEEESS-------HHHHHHHHHS--CEEETTEEEEEECCCTTCC
T ss_pred             EEEEECC-------HHHHHHHHHc--CCeeCCeEEEEEecCCCCc
Confidence            4555554       8899999974  5688999999988776543

>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=84.37  E-value=0.31  Score=35.46  Aligned_cols=35  Identities=14%  Similarity=0.117  Sum_probs=27.8

Q ss_pred             eeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeee
Q psy3930         144 VSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       144 l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      +-.|+.|.+       .++|.+|+..+++..+.++.+++..+
T Consensus        69 G~~fV~f~~-------~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           69 GNVYVKFRR-------EEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             EEEEEEESC-------HHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             EEEEEEECC-------HHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            344556655       89999999999999999998887653

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=84.30  E-value=3  Score=39.31  Aligned_cols=52  Identities=25%  Similarity=0.323  Sum_probs=42.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHh
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL  257 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~  257 (299)
                      ..++|+ +|..+...+|.++|+.||. ..|+.+.+.       .|||.|.+.+.|..++..
T Consensus       441 ~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widdt-------~a~V~~~~~~~a~~~l~~  492 (507)
T 3d45_A          441 HVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNT  492 (507)
T ss_dssp             GEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSSS-------EEEEECSCHHHHHHHHHH
T ss_pred             cEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcCC-------eEEEEECCHHHHHHHHHH
Confidence            455555 9999999999999999995 455555442       599999999999999998

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=83.54  E-value=0.078  Score=39.62  Aligned_cols=37  Identities=19%  Similarity=0.162  Sum_probs=29.3

Q ss_pred             eeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeee
Q psy3930         142 IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       142 ~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      -.+-.|+.|.+       .++|.+||. +++..+.++.++|..+.
T Consensus        60 ~~G~afV~F~~-------~~~a~~Al~-~~g~~~~gr~i~V~~a~   96 (118)
T 2db1_A           60 QSGEAFVELES-------EDDVKLALK-KDRESMGHRYIEVFKSH   96 (118)
T ss_dssp             EEEEEEEEBSS-------HHHHHHHGG-GTTEEETTEEEEEEEEC
T ss_pred             CCeEEEEEECC-------HHHHHHHHh-cCCCeECCeEEEEEECC
Confidence            34456777766       899999998 89999999998887664

>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=83.45  E-value=0.15  Score=37.05  Aligned_cols=28  Identities=14%  Similarity=0.107  Sum_probs=23.8

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      +.++|.+||.. ++..+.++.+.|.++.+
T Consensus        66 ~~~~a~~A~~~-~~~~~~gr~i~v~~~~~   93 (104)
T 1wg5_A           66 SQEIAEKALKK-HKERIGHRYIEIFKSSR   93 (104)
T ss_dssp             SHHHHHHHHTT-TTCCSSSSCCEEEEECT
T ss_pred             CHHHHHHHHHh-CcchhCCcEEEEEECCH
Confidence            38999999987 89999999999977654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=83.07  E-value=0.91  Score=32.28  Aligned_cols=42  Identities=12%  Similarity=0.027  Sum_probs=34.4

Q ss_pred             eeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         142 IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       142 ~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      -..-.|+.|.+       .++|.+|+..+++..+.++.++|..+.+..+
T Consensus        53 ~~g~afV~f~~-------~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2fc8_A           53 SKGFGFVDFNS-------EEDAKAAKEAMEDGEIDGNKVTLDWAKPKGE   94 (102)
T ss_dssp             EEEEEEEECSS-------HHHHHHHHHHHTTCEETTEECEEEECCCCCS
T ss_pred             cCcEEEEEECC-------HHHHHHHHHHhCCCeECCeEEEEEEecCCCC
Confidence            34456788876       7999999999999999999999998876544

>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=81.07  E-value=1.7  Score=31.78  Aligned_cols=36  Identities=14%  Similarity=0.137  Sum_probs=28.8

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      -.|+.|.+       .++|.+||.. ++..+.++.+.|.++.+.
T Consensus        59 ~afV~F~~-------~~~a~~Al~~-~~~~~~gr~i~v~~a~~~   94 (114)
T 2cpy_A           59 QALVQFKN-------EDDARKSERL-HRKKLNGREAFVHVVTLE   94 (114)
T ss_dssp             CEEEECSS-------HHHHHHHGGG-CSEEETTEEEEEEEECHH
T ss_pred             EEEEEECC-------HHHHHHHHHh-CCCccCCeEEEEEECCHH
Confidence            45666665       8999999977 999999999999877643

---

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	299
d2cqka1	88	a.4.5.46 (A:43-130) La-related protein 4 LARP4 {Hu	6e-23
d2cqka1	88	a.4.5.46 (A:43-130) La-related protein 4 LARP4 {Hu	2e-19
d1s29a_	92	a.4.5.46 (A:) Lupus La autoantigen N-terminal doma	1e-21
d1s29a_	92	a.4.5.46 (A:) Lupus La autoantigen N-terminal doma	8e-19
d1zh5a1	99	a.4.5.46 (A:5-103) Lupus La autoantigen N-terminal	2e-21
d1zh5a1	99	a.4.5.46 (A:5-103) Lupus La autoantigen N-terminal	1e-15
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	8e-13
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-12
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-11
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	9e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-09
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-09
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-08
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-08
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-07
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-08
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-08
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	4e-08
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-08
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	6e-08
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	7e-08
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-07
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-07
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-07
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-07
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	4e-07
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	5e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	6e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	6e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	7e-07
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	1e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-06
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-06
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-06
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-06
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-06
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	4e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-06
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-06
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	7e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	7e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-05
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	3e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	3e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	4e-05
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	5e-05
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-05
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	7e-05
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-05
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	7e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-05
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	9e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-04
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	3e-04
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-04
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	5e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	0.001
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	0.002
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	0.003
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	0.003
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.004

>d2cqka1 a.4.5.46 (A:43-130) La-related protein 4 LARP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: La-related protein 4 LARP4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 88.2 bits (219), Expect = 6e-23
 Identities = 23/78 (29%), Positives = 39/78 (50%)

Query: 107 KQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKA 166
           + L + +   +EF  S  NL KD +    +     I +       ++ +LT DPD +++ 
Sbjct: 5   EDLKECLKKQLEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEV 64

Query: 167 LRKSKLLEVTEDGTKVRR 184
           LR S +++V E G KVR 
Sbjct: 65  LRSSPMVQVDEKGEKVRP 82

>d2cqka1 a.4.5.46 (A:43-130) La-related protein 4 LARP4 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: La-related protein 4 LARP4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 78.9 bits (195), Expect = 2e-19
 Identities = 21/67 (31%), Positives = 35/67 (52%)

Query: 1  MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVT 60
          +EF  S  NL KD +    +     I +       ++ +LT DPD +++ LR S +++V 
Sbjct: 15 LEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSPMVQVD 74

Query: 61 EDGTKVK 67
          E G KV+
Sbjct: 75 EKGEKVR 81

>d1s29a_ a.4.5.46 (A:) Lupus La autoantigen N-terminal domain {Trypanosoma brucei [TaxId: 5691]} Length = 92

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: Lupus La autoantigen N-terminal domain
species: Trypanosoma brucei [TaxId: 5691]

 Score = 84.8 bits (210), Expect = 1e-21
 Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 2/79 (2%)

Query: 108 QLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPE--IEVSVFLKCNKLARLTHDPDDVVK 165
           +  Q++   +EFY SD N+++D F    + E+ E  + +   L   ++  +T D  +VV+
Sbjct: 9   ENKQKLQKQVEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVE 68

Query: 166 ALRKSKLLEVTEDGTKVRR 184
           A+R S+ L ++EDG  VRR
Sbjct: 69  AIRPSEKLVLSEDGLMVRR 87

>d1s29a_ a.4.5.46 (A:) Lupus La autoantigen N-terminal domain {Trypanosoma brucei [TaxId: 5691]} Length = 92

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: Lupus La autoantigen N-terminal domain
species: Trypanosoma brucei [TaxId: 5691]

 Score = 77.5 bits (191), Expect = 8e-19
 Identities = 23/69 (33%), Positives = 41/69 (59%), Gaps = 2/69 (2%)

Query: 1  MEFYLSDSNLRKDRFFSQLLQESPE--IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLE 58
          +EFY SD N+++D F    + E+ E  + +   L   ++  +T D  +VV+A+R S+ L 
Sbjct: 18 VEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVEAIRPSEKLV 77

Query: 59 VTEDGTKVK 67
          ++EDG  V+
Sbjct: 78 LSEDGLMVR 86

>d1zh5a1 a.4.5.46 (A:5-103) Lupus La autoantigen N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: Lupus La autoantigen N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 84.5 bits (209), Expect = 2e-21
 Identities = 33/99 (33%), Positives = 59/99 (59%), Gaps = 4/99 (4%)

Query: 101 GGRHRKKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQES-PEIEVSVFLKCNKLARLTHD 159
           G   +   L  +I + +E+Y  D NL +D+F  + ++     + + + +K N+L RLT D
Sbjct: 1   GDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTD 60

Query: 160 PDDVVKALRKSK--LLEVTEDGTKVRRTVVVQDKPDVDE 196
            + +V+AL KSK  L+E++ED TK+RR+   +  P+V +
Sbjct: 61  FNVIVEALSKSKAELMEISEDKTKIRRS-PSKPLPEVTD 98

>d1zh5a1 a.4.5.46 (A:5-103) Lupus La autoantigen N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: Lupus La autoantigen N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.0 bits (169), Expect = 1e-15
 Identities = 26/70 (37%), Positives = 46/70 (65%), Gaps = 3/70 (4%)

Query: 1  MEFYLSDSNLRKDRFFSQLLQES-PEIEVSVFLKCNKLARLTHDPDDVVKALRKSK--LL 57
          +E+Y  D NL +D+F  + ++     + + + +K N+L RLT D + +V+AL KSK  L+
Sbjct: 17 IEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELM 76

Query: 58 EVTEDGTKVK 67
          E++ED TK++
Sbjct: 77 EISEDKTKIR 86

>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 = 60.7 bits (147), Expect = 8e-13
 Identities = 20/64 (31%), Positives = 38/64 (59%)

Query: 193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
            + +  +YV  LP     D ++++F KYG +   ++ + K TG+ +G AFV ++ +EEA 
Sbjct: 3   SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 62

Query: 253 KALE 256
           +A+ 
Sbjct: 63  EAIS 66

>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 = 58.8 bits (142), Expect = 4e-12
 Identities = 13/61 (21%), Positives = 27/61 (44%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           C +++  L  +   + +   F ++G+V    + +   T + +GF FV F  +    K L 
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

Query: 257 L 257
            
Sbjct: 61  Q 61

>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 = 57.6 bits (139), Expect = 2e-11
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPK-FKSTGKLKGFAFVEFSTKEEAAK 253
               I V  +P +A    I  +FS +G++  V LPK    TG  +GF FV+F TK++A K
Sbjct: 7   TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 66

Query: 254 ALELGLN 260
           A     +
Sbjct: 67  AFNALCH 73

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.9 bits (132), Expect = 8e-11
 Identities = 15/59 (25%), Positives = 29/59 (49%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           ++YV  L P+     +   FS  G +  + + +   T +  G+A+V F    +A +AL+
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 60

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.3 bits (125), Expect = 9e-10
 Identities = 19/59 (32%), Positives = 29/59 (49%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           I+V  L P+   + I   F  +G+V  + LP    T K +GF F+ F  +E   K +E 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.5 bits (123), Expect = 2e-09
 Identities = 18/60 (30%), Positives = 29/60 (48%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           CT+YV  L      + I  +FSK G +  + +   K      GF FVE+ ++ +A  A+ 
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

>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 = 51.6 bits (123), Expect = 3e-09
 Identities = 13/69 (18%), Positives = 33/69 (47%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           + +       +++  L  E   + + + + ++GK+T   + +  ++ + +GF FV FS+ 
Sbjct: 13  KKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM 72

Query: 249 EEAAKALEL 257
            E   A+  
Sbjct: 73  AEVDAAMAA 81

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.2 bits (122), Expect = 3e-09
 Identities = 17/64 (26%), Positives = 33/64 (51%)

Query: 193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
            + +  +YV  LP       +E +FS+YG++    +   + TG  +G  F+ F  + EA 
Sbjct: 3   SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 62

Query: 253 KALE 256
           +A++
Sbjct: 63  EAIK 66

>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 = 51.4 bits (123), Expect = 3e-09
 Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 9/69 (13%)

Query: 189 QDKPDVDECTIYVEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST 247
           +  P      +++  L     +   +E++FSKYGK+   S+ K        GFAFV++  
Sbjct: 8   KTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVN 59

Query: 248 KEEAAKALE 256
           +  A  A+ 
Sbjct: 60  ERNARAAVA 68

>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 = 50.8 bits (121), Expect = 5e-09
 Identities = 21/78 (26%), Positives = 35/78 (44%)

Query: 180 TKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKG 239
           + VR  V      + D  T++  +L        +E  FS  GKV  V +   +++ + KG
Sbjct: 2   SPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG 61

Query: 240 FAFVEFSTKEEAAKALEL 257
            A+VEF   +    A+ L
Sbjct: 62  IAYVEFCEIQSVPLAIGL 79

>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 = 49.6 bits (118), Expect = 1e-08
 Identities = 15/60 (25%), Positives = 31/60 (51%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
            +++  L  E   + + S F ++G +T   + +  +T + +GF FV ++T EE   A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

>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 = 49.6 bits (118), Expect = 1e-08
 Identities = 14/65 (21%), Positives = 29/65 (44%), Gaps = 3/65 (4%)

Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
           P      +Y+  LP +   + +  +F KYG +      +  +T + +G A+V +    +A
Sbjct: 3   PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDA 59

Query: 252 AKALE 256
             A +
Sbjct: 60  KNACD 64

>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 = 49.0 bits (116), Expect = 2e-08
 Identities = 12/65 (18%), Positives = 27/65 (41%), Gaps = 5/65 (7%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKS-----TGKLKGFAFVEFSTKEEAA 252
            +YV  +P     + +   F+   ++  ++             + K FAF+EF + +E  
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 253 KALEL 257
           +A+  
Sbjct: 63  QAMAF 67

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 48.5 bits (115), Expect = 2e-08
 Identities = 13/60 (21%), Positives = 31/60 (51%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             + V  LP +     + ++F   G +    + +   TG   G+AFV+F+++ ++ +A++
Sbjct: 3   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (119), Expect = 3e-08
 Identities = 15/70 (21%), Positives = 32/70 (45%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
            +++  L  E   + + S F ++G +T   + +  +T + +GF FV ++T EE   A+  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 258 GLNPCPPDYQ 267
             +       
Sbjct: 68  RPHKVDGRVV 77

>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 = 47.7 bits (112), Expect = 3e-07
 Identities = 22/100 (22%), Positives = 40/100 (40%)

Query: 158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECTIYVEKLPPEAEHDYIESVF 217
            + D  + A        V E    V R    +    +    I+V  +  + E  ++   F
Sbjct: 59  EEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 118

Query: 218 SKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
            +YGK+  + +   + +GK +GFAFV F   +   K +  
Sbjct: 119 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158

>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 = 48.1 bits (114), Expect = 3e-08
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 3/61 (4%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVT---YVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           ++++ L      + ++ VFSK G +                  GF FVE+   E+A KAL
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 256 E 256
           +
Sbjct: 61  K 61

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 4e-08
 Identities = 16/59 (27%), Positives = 29/59 (49%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           +++  L  +     ++  FSK+G+V   +L     TG+ +GF FV F   E   K ++ 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

>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 = 48.1 bits (114), Expect = 4e-08
 Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 2/62 (3%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTY--VSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           C +++  +P   + + I    +K  +     +         K +GFAFVE+ +   AA A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 255 LE 256
             
Sbjct: 62  RR 63

>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 = 47.7 bits (113), Expect = 4e-08
 Identities = 14/58 (24%), Positives = 29/58 (50%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +++  LP     D ++ + + +G +   +L K  +TG  KG+AF E+       +A+ 
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

>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 = 47.7 bits (113), Expect = 5e-08
 Identities = 19/62 (30%), Positives = 35/62 (56%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
            + T+YV  L  +     +  +F + G V    +PK + TG+ +G+ FVEF ++E+A  A
Sbjct: 8   QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 255 LE 256
           ++
Sbjct: 68  IK 69

>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 = 47.3 bits (112), Expect = 6e-08
 Identities = 22/67 (32%), Positives = 39/67 (58%)

Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
           ++   D  TI V  L  +     ++ +F  +G ++ + L K K+TG+ KGFAF+ F  +E
Sbjct: 2   NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 61

Query: 250 EAAKALE 256
           +AA+A+ 
Sbjct: 62  DAARAIA 68

>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 = 47.7 bits (113), Expect = 6e-08
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 6/69 (8%)

Query: 188 VQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST 247
           V ++     CT+Y   +        +   FS +G++  + +   K       ++FV FST
Sbjct: 10  VVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFST 63

Query: 248 KEEAAKALE 256
            E AA A+ 
Sbjct: 64  HESAAHAIV 72

>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 = 47.3 bits (112), Expect = 7e-08
 Identities = 19/59 (32%), Positives = 28/59 (47%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            + V  LP +     ++  FS +G+V  V + K   TG  KGF FV F+  E   K + 
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

>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 = 46.6 bits (110), Expect = 1e-07
 Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
           +  PD   C + V  L        +  VFSKYG +  VS+   + + + +GFAFV F   
Sbjct: 3   RANPD-PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 61

Query: 249 EEAAKALE 256
           ++A +A E
Sbjct: 62  DDAKEAKE 69

>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 = 46.2 bits (109), Expect = 2e-07
 Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 187 VVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFS 246
           V++     ++C IYV  LPP+     IE VF KYG +  +     K+      FAFVEF 
Sbjct: 5   VIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDI---DLKNRRGGPPFAFVEFE 61

Query: 247 TKEEAAKALE 256
              +A  A+ 
Sbjct: 62  DPRDAEDAVY 71

>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 = 45.9 bits (108), Expect = 2e-07
 Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVS-LPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           I++  L PE +   +   FS +G +     + +   TG  KG+AF+ F++ + +  A+E
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 59

>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 = 44.9 bits (106), Expect = 3e-07
 Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           + V  L        I+ +F+++G +   ++   + +G+  G A V F  K +A KA++
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMK 59

>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 = 44.9 bits (106), Expect = 4e-07
 Identities = 13/63 (20%), Positives = 25/63 (39%), Gaps = 7/63 (11%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           D+  + V   P  +   YI   F++YG +    +           +  + + +K +A KA
Sbjct: 3   DDTWVTVFGFPQASA-SYILLQFAQYGNILKHVMSNTG------NWMHIRYQSKLQARKA 55

Query: 255 LEL 257
           L  
Sbjct: 56  LSK 58

>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 = 44.8 bits (105), Expect = 5e-07
 Identities = 13/61 (21%), Positives = 25/61 (40%)

Query: 196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
           ECT+++   PP      I  +      V              + FA+++ ++KE+A   +
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 256 E 256
           E
Sbjct: 61  E 61

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 6e-07
 Identities = 16/59 (27%), Positives = 28/59 (47%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            + V  LP     +   S+F   G++    L + K TG+  G+ FV +   ++A KA+ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

>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 = 45.1 bits (106), Expect = 6e-07
 Identities = 15/67 (22%), Positives = 28/67 (41%)

Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
            + D     I+V  LP       +   F  +G +    +   + TGK +G+ FV  + + 
Sbjct: 4   SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRA 63

Query: 250 EAAKALE 256
            A +A +
Sbjct: 64  AAERACK 70

>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 = 43.9 bits (103), Expect = 7e-07
 Identities = 17/59 (28%), Positives = 30/59 (50%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
           I+V  L      + ++  F ++GKV    L   K+T + +GF FV F +++   K  E+
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

>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 = 9/66 (13%), Positives = 22/66 (33%)

Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
            +  +   ++  +P       +                   + G+  G A V+F  +++A
Sbjct: 4   VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 63

Query: 252 AKALEL 257
            K+  L
Sbjct: 64  RKSERL 69

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 1e-06
 Identities = 15/66 (22%), Positives = 25/66 (37%)

Query: 192 PDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
           P     T ++  LP +   + I+  F            +  +  +LKGF + EF   +  
Sbjct: 11  PKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSL 70

Query: 252 AKALEL 257
             AL L
Sbjct: 71  LSALSL 76

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.4 bits (102), Expect = 1e-06
 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 6/67 (8%)

Query: 190 DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKE 249
           +K       ++V  LPP+   + +  +F KYGK   V + K K       F F+   T+ 
Sbjct: 2   EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRT 55

Query: 250 EAAKALE 256
            A  A  
Sbjct: 56  LAEIAKV 62

>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 = 43.2 bits (101), Expect = 2e-06
 Identities = 21/66 (31%), Positives = 36/66 (54%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
           +  V+   ++V  +  EA+ D I+  F  YG++  + L   + TG  KG+A VE+ T ++
Sbjct: 2   QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 61

Query: 251 AAKALE 256
           A  A E
Sbjct: 62  ALAAKE 67

>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 = 42.7 bits (100), Expect = 2e-06
 Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 5/60 (8%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             ++V +   +   D +   FS+YG V  V           + FAFV F+  + A     
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDV-----FIPKPFRAFAFVTFADDQIAQSLCG 60

>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 = 42.7 bits (100), Expect = 3e-06
 Identities = 21/59 (35%), Positives = 33/59 (55%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            +YV  L  E +   + + F  +G +T + +P    T K +GFAFVEF   E+AA A++
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.2 bits (101), Expect = 3e-06
 Identities = 21/62 (33%), Positives = 30/62 (48%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
               ++V  L   +  + +E +FS YG ++ +  P    T K KGFAFV F   E A KA
Sbjct: 7   GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

Query: 255 LE 256
             
Sbjct: 67  YA 68

>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 = 42.7 bits (100), Expect = 3e-06
 Identities = 16/60 (26%), Positives = 24/60 (40%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             I V+ +P     D I   F  Y  +      K+   G   G A V F +++EA  A+ 
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 42.3 bits (99), Expect = 4e-06
 Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 5/69 (7%)

Query: 188 VQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST 247
              K      T+  + L      D ++ VF    ++  V        GK KG A++EF +
Sbjct: 8   CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKS 62

Query: 248 KEEAAKALE 256
           + +A K LE
Sbjct: 63  EADAEKNLE 71

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (97), Expect = 6e-06
 Identities = 21/62 (33%), Positives = 35/62 (56%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           DE  ++V  L  +     +E VFSKYG+++ V + K + T + +GF FV F   ++A  A
Sbjct: 4   DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 255 LE 256
           + 
Sbjct: 64  MM 65

>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 = 42.1 bits (98), Expect = 6e-06
 Identities = 21/72 (29%), Positives = 26/72 (36%), Gaps = 8/72 (11%)

Query: 193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKF--------KSTGKLKGFAFVE 244
           D D   IYV+ L      D +   F + G V                K TGK KG A V 
Sbjct: 5   DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 64

Query: 245 FSTKEEAAKALE 256
           +     A  A+E
Sbjct: 65  YEDPPTAKAAVE 76

>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 = 41.9 bits (98), Expect = 7e-06
 Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 4/58 (6%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           I VE L      D +  +FSK+G V  +      +    +  A ++++    A  A  
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN----QFQALLQYADPVSAQHAKL 63

>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 = 41.7 bits (97), Expect = 7e-06
 Identities = 12/65 (18%), Positives = 17/65 (26%), Gaps = 11/65 (16%)

Query: 197 CTIYVEKLPPEAEHD-----YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 251
             +       +   +       ES+F  Y K T     K            + FS    A
Sbjct: 6   SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSA 59

Query: 252 AKALE 256
           A A  
Sbjct: 60  ADARL 64

>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 = 40.5 bits (94), Expect = 1e-05
 Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 2/66 (3%)

Query: 194 VDECTIYVEKLPPEA-EHDYIESVFSKYGKVTYVSLPKF-KSTGKLKGFAFVEFSTKEEA 251
           ++   I +  L  E  + + +   F  +G +  +++P   K        AF+ F  K+ A
Sbjct: 2   LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSA 61

Query: 252 AKALEL 257
            +AL++
Sbjct: 62  ERALQM 67

>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 = 40.4 bits (94), Expect = 2e-05
 Identities = 13/58 (22%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           + +++   E   +    +  KYG+V  +++        L G  +V+F  +E+A KA+ 
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCD-NLGDHLVGNVYVKFRREEDAEKAVI 86

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.6 bits (94), Expect = 3e-05
 Identities = 19/67 (28%), Positives = 28/67 (41%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
            P      +Y++ LP EAE+ ++   F K   V       +   GK  G  FVEF  + +
Sbjct: 13  SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEAD 72

Query: 251 AAKALEL 257
              AL  
Sbjct: 73  YKAALCR 79

>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 = 39.6 bits (92), Expect = 3e-05
 Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 2/64 (3%)

Query: 193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAA 252
           D    T+YV  L  +     I  +FS+ G      +           + FVEF    +AA
Sbjct: 5   DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAA 62

Query: 253 KALE 256
            AL 
Sbjct: 63  AALA 66

>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 = 39.4 bits (91), Expect = 4e-05
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 1/66 (1%)

Query: 192 PDVDE-CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
            DV E  T+++  L  ++E + +  V  ++G + YV +     T   KG AF +F T+E 
Sbjct: 3   SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 251 AAKALE 256
           A K L 
Sbjct: 63  AQKCLA 68

>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 = 38.9 bits (90), Expect = 5e-05
 Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 2/59 (3%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            I+++ L    ++  +   FS +G +    +   ++    KG+ FV F T+E A +A+E
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAERAIE 66

>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 = 39.3 bits (91), Expect = 6e-05
 Identities = 14/62 (22%), Positives = 25/62 (40%)

Query: 195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKA 254
           +   +++  LP E     +  +F  +G V    +   K T   K F FV +     A  A
Sbjct: 17  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 255 LE 256
           ++
Sbjct: 77  IQ 78

>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 = 38.9 bits (90), Expect = 7e-05
 Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 197 CTIYVEKLPPEA-EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKAL 255
            TIY+  L  +  + +  +S+ + + +   +       + K++G AFV F     A  AL
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 256 E 256
            
Sbjct: 64  R 64

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (90), Expect = 7e-05
 Identities = 17/67 (25%), Positives = 28/67 (41%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
               ++  + +  LP     + I   FS    V           G+  G AFV+F+++E 
Sbjct: 10  PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEI 69

Query: 251 AAKALEL 257
           A KAL+ 
Sbjct: 70  AEKALKK 76

>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 = 38.8 bits (89), Expect = 7e-05
 Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 1/71 (1%)

Query: 187 VVQDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFS 246
           +V+         +++  L P      ++   S+      ++      TG  + F +V+F 
Sbjct: 4   MVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFE 62

Query: 247 TKEEAAKALEL 257
           + E+  KALEL
Sbjct: 63  SAEDLEKALEL 73

>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 = 38.6 bits (89), Expect = 9e-05
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             +++  LP  A  + I + FS    +      +    G++ G A VEF+T E+A  A+ 
Sbjct: 16  HCVHMRGLPYRATENDIYNFFSPLNPMRVH--IEIGPDGRVTGEADVEFATHEDAVAAMA 73

Query: 257 L 257
            
Sbjct: 74  K 74

>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 = 38.5 bits (89), Expect = 9e-05
 Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 6/59 (10%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            +YV  L      + IE  F+             +   K++ +AFV FS +E+A +A++
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPG------AVERVKKIRDYAFVHFSNREDAVEAMK 62

>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 = 38.0 bits (88), Expect = 1e-04
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 12/78 (15%)

Query: 180 TKVRRTVVVQ---DKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGK 236
            +  R V+++      D ++  + + ++      + +    SK+G++  + L        
Sbjct: 5   MRHERVVIIKNMFHPMDFEDDPLVLNEI-----REDLRVECSKFGQIRKLLLFD----RH 55

Query: 237 LKGFAFVEFSTKEEAAKA 254
             G A V F   EEA   
Sbjct: 56  PDGVASVSFRDPEEADYC 73

>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 = 37.0 bits (85), Expect = 2e-04
 Identities = 16/60 (26%), Positives = 30/60 (50%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL 257
            I+V  +  + E  ++   F +YGK+  + +   + +GK +GFAFV F   +   K +  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 63

>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 = 37.0 bits (85), Expect = 3e-04
 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
           K DV   ++Y++  P +A  D I+      G+V  +   +       KG  FV F + E 
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIES 59

Query: 251 AAKALEL 257
           A K +E 
Sbjct: 60  AKKFVET 66

>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 = 36.6 bits (84), Expect = 3e-04
 Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 6/59 (10%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            +Y+  L P    D +  +F                     G+AFV++  +  A +A+E
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLA------GQVLLKSGYAFVDYPDQNWAIRAIE 55

>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 = 36.3 bits (83), Expect = 3e-04
 Identities = 17/58 (29%), Positives = 27/58 (46%)

Query: 199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           +Y+  L P      +  +   YGK+        K+T K KG+ FV+F +   A KA+ 
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 58

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (85), Expect = 4e-04
 Identities = 20/66 (30%), Positives = 34/66 (51%)

Query: 191 KPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEE 250
             D    +++V  +P EA  + ++ +FS+ G V    L   + TGK KG+ F E+  +E 
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 251 AAKALE 256
           A  A+ 
Sbjct: 63  ALSAMR 68

>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 = 36.6 bits (84), Expect = 5e-04
 Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 189 QDKPDVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 248
             +       ++V  +P       +  +F ++GK+  V +   +     KGF FV F   
Sbjct: 4   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENS 61

Query: 249 EEAAKALE 256
            +A +A E
Sbjct: 62  ADADRARE 69

>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 = 34.8 bits (79), Expect = 0.001
 Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
           T+ V+ LP     + +   F   G + +V +           FA +EF+  + A  A+ 
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN--FRFARIEFARYDGALAAIT 58

>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 = 34.7 bits (79), Expect = 0.002
 Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 6/60 (10%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             +    L      + +  V  K G V  + +P  K       ++F  + T EE+ +A  
Sbjct: 21  LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAYV 74

>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 = 34.3 bits (78), Expect = 0.003
 Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 4/60 (6%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
            T+++  +PP    + ++ +FS  G V       FK   K +  A ++  + EEA +AL 
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVK----GFKFFQKDRKMALIQMGSVEEAVQALI 66

>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 = 35.3 bits (80), Expect = 0.003
 Identities = 16/69 (23%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 189 QDKPDVDEC-TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFST 247
           Q  P+ D    + V  +P   +   +  +F +YG +  V +   + T + +G+ FV+F +
Sbjct: 34  QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93

Query: 248 KEEAAKALE 256
              A +A+ 
Sbjct: 94  GSSAQQAIA 102

>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 = 34.0 bits (77), Expect = 0.004
 Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 6/60 (10%)

Query: 197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALE 256
             ++V  L        +     K+G + YV +  FK        A VEF   + A + + 
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECVT 69

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	299
d1s29a_	92	Lupus La autoantigen N-terminal domain {Trypanosom	99.95
d2cqka1	88	La-related protein 4 LARP4 {Human (Homo sapiens) [	99.95
d1zh5a1	99	Lupus La autoantigen N-terminal domain {Human (Hom	99.95
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.79
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.77
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.77
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.77
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.77
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.77
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.76
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.75
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.75
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.75
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.75
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.75
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.75
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.74
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.74
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.73
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.73
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.73
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.73
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.73
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.72
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.72
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.72
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.71
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.71
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.7
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.7
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.7
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.69
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.69
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.68
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.68
d1s29a_	92	Lupus La autoantigen N-terminal domain {Trypanosom	99.68
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.67
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.67
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.67
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.67
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.66
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.66
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.66
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.65
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.65
d2cqka1	88	La-related protein 4 LARP4 {Human (Homo sapiens) [	99.64
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.64
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.63
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.63
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.62
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.62
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.62
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.62
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.61
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.61
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.61
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.61
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.61
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.61
d1zh5a1	99	Lupus La autoantigen N-terminal domain {Human (Hom	99.6
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.59
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.59
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.59
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.58
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.58
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.57
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.57
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.57
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.56
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.55
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.54
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.53
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.52
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.52
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.52
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.5
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.5
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.49
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.48
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.42
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	99.38
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.32
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.32
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.32
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.3
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.16
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.05
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.81
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.78
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	96.45
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	96.33
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	96.13
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	95.99
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	95.97
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	95.97
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	95.91
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	95.83
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	95.81
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	95.69
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	95.67
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	95.6
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	95.51
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	95.5
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	95.49
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	95.46
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	95.44
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	95.41
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	95.38
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	95.36
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	95.35
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	95.34
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	95.3
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	95.23
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	95.2
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	95.12
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	95.1
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	95.09
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	95.09
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	95.03
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	94.99
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	94.98
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	94.86
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	94.74
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	94.73
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	94.65
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	94.62
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	94.45
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	94.42
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	94.39
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	94.38
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	94.33
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	94.15
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	94.14
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	94.13
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	93.97
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	93.87
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	93.68
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	93.66
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	93.5
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	93.18
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	93.16
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	93.13
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	93.03
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	92.96
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	92.91
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	92.85
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	92.83
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	92.82
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	92.72
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	92.69
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	92.63
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	92.43
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	92.43
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	92.27
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	92.06
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	91.37
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	91.26
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	90.88
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	90.34
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	90.33
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	90.31
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	90.21
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	89.94
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	88.95
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	88.54
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	88.3
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	86.41
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	85.49
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	84.31
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	83.14
d1wfxa_	180	Probable RNA 2'-phosphotransferase KptA {Aeropyrum	81.1
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	80.01

>d1s29a_ a.4.5.46 (A:) Lupus La autoantigen N-terminal domain {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: Lupus La autoantigen N-terminal domain
species: Trypanosoma brucei [TaxId: 5691]

Probab=99.95  E-value=2.5e-30  Score=186.64  Aligned_cols=70  Identities=30%  Similarity=0.513  Sum_probs=67.5

Q ss_pred             CeeecCCCCcCcChHHHHhh--ccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeeccc
Q psy3930           1 MEFYLSDSNLRKDRFFSQLL--QESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGNI   70 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~--~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr~~   70 (299)
                      |||||||+||++|+||+++|  +.+|||||++|++||||++|+.|.+.|++||+.|+.|||++|+++|||+.
T Consensus        18 vEfYFSd~NL~~D~fL~~~m~~~~~G~V~i~~i~~F~rmk~lt~d~~~i~~Al~~S~~lev~ed~~~VRRk~   89 (92)
T d1s29a_          18 VEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVEAIRPSEKLVLSEDGLMVRRRD   89 (92)
T ss_dssp             HHHHTSHHHHTTCHHHHHHHTTSTTCCEEHHHHTTSHHHHTTCSCHHHHHHHHTTCSSEEECTTSSEEEESS
T ss_pred             HHHHccHhhhccCHHHHHHHhccCCCcEEhHHHhcCcCHHHhcCCHHHHHHHHhhCCeEEEeCCCCEEeeCC
Confidence            69999999999999999999  56799999999999999999999999999999999999999999999974

>d2cqka1 a.4.5.46 (A:43-130) La-related protein 4 LARP4 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: La-related protein 4 LARP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=2.2e-30  Score=185.55  Aligned_cols=73  Identities=30%  Similarity=0.492  Sum_probs=70.2

Q ss_pred             CeeecCCCCcCcChHHHHhhccCCCEEeeeeecchhhhhccCCHHHHHHHHhcCcceeeccCcceeecccccc
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVKGNIIRH   73 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~~~~v~~~~~~vrr~~~~~   73 (299)
                      |||||||+||++|.||+++|+++|||||++|++||||++||.|++.|++||+.|+.|||++|+++|||+..|+
T Consensus        15 vEfYFSd~NL~~D~fL~~~m~~~G~V~l~~i~~F~r~k~lt~d~~~i~~Al~~S~~lev~~d~~~VRr~~~r~   87 (88)
T d2cqka1          15 LEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSPMVQVDEKGEKVRPSHKRC   87 (88)
T ss_dssp             HHHHTSHHHHHHCHHHHHHSCTTSCEEHHHHHHCHHHHHHCCCHHHHHHHHHHSSSEEECSSSSEEEECCSCC
T ss_pred             HHhhCCHhhhCcCHHHHHhhcCCCCEEhHHHhcChHHHHHcCCHHHHHHHHhcCCeEEEeCCCCEeccCCCCC
Confidence            6999999999999999999999999999999999999999999999999999999999999999999987443

>d1zh5a1 a.4.5.46 (A:5-103) Lupus La autoantigen N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: Lupus La autoantigen N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=1.6e-29  Score=185.21  Aligned_cols=78  Identities=36%  Similarity=0.600  Sum_probs=71.9

Q ss_pred             CeeecCCCCcCcChHHHHhhcc-CCCEEeeeeecchhhhhccCCHHHHHHHHhcCc--ceeeccCcceeecccccccccc
Q psy3930           1 MEFYLSDSNLRKDRFFSQLLQE-SPEIEVSVFLKCNKLARLTHDPDDVVKALRKSK--LLEVTEDGTKVKGNIIRHFLVP   77 (299)
Q Consensus         1 ~e~yfs~~nl~~d~~l~~~~~~-~~~v~~~~~~~f~~~~~~~~~~~~i~~a~~~s~--~~~v~~~~~~vrr~~~~~~~~p   77 (299)
                      |||||||+||++|.||+++|+. +|||||++|++||||++|+.|.+.|++||+.|+  .|+|++|+++|||++    ..|
T Consensus        17 vEfYFSd~NL~~D~fL~~~m~~~eG~Vpl~~i~~F~r~k~l~~~~~~i~~Al~~S~~~~lev~~d~~~vRR~~----~~p   92 (99)
T d1zh5a1          17 IEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSP----SKP   92 (99)
T ss_dssp             HHHHTSTTTGGGCHHHHHHHTTTTTCEEHHHHTTSHHHHHHCCCHHHHHHHHHTCSSCCEEECTTSSEEEECT----TSC
T ss_pred             HHHhcCHhhhccCHHHHHHHhcCCCcccHHHHhcchHHHHHcCCHHHHHHHHHhCCCCeEEEcCCCceeCCCC----CCC
Confidence            6999999999999999999995 799999999999999999999999999999887  599999999999975    667


Q ss_pred             ccccc
Q psy3930          78 ISMET   82 (299)
Q Consensus        78 ~~~~~   82 (299)
                      +|+.+
T Consensus        93 lpe~~   97 (99)
T d1zh5a1          93 LPEVT   97 (99)
T ss_dssp             CCCCC
T ss_pred             CCCcc
Confidence            77654

>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=99.79  E-value=5.3e-19  Score=129.19  Aligned_cols=81  Identities=26%  Similarity=0.397  Sum_probs=74.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ...+++|||+|||+++|+++|+++|++||+|..|.+++++.+|.++|||||+|.+.++|..|++. +||  ..+.|++|.
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~-l~g--~~~~gr~i~   80 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY-ING--TRLDDRIIR   80 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-TTT--SEETTEECE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHH-hCC--CEECCEEEE
Confidence            34578999999999999999999999999999999999998999999999999999999999999 898  777899987


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus        81 V~~a   84 (93)
T d1h2vz_          81 TDWD   84 (93)
T ss_dssp             EEEE
T ss_pred             EEEc
Confidence            7653

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=1e-18  Score=129.11  Aligned_cols=83  Identities=28%  Similarity=0.380  Sum_probs=76.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||+++++++|+++|++||+|..|++++++.+|.++|||||+|.+.++|++|++. +||  ..+.|++|.|
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~-l~g--~~~~gr~i~V   82 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE-VDG--QVFQGRMLHV   82 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHH-TTT--EESSSCEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHH-cCC--CEECCEEEEE
Confidence            3457899999999999999999999999999999999988999999999999999999999999 898  7789999988


Q ss_pred             Eeeccc
Q psy3930         274 TSRLSF  279 (299)
Q Consensus       274 ~~k~~~  279 (299)
                      ......
T Consensus        83 ~~a~~~   88 (99)
T d1whwa_          83 LPSTIK   88 (99)
T ss_dssp             EECCCC
T ss_pred             EECCCC
Confidence            775543

>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=99.77  E-value=7.6e-19  Score=127.03  Aligned_cols=82  Identities=28%  Similarity=0.446  Sum_probs=74.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..++++|||+|||+++++++|+++|++||+|..|++++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~-lng--~~l~g~~l~   80 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA-LNG--AEIMGQTIQ   80 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHH-cCC--CEECCEEEE
Confidence            44578999999999999999999999999999999999988999999999999999999999999 898  778899988


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus        81 V~~a~   85 (88)
T d1rk8a_          81 VDWCF   85 (88)
T ss_dssp             EEESE
T ss_pred             EEEec
Confidence            76543

>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=99.77  E-value=1.7e-18  Score=124.34  Aligned_cols=81  Identities=31%  Similarity=0.568  Sum_probs=73.3

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ..+++|||+|||+++++++|+++|++||+|..+++++++.+|.++|||||+|.+.++|.+|++. +||..+...+++|.|
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~-l~g~~~~g~~~~l~V   82 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA-LNNVIPEGGSQPLSV   82 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTTCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHH-HCCCEeCCCCeEEEE
Confidence            4567899999999999999999999999999999999988999999999999999999999999 888655555688887


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      +.
T Consensus        83 ~~   84 (85)
T d1b7fa2          83 RL   84 (85)
T ss_dssp             EE
T ss_pred             EE
Confidence            64

>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=99.77  E-value=1.3e-18  Score=124.86  Aligned_cols=79  Identities=27%  Similarity=0.465  Sum_probs=70.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      .+++|||+|||+++++++|+++|++||+|..+++++++.+|.++|||||+|.+.++|++|++. +||..+....++|.|.
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~-lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG-LNGQKPSGATEPITVK   83 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTTCCCTTCSSCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHH-hCCCEeCCCCEEEEEE
Confidence            467899999999999999999999999999999999988999999999999999999999999 8984444344566654

>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=99.77  E-value=8.6e-19  Score=124.41  Aligned_cols=76  Identities=21%  Similarity=0.339  Sum_probs=71.3

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .+|||+|||+++|+++|+++|++||+|..|++++++.+|.++|||||+|.++++|..|++. +||  ..+.|++|+|..
T Consensus         1 aslfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~-l~g--~~~~gr~i~v~~   76 (80)
T d1cvja1           1 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT-MNF--DVIKGKPVRIMW   76 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTT-STT--CEETTEECEEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHH-cCC--CEECCEEEEEEE
Confidence            3799999999999999999999999999999999998999999999999999999999999 899  778899887754

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.7e-18  Score=126.46  Aligned_cols=78  Identities=24%  Similarity=0.453  Sum_probs=73.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||.++++++|+++|++||+|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.|.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~-l~g--~~~~g~~l~V~   84 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI-MDM--IKLYGKPIRVN   84 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHH-SSS--CBCSSCBCEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHH-cCC--CEECCEEEEEE
Confidence            457999999999999999999999999999999999988999999999999999999999999 898  77889998775


Q ss_pred             e
Q psy3930         275 S  275 (299)
Q Consensus       275 ~  275 (299)
                      .
T Consensus        85 ~   85 (93)
T d1x5ua1          85 K   85 (93)
T ss_dssp             E
T ss_pred             E
Confidence            5

>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=99.77  E-value=2e-18  Score=128.51  Aligned_cols=83  Identities=20%  Similarity=0.297  Sum_probs=74.5

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      +...++|||+|||+++++++|+++|++||.|..|++++++.+|.++|||||+|.+.++|++|++. +|+   .+.|+.|.
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~-~~~---~l~Gr~l~   82 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD-PNP---IIDGRKAN   82 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTC-SSC---EETTEECE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHH-CCC---cCCCEEEE
Confidence            44567899999999999999999999999999999999998999999999999999999999998 774   37899998


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus        83 V~~a~~~   89 (103)
T d2cqda1          83 VNLAYLG   89 (103)
T ss_dssp             EEESTTT
T ss_pred             EEEcCCC
Confidence            8765544

>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=99.76  E-value=7.3e-19  Score=125.38  Aligned_cols=77  Identities=21%  Similarity=0.385  Sum_probs=72.1

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      +++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|++|.|..
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~-lng--~~~~g~~l~v~~   78 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV-LNG--ITVRNKRLKVSY   78 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHH-HTT--CEETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHH-hCC--CEECCEEEEEEE
Confidence            57899999999999999999999999999999999988999999999999999999999999 898  778899887765

>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=99.75  E-value=2.5e-18  Score=123.16  Aligned_cols=79  Identities=20%  Similarity=0.394  Sum_probs=71.7

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||.++++++|+++|++||+|..+++++++.+|.++|||||+|.+.++|++|++.  +|  ..++|+.|.|+
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~--~~--~~i~Gr~i~V~   80 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA--RP--HKVDGRVVEPK   80 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT--CS--CEETTEECEEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHh--CC--CEECCEEEEEE
Confidence            347899999999999999999999999999999999998999999999999999999999974  65  66789999887


Q ss_pred             eec
Q psy3930         275 SRL  277 (299)
Q Consensus       275 ~k~  277 (299)
                      ...
T Consensus        81 ~A~   83 (84)
T d1l3ka1          81 RAV   83 (84)
T ss_dssp             ECC
T ss_pred             eee
Confidence            643

>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=99.75  E-value=1.2e-18  Score=124.48  Aligned_cols=76  Identities=28%  Similarity=0.385  Sum_probs=71.4

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ..++|||+|||+++|+++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|+++ +||  ..+.|++|.|
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 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER-ANG--MELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHH-HTT--EEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHH-cCC--CEECCEEeEC
Confidence            357999999999999999999999999999999999988899999999999999999999999 888  7888998876

>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=99.75  E-value=6.2e-19  Score=124.16  Aligned_cols=75  Identities=19%  Similarity=0.387  Sum_probs=70.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      |+|||+|||+++++++|+++|++||+|..+.+++++.+|.++|||||+|.++++|++|++  +|+  ..++|+.|.|+.
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~--~~~--~~i~Gr~i~V~~   75 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA--QSR--HELDSKTIDPKV   75 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH--TTT--CCCSSCCCEEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH--cCC--CEECCeEEEEEE
Confidence            689999999999999999999999999999999999899999999999999999999997  577  778899988875

>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=99.75  E-value=2.2e-18  Score=123.69  Aligned_cols=77  Identities=22%  Similarity=0.362  Sum_probs=72.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      .+|||+|||.++|+++|+++|++||+|..|++++++.+|.++|||||+|.++++|..|++. +||  ..+.|++|.|...
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   78 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG-LNG--MQLGDKKLLVQRA   78 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHT-SSS--CCCSSSCCEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHH-hCC--CEECCEEEEEEEC
Confidence            4799999999999999999999999999999999988999999999999999999999999 998  8888999887664

>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=99.75  E-value=2.4e-18  Score=124.87  Aligned_cols=80  Identities=31%  Similarity=0.517  Sum_probs=73.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..+.++|||+|||.++++++|+++|++||+|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~-l~g--~~~~g~~i~   81 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG-VSG--FGYDHLILN   81 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHH-TTT--CEETTEECE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHH-hCC--CEECCEEEE
Confidence            34567999999999999999999999999999999999988999999999999999999999999 898  778899886


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |..
T Consensus        82 v~~   84 (90)
T d2cq0a1          82 VEW   84 (90)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            654

>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=5.1e-18  Score=133.17  Aligned_cols=82  Identities=21%  Similarity=0.307  Sum_probs=75.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||+++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|..|++. +||  ..+.|+.|.|.
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~-lng--~~~~gr~l~V~  117 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG-LNG--FNILNKRLKVA  117 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHH-TTT--EECSSCEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHH-hCC--CEECCEEEEEE
Confidence            356899999999999999999999999999999999988999999999999999999999999 899  88889999998


Q ss_pred             eeccc
Q psy3930         275 SRLSF  279 (299)
Q Consensus       275 ~k~~~  279 (299)
                      .....
T Consensus       118 ~a~~~  122 (139)
T d1u6fa1         118 LAASG  122 (139)
T ss_dssp             ESSCC
T ss_pred             EcCCC
Confidence            75443

>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=99.74  E-value=1.2e-18  Score=126.23  Aligned_cols=78  Identities=28%  Similarity=0.489  Sum_probs=72.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||+++++++|+++|++||+|..|.+++++.+|.++|||||+|.+.++|++|++. +||  ..+.|++|.|.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~-l~~--~~i~g~~l~v~   80 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN-MNE--SELFGRTIRVN   80 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHH-HTT--EEETTEEEEEE
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHH-cCC--CEECCEEEEEE
Confidence            457999999999999999999999999999999999998999999999999999999999999 888  77889988776


Q ss_pred             e
Q psy3930         275 S  275 (299)
Q Consensus       275 ~  275 (299)
                      .
T Consensus        81 ~   81 (89)
T d2cqba1          81 L   81 (89)
T ss_dssp             E
T ss_pred             E
Confidence            5

>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=99.74  E-value=4.3e-18  Score=121.27  Aligned_cols=76  Identities=25%  Similarity=0.425  Sum_probs=71.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      ++|||+|||+++++++|+++|++||+|..|+++++..+|.++|||||+|.+.++|++|++. +||  ..+.|++|.|..
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~-l~g--~~~~g~~l~v~~   78 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT-LNG--LRLQTKTIKVSY   78 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH-HTT--CEETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHH-hCC--CEECCEEEEEEE
Confidence            5799999999999999999999999999999999988999999999999999999999999 898  778899887754

>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=99.73  E-value=3.8e-18  Score=120.44  Aligned_cols=76  Identities=20%  Similarity=0.267  Sum_probs=71.3

Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeec
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRL  277 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~  277 (299)
                      +|||+|||+++++++|+++|++||+|..+++++++ +|.++|||||+|.+.++|++|++. +||  ..+.|++|.|++..
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ-YNG--VPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHH-HTT--CEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHH-hCC--CEECCEEEEEEEee
Confidence            59999999999999999999999999999999987 899999999999999999999999 898  78889999988753

>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=99.73  E-value=4.3e-18  Score=126.45  Aligned_cols=80  Identities=20%  Similarity=0.266  Sum_probs=73.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      .+.+++|||+|||+++++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|+.|++. +||  ..+.|+.|.
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~-lng--~~~~g~~i~   91 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS-MNG--FQIGMKRLK   91 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHH-hCC--CEECCEEEE
Confidence            45678999999999999999999999999999999999988999999999999999999999999 898  778899887


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |..
T Consensus        92 V~~   94 (102)
T d2cpza1          92 VQL   94 (102)
T ss_dssp             EEC
T ss_pred             EEE
Confidence            655

>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=99.73  E-value=8.8e-18  Score=121.75  Aligned_cols=78  Identities=24%  Similarity=0.326  Sum_probs=69.9

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||+++|+++|+++|++||.|..|++++++.+|.++|||||+|.+.++|++|++. .+    .++|+.|.|
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~-~~----~l~Gr~i~v   80 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RH----MIDGRWCDC   80 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS-CE----EETTEEEEE
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc-CC----ccCCEEeEE
Confidence            3457899999999999999999999999999999999988999999999999999999999986 33    467888877


Q ss_pred             Eee
Q psy3930         274 TSR  276 (299)
Q Consensus       274 ~~k  276 (299)
                      +..
T Consensus        81 ~~a   83 (90)
T d2cqga1          81 KLP   83 (90)
T ss_dssp             ECC
T ss_pred             EeC
Confidence            653

>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=6e-18  Score=118.46  Aligned_cols=73  Identities=22%  Similarity=0.430  Sum_probs=67.5

Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      .|||+|||+++++++|+++|++||+|..+.+++++.+|+++|||||+|.++++|++|++  +++  ..++|+.|.|+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~--~~~--~~l~Gr~i~V~   73 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD--QKE--HKLNGKVIDPK   73 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH--TCC--CCBTTBCCEEC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh--cCC--CEECCCEEEee
Confidence            48999999999999999999999999999999999899999999999999999999997  465  56789998774

>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=99.73  E-value=7.7e-18  Score=122.12  Aligned_cols=80  Identities=28%  Similarity=0.458  Sum_probs=74.1

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      +.++|||+|||+++++++|+++|++||.|..+.++++..+|.++|||||+|.+.++|+.|++. +||  ..+.|++|.|.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-l~~--~~~~g~~l~V~   80 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA-MNG--KSVDGRQIRVD   80 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHH-HTT--CCTTSCCCEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHH-cCC--CEECCEEEEEE
Confidence            467899999999999999999999999999999998888999999999999999999999999 898  77899999987


Q ss_pred             eec
Q psy3930         275 SRL  277 (299)
Q Consensus       275 ~k~  277 (299)
                      ...
T Consensus        81 ~a~   83 (90)
T d1x5sa1          81 QAG   83 (90)
T ss_dssp             EEE
T ss_pred             EcC
Confidence            643

>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=99.72  E-value=3.4e-18  Score=119.59  Aligned_cols=74  Identities=27%  Similarity=0.454  Sum_probs=67.4

Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .|||+|||+++|+++|+++|++||+|..|.+++++.+|.++|||||+|.+.++|++|++.  ++  ..++|+.+.|+.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~--~~--~~i~g~~i~vk~   74 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK--KY--HNVGLSKCEIKV   74 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC--SS--CCBTTBCCEEEC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh--CC--CEECCEEeEEEE
Confidence            589999999999999999999999999999999998999999999999999999999974  44  567888877654

>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=1.7e-17  Score=118.98  Aligned_cols=80  Identities=23%  Similarity=0.356  Sum_probs=72.9

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||.++|+++|+++|+.||+|..|.++++. +|.++|||||+|.++++|++|++  ++|  ..+.|+.|.|+
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~--~~~--~~~~g~~l~v~   79 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE--TPG--QKYKETDLLIL   79 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT--CCC--CEETTEECEEE
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH--HCC--CEECCEEEEEE
Confidence            35799999999999999999999999999999998876 89999999999999999999996  577  88899999998


Q ss_pred             eeccc
Q psy3930         275 SRLSF  279 (299)
Q Consensus       275 ~k~~~  279 (299)
                      .+..+
T Consensus        80 ~~~dy   84 (85)
T d1zh5a2          80 FKDDY   84 (85)
T ss_dssp             EGGGC
T ss_pred             EcCCC
Confidence            86553

>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=99.72  E-value=1.8e-17  Score=121.10  Aligned_cols=82  Identities=30%  Similarity=0.438  Sum_probs=72.7

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccC-CCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFK-STGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~-~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....+|||+|||+++++++|+++|++||.|..|+++++. .+|.++|||||+|.+.++|.+|++.|.||  ..+.|++|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~--~~~~Gr~l~   83 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHS--THLYGRRLV   83 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTC--CBSSSCBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCC--cEECCEEEE
Confidence            345789999999999999999999999999999999875 47999999999999999999999994488  778899987


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus        84 V~~A~   88 (94)
T d2cpha1          84 LEWAD   88 (94)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            76643

>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=99.72  E-value=7.7e-18  Score=125.50  Aligned_cols=77  Identities=29%  Similarity=0.490  Sum_probs=72.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .++|||+|||+++++++|+++|++||+|..|++++++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.|.|..
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~-l~~--~~~~g~~i~V~~   84 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN-LNG--REFSGRALRVDN   84 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHH-SSS--BSCSSSCBEEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHH-cCC--CEECCEEEEEEE
Confidence            46899999999999999999999999999999999988999999999999999999999999 898  778899998865

>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=99.71  E-value=5.5e-18  Score=120.46  Aligned_cols=77  Identities=21%  Similarity=0.344  Sum_probs=65.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      |+|||+|||+++|+++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|++|++. +||  ..++|++|.|...
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~-l~g--~~~~g~~i~V~~a   78 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK-LNG--LKIEGYTLVTKVS   78 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHH-HTT--CEETTEECEEEEC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHH-hCC--CEECCEEEEEEEc
Confidence            7999999999999999999999999998888877777899999999999999999999999 898  7889999988763

>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=99.71  E-value=1.3e-17  Score=119.56  Aligned_cols=75  Identities=27%  Similarity=0.426  Sum_probs=68.2

Q ss_pred             EEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCC---CcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTG---KLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       199 l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g---~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      |||+|||+++|+++|+++|++||+|..|.+++++.++   .++|||||+|.+.++|++|++. +||  ..++|++|.|..
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~-~~~--~~~~g~~i~V~~   77 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ-LQG--HTVDGHKLEVRI   77 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHH-STT--CEETTEECEEEC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHH-hCC--CEECCEEEEEEE
Confidence            7999999999999999999999999999999886554   4689999999999999999999 898  778899998876


Q ss_pred             e
Q psy3930         276 R  276 (299)
Q Consensus       276 k  276 (299)
                      .
T Consensus        78 a   78 (85)
T d2cpfa1          78 S   78 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=1.3e-17  Score=119.12  Aligned_cols=74  Identities=24%  Similarity=0.458  Sum_probs=68.3

Q ss_pred             EEEecCCCCCCHHHHHHHhhcCCceEE-EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         199 IYVEKLPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       199 l~V~nLp~~~t~e~L~~~F~~~G~i~~-v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      |||+|||+++++++|+++|++||.|.. +.++++..+|+++|||||+|.+.++|++|++. +||  ..+.|++|.|..
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~g--~~~~gr~l~v~~   75 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA-MNG--QYLCNRPITVSY   75 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHT-TTT--CEETTEECEEEE
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHh-CCC--cEECCEEEEEEE
Confidence            799999999999999999999999866 47888888999999999999999999999999 898  788899987766

>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=99.71  E-value=2.7e-17  Score=116.17  Aligned_cols=76  Identities=21%  Similarity=0.384  Sum_probs=70.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .++|||+|||+++|+++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++  +||  ..++|+.|.|+.
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~--~~~--~~l~Gr~i~V~~   77 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI--QKY--HTVNGHNCEVRK   77 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH--CSC--CEETTEECEEEE
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH--hCC--CEECCEEEEEEE
Confidence            4689999999999999999999999999999999998899999999999999999999995  688  778899998875

>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=99.70  E-value=8.5e-18  Score=124.48  Aligned_cols=78  Identities=23%  Similarity=0.316  Sum_probs=72.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      +.++|||+|||.++++++|+++|+.||.|..|+++++..+|.++|||||+|.+.++|++|+ . +||  ..+.|+.|.|+
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~-l~g--~~~~G~~l~V~   92 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-G-LTG--QRLLGVPIIVQ   92 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-H-HTT--EEETTEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-H-HCC--CEECCEEEEEE
Confidence            3578999999999999999999999999999999999889999999999999999999999 4 788  78889999987


Q ss_pred             ee
Q psy3930         275 SR  276 (299)
Q Consensus       275 ~k  276 (299)
                      ..
T Consensus        93 ~a   94 (101)
T d2cq4a1          93 AS   94 (101)
T ss_dssp             EH
T ss_pred             EC
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=99.70  E-value=1.9e-17  Score=123.02  Aligned_cols=76  Identities=18%  Similarity=0.388  Sum_probs=69.9

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .++|||+|||+++++++|+++|++||.|..+.|++++.++.++|||||+|.+.++|++|++  ++|  ..++|++|.|..
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~--~~~--~~l~G~~i~V~~   95 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA--ARP--HSIDGRVVEPKR   95 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT--SCS--EEETTEEEEEEC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH--hCC--CeECCEEEEEEE
Confidence            4789999999999999999999999999999999998899999999999999999999996  577  567899988754

>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=99.70  E-value=4.3e-17  Score=118.13  Aligned_cols=77  Identities=22%  Similarity=0.300  Sum_probs=69.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      .+.++|||+|||+++++++|+++|++||+|..|.++++..++  +|||||+|.+.++|..|++. +||  ..+.|+.|.|
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~-l~~--~~~~g~~i~v   80 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAA-MNG--RKILGKEVKV   80 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHH-HTT--EEETTEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHH-cCC--CEECCEEEEE
Confidence            446899999999999999999999999999999999886544  78999999999999999999 888  6788998876


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      ..
T Consensus        81 ~~   82 (90)
T d2cqia1          81 NW   82 (90)
T ss_dssp             EE
T ss_pred             EE
Confidence            54

>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=99.69  E-value=1.2e-17  Score=136.62  Aligned_cols=141  Identities=16%  Similarity=0.259  Sum_probs=102.2

Q ss_pred             HHHHHhhhcCCCe-eeeeeec--ccccccCC----CCHHHHHHHHHhcCccccccccceeeeeeccc----CCCCCCCcE
Q psy3930         130 RFFSQLLQESPEI-EVSVFLK--CNKLARLT----HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ----DKPDVDECT  198 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l~~f~~--F~~i~~~~----~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~----~~~~~~~~~  198 (299)
                      ..|..++.+++.+ .+.+...  .+..+.+.    .+.++|.+|+.... ..+....+.+.+..+..    .......++
T Consensus        21 ~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (183)
T d1u1qa_          21 ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP-HKVDGRVVEPKRAVSREDSQRPGAHLTVKK   99 (183)
T ss_dssp             HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCS-CEETTEECEEEECCCTTGGGSTTTTCCCSE
T ss_pred             HHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcC-Ccccccchhhhhhhhcccccccccccccce
Confidence            5677777777763 2222211  11111111    56889999986544 44555555554433221    122455689


Q ss_pred             EEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       199 l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      |||+|||+.+++++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|++  +++  ..+.|+.|.|..
T Consensus       100 i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~--~~~--~~~~G~~i~V~~  172 (183)
T d1u1qa_         100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI--QKY--HTVNGHNCEVRK  172 (183)
T ss_dssp             EEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT--SSC--EEETTEEEEEEE
T ss_pred             eEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH--hCC--CeECCEEEEEEe
Confidence            9999999999999999999999999999999998899999999999999999999996  455  567899888765

>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=99.69  E-value=7.3e-17  Score=118.68  Aligned_cols=82  Identities=23%  Similarity=0.354  Sum_probs=71.7

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCC----CCCCCC
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPC----PPDYQS  268 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~----~~~~~g  268 (299)
                      ..++++|||+|||+++++++|+++|++||+|..+.++.+..++.++|||||+|.+.++|.+|++. +|+.    ...+.|
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~-l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA-ASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHH-HCTTTTTCCEESSS
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHH-cccccccCCcEECC
Confidence            34578999999999999999999999999999999999988899999999999999999999998 5521    255778


Q ss_pred             ceEEEEe
Q psy3930         269 SILTTTS  275 (299)
Q Consensus       269 ~~l~v~~  275 (299)
                      +.|.|..
T Consensus        84 r~l~v~~   90 (98)
T d1x4ha1          84 RQLKVDL   90 (98)
T ss_dssp             CEEEEEC
T ss_pred             EEEEEEE
Confidence            8877655

>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=99.68  E-value=5.4e-17  Score=120.09  Aligned_cols=81  Identities=31%  Similarity=0.402  Sum_probs=72.6

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceE--------EEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCC
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVT--------YVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPP  264 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~--------~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~  264 (299)
                      +...++|||+|||.++++++|+++|+.||.|.        .+.+.++..+|.++|||||+|.+.++|.+|++. +||  .
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~-l~g--~   81 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEW-FDG--K   81 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHH-HTT--C
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHH-hCC--C
Confidence            45678999999999999999999999999874        466777777899999999999999999999999 898  7


Q ss_pred             CCCCceEEEEee
Q psy3930         265 DYQSSILTTTSR  276 (299)
Q Consensus       265 ~~~g~~l~v~~k  276 (299)
                      .++|++|.|...
T Consensus        82 ~~~gr~i~V~~a   93 (101)
T d2cpea1          82 DFQGSKLKVSLA   93 (101)
T ss_dssp             EETTEECEEECS
T ss_pred             EECCEEEEEEEc
Confidence            889999988774

>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=99.68  E-value=1.1e-16  Score=117.27  Aligned_cols=80  Identities=23%  Similarity=0.293  Sum_probs=70.5

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCc-eEEEEeeccC-CCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGK-VTYVSLPKFK-STGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~-i~~v~i~~~~-~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      +|+|||+|||.++++++|+++|++||+ |..+.++++. .+|.++|||||+|.+.++|..|++. +++....+.|+.|.|
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~-l~~~~~~~~g~~i~V   79 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRK-LMPGRIQLWGHQIAV   79 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTT-TTTCCSCBTTBCCEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHH-HcCCCeEECCEEEEE
Confidence            478999999999999999999999996 8999999875 4688999999999999999999999 776567778888876


Q ss_pred             Eee
Q psy3930         274 TSR  276 (299)
Q Consensus       274 ~~k  276 (299)
                      ...
T Consensus        80 ~~A   82 (96)
T d2disa1          80 DWA   82 (96)
T ss_dssp             EES
T ss_pred             EEc
Confidence            543

>d1s29a_ a.4.5.46 (A:) Lupus La autoantigen N-terminal domain {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: Lupus La autoantigen N-terminal domain
species: Trypanosoma brucei [TaxId: 5691]

Probab=99.68  E-value=4.2e-18  Score=122.09  Aligned_cols=82  Identities=30%  Similarity=0.489  Sum_probs=76.1

Q ss_pred             HHHHHHHHHHhhhhcCCCCcchhHHHHHhhhc--CCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeee
Q psy3930         107 KQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQE--SPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       107 ~~~~~~i~~q~efyfsd~nL~~d~fl~~~~~~--~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      .+..++|++|+||||||+||++|.||+.+|..  .||++|+++++|++|++++.+.+.+.+|++.+..+++++++.+|+|
T Consensus         8 ~e~~~~I~~QvEfYFSd~NL~~D~fL~~~m~~~~~G~V~i~~i~~F~rmk~lt~d~~~i~~Al~~S~~lev~ed~~~VRR   87 (92)
T d1s29a_           8 SENKQKLQKQVEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVVEAIRPSEKLVLSEDGLMVRR   87 (92)
T ss_dssp             HHHHHHHHHHHHHHTSHHHHTTCHHHHHHHTTSTTCCEEHHHHTTSHHHHTTCSCHHHHHHHHTTCSSEEECTTSSEEEE
T ss_pred             HHHHHHHHHHHHHHccHhhhccCHHHHHHHhccCCCcEEhHHHhcCcCHHHhcCCHHHHHHHHhhCCeEEEeCCCCEEee
Confidence            56678899999999999999999999999954  5799999999999999999999999999999999999999999999


Q ss_pred             eecc
Q psy3930         185 TVVV  188 (299)
Q Consensus       185 ~~~~  188 (299)
                      ..|.
T Consensus        88 k~pl   91 (92)
T d1s29a_          88 RDPL   91 (92)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            7764

>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=99.67  E-value=1.7e-16  Score=115.68  Aligned_cols=80  Identities=20%  Similarity=0.299  Sum_probs=71.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||+|..|.++.+.  +.++|||||+|.+.++|.+|++. +||  ..+.|+.|.
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~-l~~--~~~~g~~l~   82 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREK-LHG--TVVEGRKIE   82 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHH-HTT--CEETTEECE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHH-cCC--CEECCEEEE
Confidence            4456789999999999999999999999999999999875  33689999999999999999999 898  788899988


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus        83 V~~A~   87 (93)
T d2cq3a1          83 VNNAT   87 (93)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            76643

>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=99.67  E-value=7.9e-17  Score=121.90  Aligned_cols=76  Identities=20%  Similarity=0.315  Sum_probs=69.5

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      .+++|||+|||.++++++|+++|++||.|..|++..   ++.++|||||+|.+.++|..|++. +||  ..+.|++|.|.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~-l~g--~~~~gr~l~V~   79 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDH-LSG--FNVCNRYLVVL   79 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHH-HTT--CEETTEECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHH-hCC--CEECCEEEEEE
Confidence            468999999999999999999999999999999975   466789999999999999999999 898  77889999887


Q ss_pred             ee
Q psy3930         275 SR  276 (299)
Q Consensus       275 ~k  276 (299)
                      ..
T Consensus        80 ~a   81 (114)
T d2f9da1          80 YY   81 (114)
T ss_dssp             EC
T ss_pred             Ec
Confidence            64

>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=99.67  E-value=6.7e-17  Score=112.91  Aligned_cols=74  Identities=23%  Similarity=0.406  Sum_probs=69.0

Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .|||+|||+++|+++|+++|++||.+..+.+++++.+|.++|||||+|.+.++|++|++  +||  ..++|++|.|+.
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~--~~~--~~l~gr~i~V~~   74 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE--IHF--HEINNKMVECKK   74 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH--CSS--CCBTTBCCEEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh--cCC--CEECCeEEEEEE
Confidence            48999999999999999999999999999999998899999999999999999999995  688  778899998864

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=5.3e-17  Score=120.21  Aligned_cols=77  Identities=16%  Similarity=0.355  Sum_probs=69.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..+.+..+. +|.++|||||+|.+.++|++|++. +||  ..+.|+++.
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~-lng--~~i~gr~~~   90 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGH-FNG--KFIKTPPGV   90 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHH-HBT--CCCCCCTTS
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHH-hCC--CEECCcCCc
Confidence            4456899999999999999999999999999999998875 889999999999999999999999 898  777788765


Q ss_pred             E
Q psy3930         273 T  273 (299)
Q Consensus       273 v  273 (299)
                      +
T Consensus        91 v   91 (101)
T d1x5oa1          91 S   91 (101)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.9e-17  Score=114.88  Aligned_cols=70  Identities=27%  Similarity=0.464  Sum_probs=65.7

Q ss_pred             EEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       199 l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      |||+|||+++|+++|+++|++||.|..+.+.+++.+|.++|||||+|.+.++|++|++. +||  ..+.|+.+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~-lng--~~~~Gr~~   70 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA-LKA--SGVQAQMA   70 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHH-HHH--HTCCEESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHH-hCC--CEECCEEC
Confidence            79999999999999999999999999999999988999999999999999999999999 888  66777765

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.66  E-value=7.7e-17  Score=115.72  Aligned_cols=78  Identities=19%  Similarity=0.320  Sum_probs=66.3

Q ss_pred             CCcEEEEecCCCCCC-HHHHHHHhhcCCceEEEEeecc-CCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         195 DECTIYVEKLPPEAE-HDYIESVFSKYGKVTYVSLPKF-KSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t-~e~L~~~F~~~G~i~~v~i~~~-~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ++++|||+|||++++ +++|+++|++||.|..|+++++ ..+|.++|||||+|.+.++|++|+ . +||  ..+.|+.|.
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al-~-~n~--~~~~gr~l~   78 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-Q-MNR--SLLGNREIS   78 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-G-GTT--EEETTEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHH-h-cCC--CEECCEEEE
Confidence            568999999999976 5569999999999999999875 468999999999999999999999 4 788  778899998


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus        79 V~~a   82 (86)
T d2ghpa3          79 VSLA   82 (86)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            8763

>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=99.66  E-value=1.5e-16  Score=116.33  Aligned_cols=76  Identities=34%  Similarity=0.513  Sum_probs=67.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ..+++|||+|||+++++++|+++|++||.|..+.+..+   +.++|||||+|.+.++|+.|++. +||  ..+.|++|.|
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~-l~g--~~~~g~~l~V   85 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYG-RDG--YDYDGYRLRV   85 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHH-HTT--CEETTEECEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHH-hCC--CEECCEEEEE
Confidence            44689999999999999999999999999999988653   45689999999999999999999 888  7788998866


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      ..
T Consensus        86 ~~   87 (95)
T d1x4aa1          86 EF   87 (95)
T ss_dssp             EC
T ss_pred             Ee
Confidence            54

>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=99.66  E-value=1e-16  Score=115.89  Aligned_cols=76  Identities=21%  Similarity=0.324  Sum_probs=68.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      ..+|||+|||+++++++|+++|++||.|..+.++.+.  +.++|||||+|.+.++|++|++. +||  ..++|++|.|..
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~-l~g--~~~~g~~i~V~~   82 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK-MNG--MLLNDRKVFVGR   82 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTS-SSE--EEETTEEEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHH-cCC--CEECCEEEEEEE
Confidence            3579999999999999999999999999999999885  34689999999999999999999 898  778899988765


Q ss_pred             e
Q psy3930         276 R  276 (299)
Q Consensus       276 k  276 (299)
                      .
T Consensus        83 a   83 (89)
T d1cvja2          83 F   83 (89)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=6e-17  Score=117.07  Aligned_cols=75  Identities=20%  Similarity=0.296  Sum_probs=67.4

Q ss_pred             CcEEEEecCCCCCCHHHH---HHHhhcCCceEEEEeeccCCCCC---cceEEEEEecCHHHHHHHHHhcCCCCCCCCCCc
Q psy3930         196 ECTIYVEKLPPEAEHDYI---ESVFSKYGKVTYVSLPKFKSTGK---LKGFAFVEFSTKEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L---~~~F~~~G~i~~v~i~~~~~~g~---~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      ..+|||+|||+++++++|   +++|++||+|..|.+++++.++.   ..|||||+|.+.++|.+|++. +||  ..+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~-lng--~~~~gr   84 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQC-VNN--VVVDGR   84 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHH-HTT--EEETTE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHH-hCC--CEECCE
Confidence            467999999999999999   77899999999999998876554   458999999999999999999 899  788899


Q ss_pred             eEEE
Q psy3930         270 ILTT  273 (299)
Q Consensus       270 ~l~v  273 (299)
                      +|++
T Consensus        85 ~lkv   88 (89)
T d2cpia1          85 TLKA   88 (89)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9876

>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=3.4e-16  Score=115.07  Aligned_cols=76  Identities=24%  Similarity=0.371  Sum_probs=66.0

Q ss_pred             CCCCcEEEEecCCC-CCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         193 DVDECTIYVEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       193 ~~~~~~l~V~nLp~-~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ....++|||+|||+ .+++++|+++|++||.|..|.+.        +|||||+|.+.++|++|++. +||  ..+.|++|
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~-lng--~~~~g~~l   80 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAG-EDG--RMIAGQVL   80 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHT-TTT--CEETTEEC
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHH-cCC--CEECCEEE
Confidence            34457899999975 67889999999999999999983        58999999999999999999 999  78899999


Q ss_pred             EEEeeccc
Q psy3930         272 TTTSRLSF  279 (299)
Q Consensus       272 ~v~~k~~~  279 (299)
                      .|......
T Consensus        81 ~V~~a~~~   88 (98)
T d1wf2a_          81 DINLAAEP   88 (98)
T ss_dssp             EEEETTSC
T ss_pred             EEEECCCC
Confidence            88875443

>d2cqka1 a.4.5.46 (A:43-130) La-related protein 4 LARP4 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: La-related protein 4 LARP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=1.2e-17  Score=118.85  Aligned_cols=81  Identities=28%  Similarity=0.469  Sum_probs=77.0

Q ss_pred             hHHHHHHHHHHhhhhcCCCCcchhHHHHHhhhcCCCeeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeee
Q psy3930         106 KKQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQESPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       106 ~~~~~~~i~~q~efyfsd~nL~~d~fl~~~~~~~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      .+++.+.|++|+||||||+||++|.||+.+|...||++|+++++|++|++++.+.+.+.+|++.+..+++++++.+|+|.
T Consensus         4 ~~~l~~~i~~QvEfYFSd~NL~~D~fL~~~m~~~G~V~l~~i~~F~r~k~lt~d~~~i~~Al~~S~~lev~~d~~~VRr~   83 (88)
T d2cqka1           4 TEDLKECLKKQLEFCFSRENLSKDLYLISQMDSDQFIPIWTVANMEEIKKLTTDPDLILEVLRSSPMVQVDEKGEKVRPS   83 (88)
T ss_dssp             HHHHHHHHHHHHHHHTSHHHHHHCHHHHHHSCTTSCEEHHHHHHCHHHHHHCCCHHHHHHHHHHSSSEEECSSSSEEEEC
T ss_pred             hHHHHHHHHHHHHhhCCHhhhCcCHHHHHhhcCCCCEEhHHHhcChHHHHHcCCHHHHHHHHhcCCeEEEeCCCCEeccC
Confidence            46788999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             e
Q psy3930         186 V  186 (299)
Q Consensus       186 ~  186 (299)
                      .
T Consensus        84 ~   84 (88)
T d2cqka1          84 H   84 (88)
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=99.64  E-value=5.3e-16  Score=115.29  Aligned_cols=79  Identities=23%  Similarity=0.387  Sum_probs=67.8

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccC-CCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFK-STGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~-~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ..++|||+|||+++++++|+++|+.|| +..+.++.+. .+|.++|||||+|.+.++|++|+ . +||  ..+.|+.|.|
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~-~~~--~~~~gr~l~V   88 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S-LNE--ESLGNKRIRV   88 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-G-GGT--CEETTEECEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-H-cCC--CEECCEEEEE
Confidence            458999999999999999999999999 7788877664 47889999999999999998776 5 787  7788999988


Q ss_pred             Eeecc
Q psy3930         274 TSRLS  278 (299)
Q Consensus       274 ~~k~~  278 (299)
                      .....
T Consensus        89 ~~a~~   93 (104)
T d1wi8a_          89 DVADQ   93 (104)
T ss_dssp             EECCC
T ss_pred             EECCC
Confidence            76443

>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=1.7e-16  Score=114.11  Aligned_cols=68  Identities=25%  Similarity=0.374  Sum_probs=61.9

Q ss_pred             EEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         198 TIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       198 ~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      +|||+|||+++++++|+++|++||+|..+.+.++       |||||+|.+.++|++|++. |||  ..+.|+.+.+..
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~-l~g--~~~~g~~i~v~~   69 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK-LDN--TKFRSHEGETAY   69 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHH-HTT--CBCCCTTSCCCB
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHH-hCC--CEECCcEeEEeE
Confidence            5999999999999999999999999999998753       6999999999999999999 898  778888887654

>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=99.63  E-value=5.8e-16  Score=114.71  Aligned_cols=81  Identities=22%  Similarity=0.232  Sum_probs=70.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ...+.+|||+|||+++|+++|+++|+.|| +..|.++.+. +|..+|||||+|.+.++|++|++  +|+  ..++|+.|.
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~--~~~--~~i~gR~I~   85 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA--KDK--ANMQHRYVE   85 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT--TSS--CCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH--cCC--CEECCEEEE
Confidence            45568999999999999999999999998 4577777776 78999999999999999999985  687  788899999


Q ss_pred             EEeeccc
Q psy3930         273 TTSRLSF  279 (299)
Q Consensus       273 v~~k~~~  279 (299)
                      |......
T Consensus        86 V~~s~~~   92 (102)
T d1weza_          86 LFLNSTA   92 (102)
T ss_dssp             EEEECCC
T ss_pred             EEEcCCC
Confidence            8775544

>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=99.62  E-value=1.2e-16  Score=118.49  Aligned_cols=80  Identities=25%  Similarity=0.365  Sum_probs=72.8

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ..+++|||+|||.++++++|+++|++||.|..+.+..+..+|.++|||||+|.+.++|.+|++. +||  ..+.|++|.|
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~-l~g--~~~~g~~l~V   92 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL-VNG--YKLYGKILVI   92 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHH-STT--CBCSSCBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHH-hCC--CEECCEEEEE
Confidence            4468999999999999999999999999999988888777899999999999999999999999 899  7788999877


Q ss_pred             Eee
Q psy3930         274 TSR  276 (299)
Q Consensus       274 ~~k  276 (299)
                      ...
T Consensus        93 ~~a   95 (102)
T d2cpxa1          93 EFG   95 (102)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            653

>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=99.62  E-value=6.5e-16  Score=110.78  Aligned_cols=74  Identities=27%  Similarity=0.421  Sum_probs=67.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||+++++++|+++|++||+|..|.+.++      +|||||+|.+.++|++|++. +||  ..+.|+.|.|.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~-l~g--~~i~g~~l~V~   77 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE-LDN--MPLRGKQLRVR   77 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHH-HTT--CCBTTBCCEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHH-hCC--CEECCEEEEEE
Confidence            4578999999999999999999999999999999865      57999999999999999999 898  78889999887


Q ss_pred             eec
Q psy3930         275 SRL  277 (299)
Q Consensus       275 ~k~  277 (299)
                      ...
T Consensus        78 ~A~   80 (86)
T d2cpja1          78 FAC   80 (86)
T ss_dssp             ESS
T ss_pred             ECC
Confidence            644

>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=99.62  E-value=4.3e-16  Score=114.09  Aligned_cols=75  Identities=24%  Similarity=0.321  Sum_probs=66.9

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..+.++|||+|||.++++++|+++|++||.|..+..     +|.++|||||+|.+.++|++|++. +||  ..+.|++|.
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~-l~~--~~~~gr~i~   84 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEE-KQG--AEIDGRSVS   84 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHH-TTE--EEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHH-cCC--CEECCEEEE
Confidence            455789999999999999999999999998766542     678899999999999999999999 898  788899998


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |..
T Consensus        85 V~~   87 (96)
T d1fjca_          85 LYY   87 (96)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            875

>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=99.62  E-value=5.6e-16  Score=113.46  Aligned_cols=72  Identities=25%  Similarity=0.481  Sum_probs=65.2

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      +..++|||+|||.++++++|+++|++||.|..|+++++      +|||||+|.+.++|+.|+.. +||  ..+.|+.|+|
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~-l~~--~~i~g~~l~v   86 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS-VNG--TTIEGHVVKC   86 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHH-HTT--CEETTEECEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHH-hCC--CEECCEEEEE
Confidence            44689999999999999999999999999999999876      57999999999999999999 888  7788888765


Q ss_pred             E
Q psy3930         274 T  274 (299)
Q Consensus       274 ~  274 (299)
                      .
T Consensus        87 ~   87 (96)
T d1x4ga1          87 Y   87 (96)
T ss_dssp             E
T ss_pred             E
Confidence            4

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.61  E-value=9.4e-16  Score=107.00  Aligned_cols=73  Identities=19%  Similarity=0.240  Sum_probs=64.6

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .+|||+|||+++++++|+++|+.||+|..|++++++.  ..+|||||+|.++++|++|+.  +||  ..++|++|.|..
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~--~~~--~~i~g~~i~V~~   73 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT--KTH--KVVGQNEIIVSH   73 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT--TTT--CEETTEECEEEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH--hcC--cEECCEEEEEEE
Confidence            4899999999999999999999999999999998863  345799999999999999985  677  678899988864

>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=99.61  E-value=3.5e-16  Score=112.20  Aligned_cols=77  Identities=26%  Similarity=0.253  Sum_probs=68.0

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEE-EEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTY-VSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~-v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...+|||+|||.++++++|+++|+.||.+.. +.+..+ .+|.++|+|||+|.+.++|++|++. +||  ..+.|++|.|
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~-l~~--~~l~gr~i~v   83 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVID-LND--RPIGSRKVKL   83 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHH-TTT--CEETTEECEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC-CCCCcceEEEEEEcCcHHHHHHHHH-cCC--CEECCEEEEE
Confidence            3567999999999999999999999998865 444444 4899999999999999999999999 998  7888999988


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      ++
T Consensus        84 ~l   85 (86)
T d2cqpa1          84 VL   85 (86)
T ss_dssp             EE
T ss_pred             EE
Confidence            75

>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=99.61  E-value=1.5e-15  Score=108.12  Aligned_cols=74  Identities=22%  Similarity=0.333  Sum_probs=64.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCC-CCceE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDY-QSSIL  271 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~-~g~~l  271 (299)
                      .+++++|||+|||.++++++|.++|++||+|..|++.+++     +|||||+|.+.++|.+|++. +||  ..+ +|++|
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~-l~g--~~~~~~~~i   76 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEA-LQG--FKITPTHAM   76 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHH-HTT--CBSSTTCBC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHH-hCC--cEeCCCcEE
Confidence            4567899999999999999999999999999999997653     67999999999999999999 888  444 46776


Q ss_pred             EEE
Q psy3930         272 TTT  274 (299)
Q Consensus       272 ~v~  274 (299)
                      .|.
T Consensus        77 ~v~   79 (83)
T d2b0ga1          77 KIT   79 (83)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            554

>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=99.61  E-value=3.9e-15  Score=110.50  Aligned_cols=80  Identities=21%  Similarity=0.220  Sum_probs=69.1

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ....+|||+|||+++|+++|+++|..+|.+..+.++.+..++.++|||||+|.++++|++|++  +|+  ..++|+.|.|
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~--~~~--~~i~gR~i~V   88 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK--KHK--ERIGHRYIEI   88 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT--TTT--CCSSSSCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh--hCC--CEEcceEEEE
Confidence            345679999999999999999999999988876666666689999999999999999999985  576  7789999988


Q ss_pred             Eeec
Q psy3930         274 TSRL  277 (299)
Q Consensus       274 ~~k~  277 (299)
                      ....
T Consensus        89 ~~~~   92 (104)
T d1wg5a_          89 FKSS   92 (104)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            7643

>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=99.61  E-value=6.2e-17  Score=117.47  Aligned_cols=79  Identities=18%  Similarity=0.301  Sum_probs=69.8

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|+++|++||.|..+.++.+. +|.++|||||+|.+.++|++|++  +||  ..+.|+.|.
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~-~g~~kg~afv~F~~~e~a~~Al~--~~g--~~~~g~~i~   84 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALE--LTG--LKVFGNEIK   84 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEE-EETTTTEEEEEESSHHHHHHHHH--GGG--EEETTEEEE
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecC-CCCccEEeEEeeCCHHHHHHHHh--cCC--cEECCEEEE
Confidence            3456799999999999999999999999999988887654 89999999999999999999995  688  788899998


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus        85 V~~a   88 (91)
T d1fjeb1          85 LEKP   88 (91)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            7653

>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=99.61  E-value=4.2e-16  Score=112.32  Aligned_cols=75  Identities=21%  Similarity=0.343  Sum_probs=63.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||+++|+++|+++|++||.|..|+++.     .++|||||+|.+.++|++|+.   ++  ..++|+.|.|.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~---~~--~~i~g~~l~v~   73 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG---ED--LIIKGISVHIS   73 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT---CE--EEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh---CC--CEECCEEeEEE
Confidence            467999999999999999999999999999998754     357899999999999998864   55  67889998887


Q ss_pred             eeccc
Q psy3930         275 SRLSF  279 (299)
Q Consensus       275 ~k~~~  279 (299)
                      .....
T Consensus        74 ~a~~k   78 (88)
T d1wf0a_          74 NAEPK   78 (88)
T ss_dssp             CCCCC
T ss_pred             eCCCC
Confidence            64433

>d1zh5a1 a.4.5.46 (A:5-103) Lupus La autoantigen N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: La domain
domain: Lupus La autoantigen N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=2.1e-16  Score=114.97  Aligned_cols=80  Identities=36%  Similarity=0.597  Sum_probs=73.7

Q ss_pred             HHHHHHHHHHhhhhcCCCCcchhHHHHHhhhc-CCCeeeeeeecccccccCCCCHHHHHHHHHhcCc--cccccccceee
Q psy3930         107 KQLYQQIMNLMEFYLSDSNLRKDRFFSQLLQE-SPEIEVSVFLKCNKLARLTHDPDDVVKALRKSKL--LEVTEDGTKVR  183 (299)
Q Consensus       107 ~~~~~~i~~q~efyfsd~nL~~d~fl~~~~~~-~~~~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~--~~~~~~~~~v~  183 (299)
                      ..+.+.|++|+||||||+||++|.||+.+|.. .+|++|+++++|++|++++.+.+.+..|++.+..  +++++++.+|+
T Consensus         7 ~~l~~~I~~QvEfYFSd~NL~~D~fL~~~m~~~eG~Vpl~~i~~F~r~k~l~~~~~~i~~Al~~S~~~~lev~~d~~~vR   86 (99)
T d1zh5a1           7 AALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIR   86 (99)
T ss_dssp             HHHHHHHHHHHHHHTSTTTGGGCHHHHHHHTTTTTCEEHHHHTTSHHHHHHCCCHHHHHHHHHTCSSCCEEECTTSSEEE
T ss_pred             HHHHHHHHHHHHHhcCHhhhccCHHHHHHHhcCCCcccHHHHhcchHHHHHcCCHHHHHHHHHhCCCCeEEEcCCCceeC
Confidence            67778999999999999999999999999985 6899999999999999999999999999998764  88999999998


Q ss_pred             eee
Q psy3930         184 RTV  186 (299)
Q Consensus       184 r~~  186 (299)
                      |..
T Consensus        87 R~~   89 (99)
T d1zh5a1          87 RSP   89 (99)
T ss_dssp             ECT
T ss_pred             CCC
Confidence            863

>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=99.59  E-value=1.4e-15  Score=109.53  Aligned_cols=81  Identities=19%  Similarity=0.323  Sum_probs=66.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      ..+|||+|||+++++++|+++|++|| +..+.+      +..+|||||+|.+.++|++|++. +||  ..+.|+.|.|+.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~-ln~--~~~~G~~l~V~~   74 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQM-FHQ--YSFRGKDLIVQL   74 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHH-HTT--EEETTEEEEEEE
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHH-hCC--CEECCEEEEEEE
Confidence            46899999999999999999999999 333333      33578999999999999999999 888  788999999988


Q ss_pred             ecccCCCCCCC
Q psy3930         276 RLSFGITPLGF  286 (299)
Q Consensus       276 k~~~~~~~r~~  286 (299)
                      .........++
T Consensus        75 a~~~~~~~~~p   85 (88)
T d1wg1a_          75 QPTDALLCSGP   85 (88)
T ss_dssp             CCCCCCCSCCC
T ss_pred             cCCCCCCCCCC
Confidence            65544444433

>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=99.59  E-value=2.2e-15  Score=113.13  Aligned_cols=72  Identities=28%  Similarity=0.309  Sum_probs=65.7

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .++|||+|||+++++++|+++|++||+|..|.|..      .+|||||+|.+.++|++|++. |||  ..+.|++|.|..
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~-lng--~~~~gr~l~v~~   80 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRH-LAY--SKFHHVPLYLEW   80 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHH-HTT--CBSSSSBCEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHH-HcC--CccCCCeEEEEE
Confidence            47899999999999999999999999999999854      368999999999999999999 899  788899998876


Q ss_pred             e
Q psy3930         276 R  276 (299)
Q Consensus       276 k  276 (299)
                      .
T Consensus        81 a   81 (111)
T d1whxa_          81 A   81 (111)
T ss_dssp             E
T ss_pred             C
Confidence            4

>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=99.59  E-value=3.2e-15  Score=111.87  Aligned_cols=73  Identities=23%  Similarity=0.287  Sum_probs=66.0

Q ss_pred             CcEEEEecCCC-CCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         196 ECTIYVEKLPP-EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       196 ~~~l~V~nLp~-~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      +++|||+|||+ .+++++|+++|+.||.|..|.+++++     +|||||+|.+.++|.+|++. +||  ..+.|+.|.|.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~-lng--~~l~g~~l~v~   73 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH-LNG--HKLHGKPIRIT   73 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHH-HTT--CBCSSSBCEEE
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHH-hCC--CEECCEEEEEE
Confidence            47899999966 58999999999999999999998864     68999999999999999999 898  77889999887


Q ss_pred             ee
Q psy3930         275 SR  276 (299)
Q Consensus       275 ~k  276 (299)
                      ..
T Consensus        74 ~s   75 (109)
T d2adca1          74 LS   75 (109)
T ss_dssp             CC
T ss_pred             EC
Confidence            64

>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=99.58  E-value=2.3e-15  Score=110.53  Aligned_cols=74  Identities=24%  Similarity=0.390  Sum_probs=66.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||+++++++|+++|++||+|..+.+.+       +|||||+|.+.++|++|++. |||  ..+.|+.|.|
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~-lng--~~~~g~~i~v   82 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRK-LDD--TKFRSHEGET   82 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHH-HSS--EEEECTTSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHH-hCC--CEeCCeEEEE
Confidence            3467899999999999999999999999999999864       47999999999999999999 898  7888888888


Q ss_pred             Eeec
Q psy3930         274 TSRL  277 (299)
Q Consensus       274 ~~k~  277 (299)
                      ....
T Consensus        83 ~~~~   86 (98)
T d1wg4a_          83 SYIR   86 (98)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            6643

>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=99.58  E-value=3.7e-15  Score=109.23  Aligned_cols=75  Identities=16%  Similarity=0.280  Sum_probs=63.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ++.++|||+|||+++++++|+++|++||+|..+++.++      ++||||+|.+.++|+.|++. +||..+...+++|.|
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~-l~~~~i~g~~~~l~v   87 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK-MRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHH-HTTCBCSSSSCBCEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHH-hCCCEeCCCceEEEE
Confidence            34689999999999999999999999999999998764      46999999999999999999 888544444455544


Q ss_pred             Ee
Q psy3930         274 TS  275 (299)
Q Consensus       274 ~~  275 (299)
                      ..
T Consensus        88 ~~   89 (97)
T d1whya_          88 DF   89 (97)
T ss_dssp             EE
T ss_pred             Ee
Confidence            43

>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=99.57  E-value=1.1e-15  Score=110.71  Aligned_cols=75  Identities=23%  Similarity=0.424  Sum_probs=66.3

Q ss_pred             CcEEEEecCCCCCCHHHHHH----HhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         196 ECTIYVEKLPPEAEHDYIES----VFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~----~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      +++|||+|||+++++++|++    +|++||+|..|.+.+   ++.++|||||+|.+.++|.+|++. +||  ..+.|++|
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~-~~~--~~~~g~~l   76 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRS-MQG--FPFYDKPM   76 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHH-HTT--CEETTEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHH-hCC--CEECCEEE
Confidence            58999999999999998864    689999999999865   567889999999999999999999 888  77889998


Q ss_pred             EEEee
Q psy3930         272 TTTSR  276 (299)
Q Consensus       272 ~v~~k  276 (299)
                      .|...
T Consensus        77 ~v~~a   81 (91)
T d1nu4a_          77 RIQYA   81 (91)
T ss_dssp             EEEEC
T ss_pred             EEEEe
Confidence            88653

>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=99.57  E-value=4.4e-15  Score=106.82  Aligned_cols=75  Identities=23%  Similarity=0.266  Sum_probs=64.0

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCC-CCceEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDY-QSSILT  272 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~-~g~~l~  272 (299)
                      ++.++|||+|||+++++++|+++|++||.|..+.+...    ..+|||||+|.+.++|.+|+.. +||  ..+ .|+.|+
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~-l~~--~~i~~g~~l~   80 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALID-LHN--HDLGENHHLR   80 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHH-HTT--CBSSSSCBCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHh-ccC--CEecCCCEEE
Confidence            45689999999999999999999999999988876543    3478999999999999999999 888  444 578887


Q ss_pred             EEe
Q psy3930         273 TTS  275 (299)
Q Consensus       273 v~~  275 (299)
                      |..
T Consensus        81 v~~   83 (88)
T d2adca2          81 VSF   83 (88)
T ss_dssp             EEE
T ss_pred             EEe
Confidence            754

>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=99.57  E-value=1.6e-15  Score=112.43  Aligned_cols=78  Identities=12%  Similarity=0.084  Sum_probs=67.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ...+|||+|||+++++++|+++|+.||.+..+.++....+|.++|||||+|.+.++|++|++  +||  ..++|+.|.|.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~--~n~--~~i~gr~i~V~   82 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER--LHR--KKLNGREAFVH   82 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG--GCS--EEETTEEEEEE
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh--cCC--CeECCcEEEEE
Confidence            34679999999999999999999999988764444444589999999999999999999995  687  78899999997


Q ss_pred             ee
Q psy3930         275 SR  276 (299)
Q Consensus       275 ~k  276 (299)
                      ..
T Consensus        83 ~~   84 (103)
T d2cpya1          83 VV   84 (103)
T ss_dssp             EE
T ss_pred             EC
Confidence            64

>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=99.56  E-value=5.4e-15  Score=110.51  Aligned_cols=76  Identities=20%  Similarity=0.112  Sum_probs=67.0

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      ..+|||+|||.++|+++|+++|++||.|..|.+.+++    .+|+|||+|.+.++|+.|+.. +||..+...++.+.+..
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~-ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLS-LDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHH-HHSCCSSTTCCCCEEEE
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHH-HCCCEeccCCcEEEEEe
Confidence            3579999999999999999999999999999998764    478999999999999999999 89966666788887755


Q ss_pred             e
Q psy3930         276 R  276 (299)
Q Consensus       276 k  276 (299)
                      .
T Consensus        82 s   82 (108)
T d2adba1          82 S   82 (108)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.55  E-value=4.5e-15  Score=106.75  Aligned_cols=77  Identities=22%  Similarity=0.295  Sum_probs=67.4

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      .+++++|||+|||+++++++|+++|++||.|..+.+.++      +|+|||+|.+.++|++|++. +++....+.|++|.
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~-~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNY-YSAVTPHLRNQPIY   77 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHH-HHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHH-HccCCCccCCCEEE
Confidence            456789999999999999999999999999999998865      46999999999999999997 55445888999998


Q ss_pred             EEee
Q psy3930         273 TTSR  276 (299)
Q Consensus       273 v~~k  276 (299)
                      |...
T Consensus        78 v~~s   81 (88)
T d2cq1a1          78 IQYS   81 (88)
T ss_dssp             EEEC
T ss_pred             EEEC
Confidence            7653

>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=99.54  E-value=3e-15  Score=105.71  Aligned_cols=73  Identities=19%  Similarity=0.342  Sum_probs=62.5

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEee
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSR  276 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k  276 (299)
                      .+|||+|||+++++++|+++|++||.|..+.+.+      .+|||||+|.+.++|++|++. +|| ...+.|++|.|...
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~-lng-~~~~~G~~i~V~~a   73 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIET-LSG-KVELHGKIMEVDYS   73 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHH-HTT-TCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHH-hCC-CeEECCEEEEEEEc
Confidence            4799999999999999999999999887666554      368999999999999999999 887 24578999988764


Q ss_pred             c
Q psy3930         277 L  277 (299)
Q Consensus       277 ~  277 (299)
                      .
T Consensus        74 ~   74 (80)
T d2cqha1          74 V   74 (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=99.53  E-value=9.9e-15  Score=102.74  Aligned_cols=71  Identities=24%  Similarity=0.323  Sum_probs=63.2

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      .+++|||+|+|  +|+++|+++|++||.|..|.+.++      +|||||+|.+.++|..|++. +||  ..+.|+.|.|.
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~-lng--~~~~g~~l~V~   72 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAE-LNG--TQVESVQLKVN   72 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHH-HTT--CBCSSCBCEEE
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHH-hCC--CEECCEEEEEE
Confidence            46899999996  899999999999999999998764      46999999999999999999 898  77889998776


Q ss_pred             ee
Q psy3930         275 SR  276 (299)
Q Consensus       275 ~k  276 (299)
                      ..
T Consensus        73 ~a   74 (79)
T d2bz2a1          73 IA   74 (79)
T ss_dssp             EC
T ss_pred             Ee
Confidence            53

>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=99.52  E-value=3.2e-14  Score=105.49  Aligned_cols=78  Identities=18%  Similarity=0.192  Sum_probs=68.1

Q ss_pred             CCCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         193 DVDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ....++|||+|||+++++++|.++|++||.|..+.+.++      +|+|||+|.+.++|+.|+.. +++..+.+.|++|.
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~-~~~~~~~~~g~~l~   84 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTF-AADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHH-HHHSCCBSSSSBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHH-HcCCCcEEeeEEEE
Confidence            345789999999999999999999999999999999764      57999999999999999998 54445888999998


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus        85 v~~s~   89 (104)
T d1wexa_          85 FNYST   89 (104)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            87653

>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=99.52  E-value=2e-14  Score=102.78  Aligned_cols=72  Identities=26%  Similarity=0.383  Sum_probs=63.3

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTT  274 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~  274 (299)
                      ..++|||+|||+++++++|+++|++||.+..+.+.+      ++|||||+|.+.++|..|+.. +||  ..+.|+.|.|.
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~-l~~--~~i~g~~i~V~   77 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKA-LNG--KVLDGSPIEVT   77 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHH-HSS--EEETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHH-cCC--CEECCEEEEEE
Confidence            347899999999999999999999999988777643      468999999999999999999 888  77889988765


Q ss_pred             e
Q psy3930         275 S  275 (299)
Q Consensus       275 ~  275 (299)
                      .
T Consensus        78 ~   78 (86)
T d2cpda1          78 L   78 (86)
T ss_dssp             C
T ss_pred             e
Confidence            4

>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=99.52  E-value=2.2e-14  Score=99.87  Aligned_cols=69  Identities=23%  Similarity=0.408  Sum_probs=60.6

Q ss_pred             EEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEeec
Q psy3930         199 IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTSRL  277 (299)
Q Consensus       199 l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~k~  277 (299)
                      |||+|||+++++++|+++|++|| +..+.+      +.++|||||+|.+.++|++|++. +||  ..+.|++|.|+...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~-ln~--~~~~g~~l~V~~a~   69 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINT-FHQ--SRLRERELSVQLQP   69 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHH-HTT--EESSSCEEEEEECC
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHH-hCC--ccCCCCEEEEEEeC
Confidence            79999999999999999999999 555554      34578999999999999999999 898  88889999888754

>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=99.50  E-value=1.1e-14  Score=109.61  Aligned_cols=79  Identities=23%  Similarity=0.289  Sum_probs=68.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEE
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTT  273 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v  273 (299)
                      ...++|||+|||+++|+++|+++|+.||.+..+.++.+..+|.++|+|||+|.+.++|++|++  +||  ..++|+.|.|
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~--~~~--~~i~gR~i~V   91 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC--RHK--QYMGNRFIQV   91 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT--SCS--BCSTTSCBEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH--cCC--CcCCCEEEEE
Confidence            456799999999999999999999999988765555555599999999999999999999995  688  7789999988


Q ss_pred             Eee
Q psy3930         274 TSR  276 (299)
Q Consensus       274 ~~k  276 (299)
                      ...
T Consensus        92 ~~~   94 (112)
T d1wela1          92 HPI   94 (112)
T ss_dssp             EEE
T ss_pred             EEc
Confidence            653

>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=99.50  E-value=1.6e-14  Score=106.11  Aligned_cols=78  Identities=19%  Similarity=0.207  Sum_probs=66.2

Q ss_pred             CCCCcEEEEecCCCC-CCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         193 DVDECTIYVEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~-~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ...+++|||+|||.+ +|+++|.++|++||.|..+.+.++      +|+|||+|.+.++|.+|++. ++.....+.|++|
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~-~~~~~~~~~gr~l   87 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDH-CLKKALWFQGRCV   87 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHH-HHHSCCCSSSSCC
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHH-HhcCCceECCEEE
Confidence            445789999999985 899999999999999999999865      47999999999999999985 3323388999999


Q ss_pred             EEEeec
Q psy3930         272 TTTSRL  277 (299)
Q Consensus       272 ~v~~k~  277 (299)
                      .|....
T Consensus        88 ~V~~s~   93 (99)
T d1x4fa1          88 KVDLSE   93 (99)
T ss_dssp             EEEEEC
T ss_pred             EEEEcC
Confidence            887643

>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=99.49  E-value=4.5e-16  Score=112.60  Aligned_cols=79  Identities=18%  Similarity=0.292  Sum_probs=66.2

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeec-----cCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPK-----FKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~-----~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      ++|||+|||.++++++|+++|++||.+..+.+..     +..++.++|||||+|.+.++|++|+ . +||  ..+.|++|
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~-l~g--~~~~Gr~l   77 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-A-FDG--IIFQGQSL   77 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-G-GSS--CCSSSSCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-h-hCC--cEECCEEE
Confidence            6899999999999999999999999877665532     3346788999999999999999998 5 788  88899999


Q ss_pred             EEEeeccc
Q psy3930         272 TTTSRLSF  279 (299)
Q Consensus       272 ~v~~k~~~  279 (299)
                      .|.....+
T Consensus        78 ~V~r~k~~   85 (90)
T d1u2fa_          78 KIRRPHDY   85 (90)
T ss_dssp             CCBCTTCC
T ss_pred             EECCCCCC
Confidence            88643333

>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=99.48  E-value=2.6e-14  Score=102.89  Aligned_cols=77  Identities=12%  Similarity=0.119  Sum_probs=66.7

Q ss_pred             CCCcEEEEecCCCC-CCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEE
Q psy3930         194 VDECTIYVEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILT  272 (299)
Q Consensus       194 ~~~~~l~V~nLp~~-~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~  272 (299)
                      ..+++|||+|||.. +|+++|.++|++||.|..|.+.+++      ++|||+|.+.++|..|++. +++....+.|++|.
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~-l~~~~~~~~gr~l~   78 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDY-YTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHH-HHHSCCEETTEECE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHH-HhhCCCccCCceEE
Confidence            44689999999997 7899999999999999999998753      5899999999999999997 55445889999998


Q ss_pred             EEeec
Q psy3930         273 TTSRL  277 (299)
Q Consensus       273 v~~k~  277 (299)
                      |....
T Consensus        79 V~~s~   83 (89)
T d1x4da1          79 VHLSQ   83 (89)
T ss_dssp             EEEEC
T ss_pred             EEECC
Confidence            87643

>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=99.42  E-value=4.5e-13  Score=100.61  Aligned_cols=76  Identities=14%  Similarity=0.187  Sum_probs=62.8

Q ss_pred             CCCCcE-EEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCH-HHHHHHHHhcCCCCCCCCCCce
Q psy3930         193 DVDECT-IYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK-EEAAKALELGLNPCPPDYQSSI  270 (299)
Q Consensus       193 ~~~~~~-l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~-~~A~~Al~~~lng~~~~~~g~~  270 (299)
                      .+.++. +||||||+++|+++|+++|++||+|.+|+++++      +|||||+|.++ ++|..|+.. +||..+...+..
T Consensus         7 ~~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~-~~~~~l~~~~~~   79 (113)
T d1owxa_           7 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKD-ANNGNLQLRNKE   79 (113)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHH-TTTSCBCTTSSS
T ss_pred             CCCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHH-hcCCceecCceE
Confidence            344555 599999999999999999999999999999865      57999999985 789999999 888666666666


Q ss_pred             EEEEe
Q psy3930         271 LTTTS  275 (299)
Q Consensus       271 l~v~~  275 (299)
                      +.+..
T Consensus        80 v~~~~   84 (113)
T d1owxa_          80 VTWEV   84 (113)
T ss_dssp             EEEEE
T ss_pred             EEEee
Confidence            65544

>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=99.38  E-value=2.2e-14  Score=106.32  Aligned_cols=75  Identities=20%  Similarity=0.231  Sum_probs=68.7

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      ..++|.+++.++++++|+++|++||+|..|.|+++. +|.++|+|||+|.+.++|.+|++. +||  ..++|++|.+..
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~-lng--~~~~gr~i~v~~  102 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVID-LNN--RWFNGQPIHAEL  102 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHH-HTT--CEETTEECCEEE
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHH-HCC--CEECCEEEEEEE
Confidence            357788888889999999999999999999999875 899999999999999999999999 999  888999998765

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=3e-12  Score=103.85  Aligned_cols=76  Identities=20%  Similarity=0.353  Sum_probs=66.4

Q ss_pred             CcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         196 ECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       196 ~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .++|||+|||+++|+++|+++|++||.|..+.++++..+|.++|||||+|.+.++|.+|+.. ++   ..+.++.+.+..
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~---~~~~~~~~~~~~   81 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RP---HKVDGRVVEPKR   81 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CS---CEETTEECEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cC---Ccccccchhhhh
Confidence            47999999999999999999999999999999999988999999999999999999999997 44   344455555443

>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=99.32  E-value=1.4e-12  Score=96.35  Aligned_cols=73  Identities=18%  Similarity=0.101  Sum_probs=63.4

Q ss_pred             CCcEEEEecCCCCC-C----HHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCc
Q psy3930         195 DECTIYVEKLPPEA-E----HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSS  269 (299)
Q Consensus       195 ~~~~l~V~nLp~~~-t----~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~  269 (299)
                      ..++|||+||+.++ +    +++|+.+|++||.|..+.+.+.      +++|||+|.+.++|.+|++. |||  ..+.|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~-lng--~~~~g~   74 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLR-LHK--TEFLGK   74 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHT-STT--SEETTE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHH-hcc--cccCCC
Confidence            45789999999886 3    3569999999999999998753      56999999999999999999 999  888899


Q ss_pred             eEEEEee
Q psy3930         270 ILTTTSR  276 (299)
Q Consensus       270 ~l~v~~k  276 (299)
                      +|.|...
T Consensus        75 ~l~v~~a   81 (104)
T d1weya_          75 EMKLYFA   81 (104)
T ss_dssp             ECEEECC
T ss_pred             EeEEeec
Confidence            9988653

>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=99.32  E-value=1.3e-12  Score=96.03  Aligned_cols=78  Identities=23%  Similarity=0.256  Sum_probs=61.8

Q ss_pred             CCCcEEEE--ecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceE
Q psy3930         194 VDECTIYV--EKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSIL  271 (299)
Q Consensus       194 ~~~~~l~V--~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l  271 (299)
                      .+..++||  ||||+++|+++|+++|++||.|..|.+.++      +|||||+|.+.++|.+|+.. |||..+ ..+..+
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~-lng~~i-~~~~~~   87 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVT-LNGKEV-VDDLGQ   87 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHH-TTTCEE-ECTTSC
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHH-hCCCCC-CCCCCc
Confidence            33567888  559999999999999999999999998765      46999999999999999999 898332 234444


Q ss_pred             EEEeeccc
Q psy3930         272 TTTSRLSF  279 (299)
Q Consensus       272 ~v~~k~~~  279 (299)
                      .+.+-++|
T Consensus        88 ~i~~~~~~   95 (101)
T d2cq2a1          88 KITLYLNF   95 (101)
T ss_dssp             EEECEEEE
T ss_pred             EEEEEEEe
Confidence            45444444

>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=99.30  E-value=3.1e-12  Score=89.95  Aligned_cols=72  Identities=18%  Similarity=0.305  Sum_probs=59.6

Q ss_pred             CCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCce-EEE
Q psy3930         195 DECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSI-LTT  273 (299)
Q Consensus       195 ~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~-l~v  273 (299)
                      +.+.|+|+|+|++.+++.| +.|++||+|..+++.++      +|||||+|.++++|++||+  +||  ..++|+. +.|
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~--~nG--~~~~g~~~vgV   71 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS--KDG--RIFGESIMIGV   71 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHT--TTT--CEETTTEECEE
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHh--cCC--CeECCcEEEEE
Confidence            4578999999999987655 57999999999987543      5799999999999999995  798  7888874 567


Q ss_pred             Eeec
Q psy3930         274 TSRL  277 (299)
Q Consensus       274 ~~k~  277 (299)
                      ++..
T Consensus        72 ~~~~   75 (81)
T d1wwha1          72 KPCI   75 (81)
T ss_dssp             EECC
T ss_pred             EeCC
Confidence            6643

>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=99.16  E-value=4.8e-11  Score=87.10  Aligned_cols=77  Identities=19%  Similarity=0.256  Sum_probs=64.9

Q ss_pred             CCCCcEEEEecC--CCCC---------CHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCC
Q psy3930         193 DVDECTIYVEKL--PPEA---------EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNP  261 (299)
Q Consensus       193 ~~~~~~l~V~nL--p~~~---------t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng  261 (299)
                      ....++|+|.|+  |.+.         .+++|++.|++||.|..|.++.+    ..+|+|||+|.+.++|.+|+.. +||
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~-lng   79 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQT-LDG   79 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHH-STT
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHH-hCC
Confidence            345689999998  6543         23689999999999999988754    3578999999999999999999 999


Q ss_pred             CCCCCCCceEEEEee
Q psy3930         262 CPPDYQSSILTTTSR  276 (299)
Q Consensus       262 ~~~~~~g~~l~v~~k  276 (299)
                        ..++|++|.+..-
T Consensus        80 --~~~~gr~i~v~~~   92 (99)
T d2dita1          80 --RWFGGRQITAQAW   92 (99)
T ss_dssp             --CEETTEECEEEEC
T ss_pred             --cEECCEEEEEEEe
Confidence              8899999998763

>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=99.05  E-value=1.7e-10  Score=84.87  Aligned_cols=78  Identities=22%  Similarity=0.299  Sum_probs=65.5

Q ss_pred             CCcEEEEecC--CCCC--------CHHHHHHHhhcCCceEEEEeeccCCC--CCcceEEEEEecCHHHHHHHHHhcCCCC
Q psy3930         195 DECTIYVEKL--PPEA--------EHDYIESVFSKYGKVTYVSLPKFKST--GKLKGFAFVEFSTKEEAAKALELGLNPC  262 (299)
Q Consensus       195 ~~~~l~V~nL--p~~~--------t~e~L~~~F~~~G~i~~v~i~~~~~~--g~~kg~~fV~F~~~~~A~~Al~~~lng~  262 (299)
                      +.++|.+.|+  |.+.        ..++|++.|++||.|..|.|+++..+  ....|++||+|.+.++|.+|+.. ||| 
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~-l~G-   80 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQG-LTG-   80 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHH-HSS-
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHH-HCC-
Confidence            4678999999  5443        34679999999999999999886533  34568999999999999999999 999 


Q ss_pred             CCCCCCceEEEEe
Q psy3930         263 PPDYQSSILTTTS  275 (299)
Q Consensus       263 ~~~~~g~~l~v~~  275 (299)
                       ..++|++|.+..
T Consensus        81 -r~f~gR~v~v~f   92 (104)
T d1o0pa_          81 -RKFANRVVVTKY   92 (104)
T ss_dssp             -CCSSSSCCEEEE
T ss_pred             -CEECCeEEEEEE
Confidence             899999998865

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.81  E-value=0.0021  Score=44.46  Aligned_cols=65  Identities=11%  Similarity=0.253  Sum_probs=54.1

Q ss_pred             cEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCC--cceEEEEEecCHHHHHHHHHhcCCCC
Q psy3930         197 CTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGK--LKGFAFVEFSTKEEAAKALELGLNPC  262 (299)
Q Consensus       197 ~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~--~kg~~fV~F~~~~~A~~Al~~~lng~  262 (299)
                      .+|.|+.||+..|++++.+.++..|.+.+......+.+..  .-.-|||.|.+.++.....+. .+|+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~-f~g~   68 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDR-FDGY   68 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHH-HTTC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHH-cCCc
Confidence            4789999999999999999999999999888776653322  223589999999999999998 8873

>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=96.78  E-value=0.00083  Score=46.00  Aligned_cols=72  Identities=15%  Similarity=0.274  Sum_probs=55.8

Q ss_pred             CCCCcEEEEecCCCCCC---------HHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCC
Q psy3930         193 DVDECTIYVEKLPPEAE---------HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCP  263 (299)
Q Consensus       193 ~~~~~~l~V~nLp~~~t---------~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~  263 (299)
                      .+...||.|.=..++..         ..+|.+.|+.||+|.-||++.+.        -+|+|.+-.+|.+|++  ++|  
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d~--------mwVTF~dG~SAL~al~--l~g--   79 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD--VDG--   79 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH--GGG--
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCCe--------EEEEECCcHHHHHHhc--cCC--
Confidence            34456777754433322         35778889999999999998763        8999999999999999  577  


Q ss_pred             CCCCCceEEEEee
Q psy3930         264 PDYQSSILTTTSR  276 (299)
Q Consensus       264 ~~~~g~~l~v~~k  276 (299)
                      .++.|+.|.+..+
T Consensus        80 ~~v~G~~l~It~~   92 (95)
T d1ufwa_          80 MKVKGRAVKISGP   92 (95)
T ss_dssp             SEETTEEEEEECC
T ss_pred             eEEcceEEEEecC
Confidence            8899999988764

>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=96.45  E-value=6.3e-05  Score=51.45  Aligned_cols=30  Identities=17%  Similarity=0.097  Sum_probs=26.6

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .+.++|.+|++.+++..+.++.++|.++.|
T Consensus        52 ~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          52 TSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            458999999999999999999999988754

>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=96.33  E-value=0.0001  Score=51.41  Aligned_cols=32  Identities=16%  Similarity=0.086  Sum_probs=27.7

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .+.++|..|++.+++..+.++.++|.++.+..
T Consensus        56 ~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~   87 (90)
T d2cqia1          56 YEHRDAAAALAAMNGRKILGKEVKVNWATTPS   87 (90)
T ss_dssp             SSHHHHHHHHHHHTTEEETTEEEEEEECCCTT
T ss_pred             CCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            45899999999999999999999999876543

>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=96.13  E-value=0.00023  Score=49.85  Aligned_cols=32  Identities=9%  Similarity=0.181  Sum_probs=28.0

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .+.++|.+|++.+++..+.++.++|+++.+..
T Consensus        59 ~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~   90 (93)
T d1x5ua1          59 LSEEDADYAIKIMDMIKLYGKPIRVNKASAHN   90 (93)
T ss_dssp             SSHHHHHHHHHHSSSCBCSSCBCEEEETTTTS
T ss_pred             CCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            45899999999999999999999998876543

>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=95.99  E-value=0.00026  Score=49.10  Aligned_cols=33  Identities=18%  Similarity=0.123  Sum_probs=28.4

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .+.++|..|++.+++..+.|+.++|+++.+..+
T Consensus        55 ~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~~~   87 (90)
T d1x5sa1          55 ENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   87 (90)
T ss_dssp             SSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             CCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            458999999999999999999999998775543

>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=95.97  E-value=0.00017  Score=49.13  Aligned_cols=30  Identities=27%  Similarity=0.256  Sum_probs=26.6

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .+.++|..|++.+++..+.++.++|.++.|
T Consensus        52 ~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          52 IDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            568999999999999999999999988764

>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=95.97  E-value=0.00032  Score=47.64  Aligned_cols=32  Identities=16%  Similarity=0.111  Sum_probs=26.9

Q ss_pred             CHHHHHHHHHhcCc-cccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKL-LEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~-~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|.+|++.+++ ..+.|+.++|+++.|...
T Consensus        46 ~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1          46 DQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             CHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             CHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            38999999999987 579999999998876543

>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=95.91  E-value=0.00026  Score=49.13  Aligned_cols=32  Identities=13%  Similarity=0.095  Sum_probs=27.4

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .+.++|.+|+..+++..+.++.++|.++.|..
T Consensus        55 ~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~~   86 (89)
T d2cqba1          55 ELAEDAAAAIDNMNESELFGRTIRVNLAKPMR   86 (89)
T ss_dssp             SSHHHHHHHHHHHTTEEETTEEEEEEECCCCC
T ss_pred             CCHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            44899999999999999999999998876543

>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=95.83  E-value=0.00045  Score=47.42  Aligned_cols=59  Identities=12%  Similarity=0.064  Sum_probs=39.8

Q ss_pred             HHHHHhhhcCCCe-eeeeeecc--cccccCC----CCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         130 RFFSQLLQESPEI-EVSVFLKC--NKLARLT----HDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l~~f~~F--~~i~~~~----~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .-|.+++..+|.+ .+.+...-  |.-+.+.    .+.++|..|++.+++..+.++.+.|.++.+.
T Consensus        16 ~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_          16 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             HHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             HHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            5677787777762 22332211  1111111    5689999999999999999999999987643

>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=95.81  E-value=0.00045  Score=47.06  Aligned_cols=32  Identities=9%  Similarity=-0.088  Sum_probs=27.6

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .+.++|.+|++.+++..+.++.++|..+.+..
T Consensus        49 ~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1          49 ASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             SSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            45899999999999999999999998876543

>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=95.69  E-value=0.00036  Score=48.04  Aligned_cols=31  Identities=10%  Similarity=-0.072  Sum_probs=26.8

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .+.++|.+|++.+++..+.++.++|+++.+.
T Consensus        52 ~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1          52 ETRTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             SSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CCHHHHHHHHHHhCCCEECCEEEEEEECCCc
Confidence            4589999999999999999999999887643

>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=95.67  E-value=0.00039  Score=48.22  Aligned_cols=31  Identities=13%  Similarity=0.036  Sum_probs=27.0

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .+.++|.+|++.+++..+.++.++|.++.|.
T Consensus        58 ~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~   88 (90)
T d2cq0a1          58 HRREDAARAIAGVSGFGYDHLILNVEWAKPS   88 (90)
T ss_dssp             SSHHHHHHHHHHTTTCEETTEECEEEESSCC
T ss_pred             CCHHHHHHHHHHhCCCEECCEEEEEEeeeCC
Confidence            3489999999999999999999999987654

>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=95.60  E-value=0.00035  Score=48.29  Aligned_cols=30  Identities=13%  Similarity=0.070  Sum_probs=26.5

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .+.++|.+|+..+++..+.++.++|.++.+
T Consensus        57 ~~~~~A~~A~~~lng~~l~g~~l~V~~a~~   86 (88)
T d1rk8a_          57 ETHKQALAAKEALNGAEIMGQTIQVDWCFV   86 (88)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEEESEE
T ss_pred             CCHHHHHHHHHHcCCCEECCEEEEEEEecC
Confidence            448999999999999999999999988765

>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=95.51  E-value=0.00059  Score=51.32  Aligned_cols=54  Identities=17%  Similarity=0.151  Sum_probs=39.5

Q ss_pred             HHHHHhhhcCCCe-eee-------------eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         130 RFFSQLLQESPEI-EVS-------------VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l~-------------~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .-|..++..++.+ .+.             .|+.|.       +.++|..||+.+++..+.++.++|+++.+...
T Consensus        57 ~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~-------~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~~  124 (139)
T d1u6fa1          57 VQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQ-------SGSSAQQAIAGLNGFNILNKRLKVALAASGHQ  124 (139)
T ss_dssp             HHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEES-------SHHHHHHHHHHTTTEECSSCEEEEEESSCCCC
T ss_pred             HHHHHHHHhhccccccccccccccccccceeeEEEC-------CHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            5677777777652 222             344444       48999999999999999999999998765443

>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=95.50  E-value=0.00037  Score=47.26  Aligned_cols=30  Identities=10%  Similarity=0.024  Sum_probs=26.7

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .+.++|.+|++.+++..+.++.++|+.+.|
T Consensus        51 ~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1          51 TSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            458999999999999999999999988765

>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=95.49  E-value=0.00051  Score=47.95  Aligned_cols=60  Identities=13%  Similarity=0.067  Sum_probs=38.8

Q ss_pred             HHHHHhhhcCCCee-eeeeecccccccCC----CCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         130 RFFSQLLQESPEIE-VSVFLKCNKLARLT----HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       130 ~fl~~~~~~~~~~~-l~~f~~F~~i~~~~----~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .-|..++..++.+. +.++..-+.-+.+.    .+.++|.+|+..+++..+.++.++|+++.+..
T Consensus        26 ~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~   90 (93)
T d2cq3a1          26 PDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV   90 (93)
T ss_dssp             HHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSC
T ss_pred             HHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCC
Confidence            45666776666522 22222111111111    45899999999999999999999999887543

>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=95.46  E-value=0.00073  Score=47.69  Aligned_cols=39  Identities=10%  Similarity=-0.023  Sum_probs=31.7

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      -.|+.|.+       .++|.+|++.+++..+.++.++|.++.+.+.
T Consensus        60 ~afV~f~~-------~~~a~~Ai~~l~g~~~~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          60 DATVSYED-------PPTAKAAVEWFDGKDFQGSKLKVSLARKKPP   98 (101)
T ss_dssp             EEEEEBSS-------HHHHHHHHHHHTTCEETTEECEEECSSCCCC
T ss_pred             eeeEEecC-------HHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            35666655       8999999999999999999999998775443

>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=95.44  E-value=0.00061  Score=46.89  Aligned_cols=51  Identities=14%  Similarity=0.200  Sum_probs=35.9

Q ss_pred             HHHHHhhhcCCCe---ee----eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         130 RFFSQLLQESPEI---EV----SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       130 ~fl~~~~~~~~~~---~l----~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .-|..++..++.+   .+    -.|++|.+       .++|.+||..+++..+.++.+++....+
T Consensus        15 ~~l~~~F~~~G~v~~~~i~~~g~afV~f~~-------~~~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1          15 QDLKDHMREAGDVCYADVYRDGTGVVEFVR-------KEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             THHHHHHGGGSCEEEEEECTTSEEEEEESS-------HHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             HHHHHHHhhhcccccccccccceeeEEeCC-------HHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            3466666666641   11    23455544       8999999999999999999988876543

>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=95.41  E-value=0.00033  Score=49.36  Aligned_cols=31  Identities=6%  Similarity=-0.068  Sum_probs=26.8

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .+.++|..|+..+++..+.++.++|.++.+.
T Consensus        62 ~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          62 STHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             SSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             CCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            3489999999999999999999999887653

>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=95.38  E-value=0.00075  Score=47.62  Aligned_cols=51  Identities=6%  Similarity=-0.002  Sum_probs=36.2

Q ss_pred             HHHHhhhcCCC---eee---eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         131 FFSQLLQESPE---IEV---SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       131 fl~~~~~~~~~---~~l---~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      -|..++.+++.   +.+   -.|+.|.+       .++|.+|++.+++..+.++.++|..+.+.
T Consensus        32 ~L~~~F~~~G~i~~~~i~rg~aFV~f~~-------~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          32 DVEAIFSKYGKIVGCSVHKGFAFVQYVN-------ERNARAAVAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             HHHHSSTTSSCEEEEEEETEEEEEEESS-------HHHHHHHHHTTTTCEETTEECEEEETTSC
T ss_pred             HHHHHHhhcCCEEEEEEeCCeEEEEECC-------HHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            35555555554   111   22555544       89999999999999999999999887543

>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=95.36  E-value=0.00034  Score=50.78  Aligned_cols=75  Identities=13%  Similarity=0.115  Sum_probs=49.8

Q ss_pred             HHHHHhhhcCCCe-eee----------eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccCCCCCCCcE
Q psy3930         130 RFFSQLLQESPEI-EVS----------VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQDKPDVDECT  198 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l~----------~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~~~~~~~~~  198 (299)
                      ..|..++..+|.+ .+.          .|+.|       .+.++|..|++.+++..+.++.+.|..+.+.....      
T Consensus        22 ~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f-------~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~~~~~------   88 (114)
T d2f9da1          22 EEMYDIFGKYGPIRQIRVGNTPETRGTAYVVY-------EDIFDAKNACDHLSGFNVCNRYLVVLYYNANRAFQ------   88 (114)
T ss_dssp             HHHHHHHHTTSCEEEEEEECSTTTTTEEEEEE-------SSHHHHHHHHHHHTTCEETTEECEEEECCHHHHTT------
T ss_pred             HHHHHHHhhcCCeEeecccccCCcCCeEEEEE-------CCHHHHHHHHHHhCCCEECCEEEEEEEcCCCchhh------
Confidence            4566677777652 222          34444       44899999999999999999999998765432211      


Q ss_pred             EEEecCCCCCCHHHHHHHhhcCC
Q psy3930         199 IYVEKLPPEAEHDYIESVFSKYG  221 (299)
Q Consensus       199 l~V~nLp~~~t~e~L~~~F~~~G  221 (299)
                          .......++.+..+..++|
T Consensus        89 ----~~~~~~~~~~~~~~~~~~g  107 (114)
T d2f9da1          89 ----KMDTKKKEEQLKLLKEKYG  107 (114)
T ss_dssp             ----TSCHHHHHHHHHHHHHHHC
T ss_pred             ----hhHHHHHHHHHHHHHHHhC
Confidence                1122345677888888887

>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=95.35  E-value=0.00038  Score=46.94  Aligned_cols=29  Identities=10%  Similarity=0.185  Sum_probs=25.2

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      .+.++|.+|++.+++..+.++.++|+.+.
T Consensus        49 ~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_          49 ERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             SCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            45899999999999999999999987654

>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=95.34  E-value=0.00055  Score=48.69  Aligned_cols=32  Identities=16%  Similarity=0.169  Sum_probs=27.7

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      +.++|..||+.+++..+.++.++|+++.+..+
T Consensus        69 ~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k~~  100 (102)
T d2cpza1          69 NPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND  100 (102)
T ss_dssp             SHHHHHHHHHHHTTCEETTEECEEECCCCSCC
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEEeCCCCC
Confidence            48999999999999999999999998776543

>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=95.30  E-value=0.00084  Score=47.47  Aligned_cols=38  Identities=8%  Similarity=-0.032  Sum_probs=31.6

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .|+.|.+       .++|..|++.+++..+.++.++|..+.+..+
T Consensus        63 ~fV~f~~-------~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k~~  100 (102)
T d2cpxa1          63 AFITFPN-------KEIAWQALHLVNGYKLYGKILVIEFGKNKKQ  100 (102)
T ss_dssp             EEEECSS-------HHHHHHHHHHSTTCBCSSCBCEEEECCCCSC
T ss_pred             ceEEecc-------HHHHHHHHHHhCCCEECCEEEEEEeCCCccc
Confidence            4566655       8999999999999999999999998876543

>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=95.23  E-value=0.0037  Score=41.88  Aligned_cols=31  Identities=13%  Similarity=-0.018  Sum_probs=27.0

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .+.++|..|+..+++..+.++.++|.++.+.
T Consensus        47 ~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1          47 EKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             SSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             cccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            3489999999999999999999999887643

>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=95.20  E-value=0.00072  Score=48.57  Aligned_cols=30  Identities=13%  Similarity=0.108  Sum_probs=26.2

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .+.++|.+|++.+++..+.++.+.|.++..
T Consensus        54 ~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_          54 LEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             SCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             cCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            458999999999999999999999987653

>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=95.12  E-value=0.00053  Score=48.65  Aligned_cols=31  Identities=3%  Similarity=-0.125  Sum_probs=25.9

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .+.++|.+|++.+|+..+.++.+.+....|.
T Consensus        67 ~~~~~A~~Ai~~lng~~i~gr~~~v~~~~Pl   97 (101)
T d1x5oa1          67 ESTEKCEAVIGHFNGKFIKTPPGVSAPTEPL   97 (101)
T ss_dssp             SCHHHHHHHHHHHBTCCCCCCTTSCCCSSCB
T ss_pred             CCHHHHHHHHHHhCCCEECCcCCccCCCCCc
Confidence            4589999999999999999999888665543

>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=95.10  E-value=0.00077  Score=47.54  Aligned_cols=33  Identities=15%  Similarity=0.087  Sum_probs=27.9

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .+.++|.+|++.+++..+.++.++|..+.+..+
T Consensus        58 ~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~~   90 (99)
T d1whwa_          58 MFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKE   90 (99)
T ss_dssp             SSHHHHHHHHHHTTTEESSSCEEEEEECCCCST
T ss_pred             CCHHHHHHHHHHcCCCEECCEEEEEEECCCCCc
Confidence            448999999999999999999999988775443

>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=95.09  E-value=0.00081  Score=46.91  Aligned_cols=30  Identities=10%  Similarity=-0.008  Sum_probs=26.2

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .+.++|..|++.+++..+.++.++|.++.+
T Consensus        57 ~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~~   86 (93)
T d1h2vz_          57 YSRADAENAMRYINGTRLDDRIIRTDWDAG   86 (93)
T ss_dssp             SSHHHHHHHHHHTTTSEETTEECEEEEESC
T ss_pred             CCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            448999999999999999999999988654

>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=95.09  E-value=0.00085  Score=46.87  Aligned_cols=31  Identities=10%  Similarity=-0.057  Sum_probs=26.7

Q ss_pred             CCHHHHHHHHHhc-Cccccccccceeeeeecc
Q psy3930         158 HDPDDVVKALRKS-KLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       158 ~~~~~a~~Al~~~-~~~~~~~~~~~v~r~~~~  188 (299)
                      .+.++|.+|++.+ ++..+.|+.+.|.++.+.
T Consensus        59 ~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~   90 (94)
T d2cpha1          59 ITKQDAKKAFNALCHSTHLYGRRLVLEWADSE   90 (94)
T ss_dssp             SSHHHHHHHHHHHHTCCBSSSCBCEEEECCCC
T ss_pred             CCHHHHHHHHHHccCCcEECCEEEEEEEcCCC
Confidence            4589999999987 889999999999987653

>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=95.03  E-value=0.001  Score=44.06  Aligned_cols=27  Identities=15%  Similarity=0.202  Sum_probs=22.9

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      .+.++|.+|++ +++..+.++.++|+++
T Consensus        49 ~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_          49 ESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             SCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            34889999995 8999999999999764

>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=94.99  E-value=0.00076  Score=46.06  Aligned_cols=29  Identities=24%  Similarity=0.287  Sum_probs=25.5

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      .+.++|.+|++.+++..+.++.+.|.++.
T Consensus        51 ~~~~~A~~A~~~~~~~~~~g~~i~V~~a~   79 (85)
T d2cpfa1          51 KKPEQAQKALKQLQGHTVDGHKLEVRISE   79 (85)
T ss_dssp             SSHHHHHHHHHHSTTCEETTEECEEECSS
T ss_pred             CCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            34899999999999999999999998764

>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=94.98  E-value=0.00074  Score=46.27  Aligned_cols=32  Identities=16%  Similarity=0.147  Sum_probs=27.4

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .+.++|..|+..+++..+.++.++|..+.|..
T Consensus        52 ~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~   83 (86)
T d2cpda1          52 SNREDAVEAMKALNGKVLDGSPIEVTLAKPVD   83 (86)
T ss_dssp             SSHHHHHHHHHHHSSEEETTEEEEEECCCCCC
T ss_pred             CCHHHHHHHHHHcCCCEECCEEEEEEeccCCC
Confidence            34899999999999999999999999876543

>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=94.86  E-value=0.0013  Score=46.33  Aligned_cols=54  Identities=15%  Similarity=0.184  Sum_probs=38.0

Q ss_pred             HHHHHhhhcCCCe---ee----eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         130 RFFSQLLQESPEI---EV----SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       130 ~fl~~~~~~~~~~---~l----~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .-|.+++..++.+   .+    -.|+.|.+       .++|.+||+.+|+..+.++.+++....+..+
T Consensus        30 ~~L~~~F~~~G~v~~~~i~~~g~afV~f~~-------~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~~   90 (98)
T d1wg4a_          30 QDLKDHMREAGDVCYADVQKDGMGMVEYLR-------KEDMEYALRKLDDTKFRSHEGETSYIRVYPE   90 (98)
T ss_dssp             HHHHHHHTTSSCEEEEEEETTTEEEEEESS-------HHHHHHHHHHHSSEEEECTTSCEEEEEEECC
T ss_pred             HHHHHHHHhhcccccccccccceEEEEECC-------HHHHHHHHHHhCCCEeCCeEEEEEEEecCCC
Confidence            3456666666542   11    23555544       8999999999999999999999987765443

>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=94.74  E-value=0.00086  Score=46.91  Aligned_cols=30  Identities=17%  Similarity=0.103  Sum_probs=26.5

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .+.++|..||+.+++..+.++.++|+.+.+
T Consensus        61 ~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          61 EDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             SCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            458999999999999999999999987654

>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=94.73  E-value=0.00087  Score=45.27  Aligned_cols=29  Identities=14%  Similarity=0.238  Sum_probs=25.3

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      .+.++|..|++.+++..+.++.++|.++.
T Consensus        50 ~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1          50 QQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             SSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             CCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45899999999999999999999987653

>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=94.65  E-value=0.001  Score=44.36  Aligned_cols=27  Identities=15%  Similarity=0.223  Sum_probs=22.1

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      .+.++|.+||+ +++..+.|+.+.|+++
T Consensus        49 ~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_          49 KESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             SSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            55899999996 6777899999888764

>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=94.62  E-value=0.022  Score=38.76  Aligned_cols=60  Identities=12%  Similarity=0.058  Sum_probs=39.3

Q ss_pred             HHHHHhhhcCCCe-eeeeeecccccccCC----CCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         130 RFFSQLLQESPEI-EVSVFLKCNKLARLT----HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l~~f~~F~~i~~~~----~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .-|..++..++.+ .+.+...-+.-+.+.    .+.++|.+|++.+++..+.++.++|.++.+..
T Consensus        23 ~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~   87 (89)
T d1cvja2          23 KALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK   87 (89)
T ss_dssp             HHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTT
T ss_pred             HHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            4566666666652 222222222211111    55899999999999999999999998877544

>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=94.45  E-value=0.00089  Score=45.49  Aligned_cols=25  Identities=20%  Similarity=0.299  Sum_probs=21.3

Q ss_pred             CCHHHHHHHHHhcCcccccccccee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKV  182 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v  182 (299)
                      .+.++|.+|++.+++..+.++.++|
T Consensus        59 ~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          59 ENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             SSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4489999999999999999887765

>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=94.42  E-value=0.0018  Score=46.16  Aligned_cols=50  Identities=6%  Similarity=0.062  Sum_probs=36.7

Q ss_pred             HHHHHhhhcCCCeee-e--------eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeee
Q psy3930         130 RFFSQLLQESPEIEV-S--------VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       130 ~fl~~~~~~~~~~~l-~--------~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      .-|.+++..+|.+.- .        .|+.|       .+.++|.+|++.+++..+.++.++|..+.
T Consensus        18 ~~L~~~F~~fG~I~~v~i~~~~kg~afV~f-------~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1          18 QSLFILFGVYGDVQRVKILFNKKENALVQM-------ADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             HHHHHHHHHHTCEEEEEECCTTSCCEEEEE-------SCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             HHHHHHHhhccccceEEEEecccceEEEEE-------CCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            357777777775222 2        23444       45899999999999999999999998764

>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=94.39  E-value=0.0014  Score=46.46  Aligned_cols=29  Identities=17%  Similarity=0.244  Sum_probs=25.3

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      +.++|.+|++.+++..+.++.++|.++.+
T Consensus        59 ~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_          59 DQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             CHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            48999999999999999999999987643

>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=94.38  E-value=0.0014  Score=44.71  Aligned_cols=27  Identities=11%  Similarity=0.085  Sum_probs=21.7

Q ss_pred             CCHHHHHHHHHhcCcccccc--ccceeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTE--DGTKVRR  184 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~--~~~~v~r  184 (299)
                      .+.++|.+|++.+++..+.+  +.++|++
T Consensus        56 ~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2          56 NKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             SSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            45899999999999988866  5577765

>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=94.33  E-value=0.0013  Score=46.11  Aligned_cols=31  Identities=16%  Similarity=0.067  Sum_probs=27.2

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      +.++|.+|++.+++..+.++.++|.++.+..
T Consensus        62 ~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~   92 (96)
T d1fjca_          62 SEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             SHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CHHHHHHHHHHcCCCEECCEEEEEEEeCCCC
Confidence            3899999999999999999999999877544

>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=94.15  E-value=0.071  Score=34.32  Aligned_cols=60  Identities=22%  Similarity=0.275  Sum_probs=47.8

Q ss_pred             HHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHhcCCCCCCCCCCceEEEEe
Q psy3930         210 HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALELGLNPCPPDYQSSILTTTS  275 (299)
Q Consensus       210 ~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~~lng~~~~~~g~~l~v~~  275 (299)
                      .+.|...|.++|.|..+.+.... .|..  .|-|...+..+|.-|+.. ++.  ..+++++|.|..
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~~-dg~~--~A~V~v~~~q~A~~~v~~-LhR--~KiG~KRI~Vs~   69 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPHT-DYQL--KAVVQMENLQDAIGAVNS-LHR--YKIGSKKILVSL   69 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSCC-STTC--CEEEEESSHHHHHHHHHH-HTT--EEETTEEEEEEE
T ss_pred             HHHHHHHHHhheeEEEEEEEecc-CCcE--EEEEEcCCHHHHHHHHHH-HHH--HhcCCeEEEEEE
Confidence            34566789999999999986543 4554  499999999999999999 554  777888887765

>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=94.14  E-value=0.0028  Score=45.06  Aligned_cols=27  Identities=11%  Similarity=-0.028  Sum_probs=23.7

Q ss_pred             CCHHHHHHHHHhcCccccccccceeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      .+.++|.+|+..+++..+.|+.+++..
T Consensus        76 ~~~~~A~~Ai~~lng~~~~gr~i~v~~  102 (104)
T d1jmta_          76 RREEDAEKAVIDLNNRWFNGQPIHAEL  102 (104)
T ss_dssp             SCHHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             echhHHHHHHHHHCCCEECCEEEEEEE
Confidence            348999999999999999999988764

>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=94.13  E-value=0.0022  Score=42.87  Aligned_cols=27  Identities=19%  Similarity=0.135  Sum_probs=22.1

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      .+.++|.+|++ +++..++|+.+.|+.+
T Consensus        50 ~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_          50 MDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            45789999996 6888999999888754

>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=93.97  E-value=0.0011  Score=45.96  Aligned_cols=34  Identities=21%  Similarity=0.248  Sum_probs=27.8

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .|+.|.+       .++|.+||+ +++..+.++.++|+++.+
T Consensus        57 afv~F~~-------~e~a~~Al~-~~g~~~~g~~i~V~~ak~   90 (91)
T d1fjeb1          57 GYVDFES-------AEDLEKALE-LTGLKVFGNEIKLEKPKG   90 (91)
T ss_dssp             EEEEESS-------HHHHHHHHH-GGGEEETTEEEEEECCCC
T ss_pred             eEEeeCC-------HHHHHHHHh-cCCcEECCEEEEEEecCC
Confidence            4666655       889999995 899999999999987653

>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=93.87  E-value=0.0017  Score=44.47  Aligned_cols=29  Identities=14%  Similarity=0.039  Sum_probs=24.6

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      +.++|.+|++ +++..+.++.++|..+.+.
T Consensus        57 ~~~~a~~Al~-~n~~~~~gr~l~V~~a~~k   85 (86)
T d2ghpa3          57 NKDSAERALQ-MNRSLLGNREISVSLADKK   85 (86)
T ss_dssp             SHHHHHHHGG-GTTEEETTEEEEEEECCCC
T ss_pred             CHHHHHHHHh-cCCCEECCEEEEEEEcCCC
Confidence            4889999995 8999999999999887643

>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=93.68  E-value=0.0019  Score=44.46  Aligned_cols=30  Identities=13%  Similarity=0.254  Sum_probs=25.0

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCcccccccccee
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKV  182 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v  182 (299)
                      .|++|.+       .++|.+|++.+|+..+.|+.+++
T Consensus        59 aFV~f~~-------~~~A~~Ai~~lng~~~~gr~lkv   88 (89)
T d2cpia1          59 AYVTYIR-------SEDALRAIQCVNNVVVDGRTLKA   88 (89)
T ss_dssp             EEEEESS-------HHHHHHHHHHHTTEEETTEEEEE
T ss_pred             EEEeccc-------chhHHHHHHHhCCCEECCEEEEE
Confidence            3555555       89999999999999999988876

>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=93.66  E-value=0.0024  Score=43.47  Aligned_cols=27  Identities=7%  Similarity=-0.011  Sum_probs=21.4

Q ss_pred             CCHHHHHHHHHhcCcccccccc--ceeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDG--TKVRR  184 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~--~~v~r  184 (299)
                      .+.++|.+|++.+++..+.|+.  ++|.+
T Consensus        56 ~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2          56 DKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             SSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             cCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            4589999999999999998755  55543

>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=93.50  E-value=0.0025  Score=43.39  Aligned_cols=28  Identities=18%  Similarity=0.228  Sum_probs=22.8

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      .+.++|.+|++ +++..+.|+.++|+++.
T Consensus        56 ~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          56 ATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             SSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             cCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            44899999996 47788999999998764

>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=93.18  E-value=0.041  Score=36.02  Aligned_cols=34  Identities=12%  Similarity=0.090  Sum_probs=28.9

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeee
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      .|+.|.+       .++|.+|+..+++..+.|+.++|+.+.
T Consensus        36 afv~f~~-------~~~A~~Ai~~ln~~~~~g~~l~V~~a~   69 (75)
T d1wi6a1          36 AFVTLLN-------GEQAEAAINTFHQSRLRERELSVQLQP   69 (75)
T ss_dssp             EEEEESS-------HHHHHHHHHHHTTEESSSCEEEEEECC
T ss_pred             EEEEECC-------HHHHHHHHHHhCCccCCCCEEEEEEeC
Confidence            4566655       899999999999999999999998764

>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=93.16  E-value=0.0034  Score=42.49  Aligned_cols=29  Identities=10%  Similarity=-0.014  Sum_probs=22.9

Q ss_pred             CCHHHHHHHHHhcCccccc-cccceeeeee
Q psy3930         158 HDPDDVVKALRKSKLLEVT-EDGTKVRRTV  186 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~-~~~~~v~r~~  186 (299)
                      .+.++|..|++.+++..+. +..++|.+++
T Consensus        53 ~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          53 TTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             SSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             CCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            4589999999999998885 4667887653

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.13  E-value=0.16  Score=34.89  Aligned_cols=56  Identities=21%  Similarity=0.286  Sum_probs=44.5

Q ss_pred             CCCcEEEEecCCCCCCHHHHHHHhhcCCceEEEEeeccCCCCCcceEEEEEecCHHHHHHHHHh
Q psy3930         194 VDECTIYVEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAAKALEL  257 (299)
Q Consensus       194 ~~~~~l~V~nLp~~~t~e~L~~~F~~~G~i~~v~i~~~~~~g~~kg~~fV~F~~~~~A~~Al~~  257 (299)
                      +...-||.-.+|......+|.++|+.||.|. |..+.+.       -|||.....++|+.++..
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~   68 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHH
Confidence            3445688889999999999999999999653 3333332       599999999999998876

>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=93.03  E-value=0.0038  Score=43.58  Aligned_cols=51  Identities=10%  Similarity=0.083  Sum_probs=34.3

Q ss_pred             HHHHHhhhcCCCeee-e-------eeecccccccCCCCHHHHHHHHHhcCccccccc--cceeeeeec
Q psy3930         130 RFFSQLLQESPEIEV-S-------VFLKCNKLARLTHDPDDVVKALRKSKLLEVTED--GTKVRRTVV  187 (299)
Q Consensus       130 ~fl~~~~~~~~~~~l-~-------~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~--~~~v~r~~~  187 (299)
                      .-|++++..++.+.- .       .|++|       .+.++|..|++.+++..+.+.  .++|.++.+
T Consensus        32 ~~l~~~f~~~G~i~~~~~~~~~~~afV~f-------~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~   92 (97)
T d1whya_          32 AALAREFDRFGSIRTIDHVKGDSFAYIQY-------ESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS   92 (97)
T ss_dssp             HHHHHHHHTTSCEEEEEECSSSCCEEEEE-------SSHHHHHHHHHHHTTCBCSSSSCBCEEEECCC
T ss_pred             HHHHHHHHhhcccceEeeeccccEEEecc-------CCHHHHHHHHHHhCCCEeCCCceEEEEEeCCC
Confidence            457777777765221 1       23444       448999999999999999775  467766553

>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=92.96  E-value=0.0062  Score=42.66  Aligned_cols=31  Identities=16%  Similarity=0.073  Sum_probs=24.7

Q ss_pred             CCHHHHHHHHH--hcCccccccccceeeeeecc
Q psy3930         158 HDPDDVVKALR--KSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       158 ~~~~~a~~Al~--~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .+.++|..|++  .++++.+.|+.++|..+...
T Consensus        63 ~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~   95 (99)
T d1x4fa1          63 ETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY   95 (99)
T ss_dssp             SSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             cchHHHHHHHHHHhcCCceECCEEEEEEEcCCc
Confidence            44889999997  46788899999999876543

>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=92.91  E-value=0.06  Score=37.71  Aligned_cols=30  Identities=13%  Similarity=0.051  Sum_probs=26.5

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      +.++|.+|+..+++..+.++.++|..+.+.
T Consensus        55 ~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~   84 (104)
T d1weya_          55 NPLSAADARLRLHKTEFLGKEMKLYFAQTL   84 (104)
T ss_dssp             STTHHHHHHHTSTTSEETTEECEEECCCCS
T ss_pred             CHHHHHHHHHHhcccccCCCEeEEeecccC
Confidence            379999999999999999999999887544

>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=92.85  E-value=0.0037  Score=44.29  Aligned_cols=31  Identities=13%  Similarity=0.156  Sum_probs=24.9

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .+.++|.+|+ .+++..+.|+.+.|+++.+..
T Consensus        70 ~~~~~a~~al-~~~~~~l~G~~i~V~~a~~ke  100 (103)
T d1x4ba1          70 SSMAEVDAAM-AARPHSIDGRVVEPKRAVARE  100 (103)
T ss_dssp             SSHHHHHHHH-TSCSEEETTEEEEEECCSSCC
T ss_pred             CCHHHHHHHH-HhCCCeECCEEEEEEECcccC
Confidence            4588999998 468888999999998877544

>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=92.83  E-value=0.0027  Score=43.80  Aligned_cols=30  Identities=10%  Similarity=0.070  Sum_probs=22.7

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      .+.++|.+||+..+  .++|+.+.|+++.+..
T Consensus        58 ~~~~~a~~al~~~~--~l~Gr~i~v~~a~~k~   87 (90)
T d2cqga1          58 TEYETQVKVMSQRH--MIDGRWCDCKLPNSKQ   87 (90)
T ss_dssp             SSHHHHHHHHHSCE--EETTEEEEEECCCTTC
T ss_pred             CCHHHHHHHHhcCC--ccCCEEeEEEeCCCCC
Confidence            44899999997544  6888888888776544

>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=92.82  E-value=0.0032  Score=42.06  Aligned_cols=27  Identities=30%  Similarity=0.362  Sum_probs=22.0

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      .+.+++.+|+ .+++..+.|+.++|+++
T Consensus        52 ~~~e~~~~al-~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          52 DDHDSVDKIV-IQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SSHHHHHHHH-HCSCCEETTEECEEEEC
T ss_pred             cCHHHHHHHH-HhCCCEECCEEEEEEEC
Confidence            4478888888 57999999999999765

>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=92.72  E-value=0.0019  Score=42.42  Aligned_cols=24  Identities=25%  Similarity=0.220  Sum_probs=20.4

Q ss_pred             CCHHHHHHHHHhcCccccccccce
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTK  181 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~  181 (299)
                      .+.++|.+|++.+|+..+.++.++
T Consensus        48 ~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1          48 DSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             SCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CCHHHHHHHHHHhCCCEECCEECc
Confidence            458999999999999999887654

>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=92.69  E-value=0.0031  Score=41.85  Aligned_cols=27  Identities=15%  Similarity=0.087  Sum_probs=22.1

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      .+.++|.+|+ .+++..++++.+.|.+.
T Consensus        48 ~~~~~a~~Al-~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2          48 ARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             SSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             cchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            4589999998 57888999999888653

>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=92.63  E-value=0.0043  Score=43.13  Aligned_cols=32  Identities=19%  Similarity=0.144  Sum_probs=23.9

Q ss_pred             CCHHHHHHHHHhcC------ccccccccceeeeeeccc
Q psy3930         158 HDPDDVVKALRKSK------LLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       158 ~~~~~a~~Al~~~~------~~~~~~~~~~v~r~~~~~  189 (299)
                      .+.++|.+|++.++      +..+.++.++|.++.+..
T Consensus        58 ~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k~   95 (98)
T d1x4ha1          58 MTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD   95 (98)
T ss_dssp             SSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCC
T ss_pred             cCHHHHHHHHHHcccccccCCcEECCEEEEEEECCCCC
Confidence            34899999998765      567788888888776543

>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=92.43  E-value=0.0033  Score=43.08  Aligned_cols=31  Identities=6%  Similarity=-0.049  Sum_probs=24.0

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      .+.++|.+|+.  ++..+.++.++|+++.+...
T Consensus        50 ~~~~~a~~a~~--~~~~i~g~~l~v~~a~~k~~   80 (88)
T d1wf0a_          50 ADDQIAQSLCG--EDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             SCHHHHHHTTT--CEEEETTEEEEEECCCCCCC
T ss_pred             CCHHHHHHHHh--CCCEECCEEeEEEeCCCCCC
Confidence            44788888885  67789999999988765543

>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=92.43  E-value=0.0043  Score=43.83  Aligned_cols=29  Identities=10%  Similarity=0.102  Sum_probs=23.6

Q ss_pred             CCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .+.++|.+||+.+++ .+.++.++|..+.+
T Consensus        60 ~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~   88 (103)
T d2cqda1          60 ADRAAAERACKDPNP-IIDGRKANVNLAYL   88 (103)
T ss_dssp             SSHHHHHHHHTCSSC-EETTEECEEEESTT
T ss_pred             CCHHHHHHHHHHCCC-cCCCEEEEEEEcCC
Confidence            458999999988876 68999999987653

>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=92.27  E-value=0.02  Score=39.16  Aligned_cols=36  Identities=11%  Similarity=0.161  Sum_probs=29.8

Q ss_pred             eeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecc
Q psy3930         146 VFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       146 ~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~  188 (299)
                      .|+.|.+       .++|.+|++.+++..+.++.+.|.++.+.
T Consensus        49 afV~F~~-------~~~A~~A~~~~~~~~~~g~~l~v~~ak~~   84 (91)
T d1nu4a_          49 AFVIFKE-------VSSATNALRSMQGFPFYDKPMRIQYAKTD   84 (91)
T ss_dssp             EEEEESS-------HHHHHHHHHHHTTCEETTEECEEEECSSC
T ss_pred             eEEEECC-------HHHHHHHHHHhCCCEECCEEEEEEEeCCC
Confidence            4556655       89999999999999999999999887643

>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=92.06  E-value=0.1  Score=35.07  Aligned_cols=29  Identities=7%  Similarity=0.031  Sum_probs=25.8

Q ss_pred             CHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      +.++|.+|++.+++..+.++.++|+.+.+
T Consensus        49 ~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_          49 NGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            38999999999999999999999987643

>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=91.37  E-value=0.01  Score=40.13  Aligned_cols=36  Identities=8%  Similarity=-0.001  Sum_probs=30.0

Q ss_pred             eeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeee
Q psy3930         142 IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       142 ~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      ..+..|+.|.+       .++|.+|++.+++..+.++.++|..
T Consensus        50 ~~G~afV~f~~-------~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1          50 PTGEAMVAFES-------RDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             EEEEEEEEESC-------HHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             cceEEEEEEcC-------cHHHHHHHHHcCCCEECCEEEEEEE
Confidence            44467888877       8999999999999999999988753

>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=91.26  E-value=0.0033  Score=44.36  Aligned_cols=57  Identities=9%  Similarity=0.069  Sum_probs=35.2

Q ss_pred             HHHHHhhhcCCCe-eeeeeecc--cccccCC----CCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         130 RFFSQLLQESPEI-EVSVFLKC--NKLARLT----HDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l~~f~~F--~~i~~~~----~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      .-|++++..+|.+ ++.+...-  |..+.+.    .+.++|.+|+ .+++..+.|+.++|..+.+
T Consensus        33 ~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          33 RDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             HHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCCEECCEEEEEEECCC
Confidence            4567777776653 22322211  1111111    4578899999 5899999999999987654

>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=90.88  E-value=0.032  Score=37.98  Aligned_cols=31  Identities=13%  Similarity=-0.002  Sum_probs=24.6

Q ss_pred             CCHHHHHHHHHhc--Cccccccccceeeeeecc
Q psy3930         158 HDPDDVVKALRKS--KLLEVTEDGTKVRRTVVV  188 (299)
Q Consensus       158 ~~~~~a~~Al~~~--~~~~~~~~~~~v~r~~~~  188 (299)
                      .+.++|..|++.+  ++..+.|+.++|..+.+.
T Consensus        53 ~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~   85 (89)
T d1x4da1          53 ATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   85 (89)
T ss_dssp             SSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             cchhhHHHHHHHHhhCCCccCCceEEEEECCCc
Confidence            4588999999854  678899999999887643

>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=90.34  E-value=0.0094  Score=42.33  Aligned_cols=50  Identities=10%  Similarity=0.135  Sum_probs=33.5

Q ss_pred             HHHHHhhhcCCCe-eeee---------eecccccccCCCCHHHHHHHHHhcCccccccc--cceeeeee
Q psy3930         130 RFFSQLLQESPEI-EVSV---------FLKCNKLARLTHDPDDVVKALRKSKLLEVTED--GTKVRRTV  186 (299)
Q Consensus       130 ~fl~~~~~~~~~~-~l~~---------f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~--~~~v~r~~  186 (299)
                      ..|..++..+|.+ .+.+         |+.|       .+.++|..|+..+++..+.+.  .+++..+.
T Consensus        22 ~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f-------~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~   83 (108)
T d2adba1          22 DVLHQIFSKFGTVLKIITFTKNNQFQALLQY-------ADPVSAQHAKLSLDGQNIYNACCTLRIDFSK   83 (108)
T ss_dssp             HHHHHHHTTTSCEEEEEEEEETTEEEEEEEE-------SCHHHHHHHHHHHHSCCSSTTCCCCEEEECS
T ss_pred             HHHHHHHccCCcEEEEEEEeeCCCCeEEEEE-------CCHHHHHHHHHHHCCCEeccCCcEEEEEecC
Confidence            5677788888762 2222         4444       448999999999999988654  45554443

>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=90.33  E-value=0.0055  Score=40.66  Aligned_cols=26  Identities=19%  Similarity=0.270  Sum_probs=19.7

Q ss_pred             CCHHHHHHHHHhcCccccccccceeee
Q psy3930         158 HDPDDVVKALRKSKLLEVTEDGTKVRR  184 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~~~~~v~r  184 (299)
                      .+.++|.+||+. ++..++++.+.|+.
T Consensus        49 ~~~~~a~~al~~-~~~~i~g~~i~vk~   74 (75)
T d1x0fa1          49 KEEEPVKKIMEK-KYHNVGLSKCEIKV   74 (75)
T ss_dssp             SSSHHHHHHTTC-SSCCBTTBCCEEEC
T ss_pred             CCHHHHHHHHhh-CCCEECCEEeEEEE
Confidence            458899999954 66678888877764

>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=90.31  E-value=0.011  Score=41.03  Aligned_cols=34  Identities=15%  Similarity=-0.013  Sum_probs=26.2

Q ss_pred             CCHHHHHHHHHhcC--ccccccccceeeeeecccCC
Q psy3930         158 HDPDDVVKALRKSK--LLEVTEDGTKVRRTVVVQDK  191 (299)
Q Consensus       158 ~~~~~a~~Al~~~~--~~~~~~~~~~v~r~~~~~~~  191 (299)
                      .+.++|..|++.++  ++.+.++.++|.++.|..+.
T Consensus        53 ~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~~~   88 (96)
T d2disa1          53 ESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDV   88 (96)
T ss_dssp             SSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCST
T ss_pred             cCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCCCCC
Confidence            34899999998874  45667889999998765543

>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=90.21  E-value=0.0073  Score=40.99  Aligned_cols=26  Identities=8%  Similarity=-0.041  Sum_probs=21.7

Q ss_pred             CHHHHHHHHHhcCccccccccceeeee
Q psy3930         159 DPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       159 ~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      +.++|.+|| .+++..+.++.+.|.++
T Consensus        56 ~~e~a~~al-~~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2          56 SIESAKKFV-ETPGQKYKETDLLILFK   81 (85)
T ss_dssp             CHHHHHHHH-TCCCCEETTEECEEEEG
T ss_pred             CHHHHHHHH-HHCCCEECCEEEEEEEc
Confidence            489999999 46889999999988754

>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=89.94  E-value=0.35  Score=32.09  Aligned_cols=29  Identities=14%  Similarity=0.121  Sum_probs=23.9

Q ss_pred             CCHHHHHHHHHhcCccccc-cccceeeeee
Q psy3930         158 HDPDDVVKALRKSKLLEVT-EDGTKVRRTV  186 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~-~~~~~v~r~~  186 (299)
                      .+.++|.+|+..+++..+. ++.++|..++
T Consensus        56 ~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk   85 (88)
T d2adca2          56 GSVEEAVQALIDLHNHDLGENHHLRVSFSK   85 (88)
T ss_dssp             SSHHHHHHHHHHHTTCBSSSSCBCEEEECS
T ss_pred             CCHHHHHHHHHhccCCEecCCCEEEEEeCC
Confidence            4589999999999998884 6788888764

>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=88.95  E-value=0.015  Score=39.53  Aligned_cols=30  Identities=0%  Similarity=-0.041  Sum_probs=23.0

Q ss_pred             CCHHHHHHHHHhc--Cccccccccceeeeeec
Q psy3930         158 HDPDDVVKALRKS--KLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       158 ~~~~~a~~Al~~~--~~~~~~~~~~~v~r~~~  187 (299)
                      .+.++|.+|++.+  ++..+.++.++|..+..
T Consensus        52 ~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~   83 (88)
T d2cq1a1          52 ATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH   83 (88)
T ss_dssp             SSHHHHHHHHHHHHHSCCEETTEECEEEECSC
T ss_pred             CCHHHHHHHHHHHccCCCccCCCEEEEEECCC
Confidence            3488999999854  56788999999887653

>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=88.54  E-value=0.0052  Score=42.13  Aligned_cols=26  Identities=19%  Similarity=0.238  Sum_probs=21.4

Q ss_pred             HHHHHHHHHhcCccccccccceeeeee
Q psy3930         160 PDDVVKALRKSKLLEVTEDGTKVRRTV  186 (299)
Q Consensus       160 ~~~a~~Al~~~~~~~~~~~~~~v~r~~  186 (299)
                      .++|.+|+ .+++..+.++.++|++..
T Consensus        58 ~e~a~~a~-~l~g~~~~Gr~l~V~r~k   83 (90)
T d1u2fa_          58 VDETTQAM-AFDGIIFQGQSLKIRRPH   83 (90)
T ss_dssp             CTTTTTGG-GGSSCCSSSSCCCCBCTT
T ss_pred             HHHHHHHH-hhCCcEECCEEEEECCCC
Confidence            66777888 599999999999997643

>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=88.30  E-value=0.025  Score=39.67  Aligned_cols=50  Identities=8%  Similarity=0.045  Sum_probs=32.8

Q ss_pred             HHHHhhhcCCCee-e-------eeeecccccccCCCCHHHHHHHHHhc--Cccccccccceeeeeec
Q psy3930         131 FFSQLLQESPEIE-V-------SVFLKCNKLARLTHDPDDVVKALRKS--KLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       131 fl~~~~~~~~~~~-l-------~~f~~F~~i~~~~~~~~~a~~Al~~~--~~~~~~~~~~~v~r~~~  187 (299)
                      -|..++..++.+. +       -.|+.|.+       .++|..|+..+  +.+.+.+..++|..+..
T Consensus        31 ~l~~~F~~fG~I~~~~~~~~k~~AfV~f~~-------~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~   90 (104)
T d1wexa_          31 DLVEALEKFGTICYVMMMPFKRQALVEFEN-------IDSAKECVTFAADVPVYIAGQQAFFNYSTS   90 (104)
T ss_dssp             HHHHHHTTTSCEEEEEEETTTTEEEEEESS-------HHHHHHHHHHHHHSCCBSSSSBCEEEECSS
T ss_pred             HHHHhhhhcccceEEEEEecceeEEEEeCC-------HHHHHHHHHHHcCCCcEEeeEEEEEEEcCC
Confidence            4566666665411 1       13555544       78999999865  56678899999987653

>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=86.41  E-value=0.74  Score=31.43  Aligned_cols=38  Identities=16%  Similarity=0.125  Sum_probs=28.4

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeecccC
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQD  190 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~~  190 (299)
                      -.|++|.+       .++|++|+ .+++..+.++.++|..+.+...
T Consensus        59 ~afV~f~~-------~e~a~~~~-~~~~~~~~gr~l~V~~a~~~~~   96 (104)
T d1wi8a_          59 FGYAEFED-------LDSLLSAL-SLNEESLGNKRIRVDVADQAQD   96 (104)
T ss_dssp             CEEEEESS-------HHHHHHHH-GGGTCEETTEECEEEECCCCCC
T ss_pred             eeeEEECC-------HHHHHHHH-HcCCCEECCEEEEEEECCCCCC
Confidence            45666655       67777666 6899999999999988765543

>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=85.49  E-value=0.23  Score=34.16  Aligned_cols=36  Identities=3%  Similarity=-0.123  Sum_probs=30.1

Q ss_pred             eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeec
Q psy3930         145 SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVV  187 (299)
Q Consensus       145 ~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~  187 (299)
                      -+|+.|.+       .++|.+|+..+++..+.++.+.+....+
T Consensus        59 ~~fV~f~~-------~e~A~~A~~~lng~~~~gr~i~v~~~~g   94 (99)
T d2dita1          59 VASVSFRD-------PEEADYCIQTLDGRWFGGRQITAQAWDG   94 (99)
T ss_dssp             EEEEECSC-------HHHHHHHHHHSTTCEETTEECEEEECCS
T ss_pred             EEEEEECC-------HHHHHHHHHHhCCcEECCEEEEEEEeCC
Confidence            35677766       8999999999999999999999886543

>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=84.31  E-value=0.041  Score=39.16  Aligned_cols=50  Identities=8%  Similarity=0.102  Sum_probs=30.9

Q ss_pred             HHHHHhhhcCCC---eee-----eeeecccccccCCCCHHHHHHHHHhcCccccccccceeeee
Q psy3930         130 RFFSQLLQESPE---IEV-----SVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRT  185 (299)
Q Consensus       130 ~fl~~~~~~~~~---~~l-----~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~  185 (299)
                      .-|+.++..++.   +++     ..|+.|.+      ..++|.+|+..+++..+.++...+...
T Consensus        26 e~Lk~~F~~fG~V~~v~i~~~kg~gfV~F~~------~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          26 EDLHILFSNHGEIKWIDFVRGAKEGIILFKE------KAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             HHHHHHTCSSCCEEEEECCTTCSEEEEEESS------CHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             HHHHHHHHhcCChheEEEecCCceEEEEecC------cHHHHHHHHHHhcCCceecCceEEEEe
Confidence            456666666665   222     12344422      246788899999988887777666554

>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=83.14  E-value=2.3  Score=28.82  Aligned_cols=40  Identities=13%  Similarity=0.101  Sum_probs=30.4

Q ss_pred             eeeeeeecccccccCCCCHHHHHHHHHhcCccccccccceeeeeeccc
Q psy3930         142 IEVSVFLKCNKLARLTHDPDDVVKALRKSKLLEVTEDGTKVRRTVVVQ  189 (299)
Q Consensus       142 ~~l~~f~~F~~i~~~~~~~~~a~~Al~~~~~~~~~~~~~~v~r~~~~~  189 (299)
                      -.+..|+.|.+       .++|.+|+ .+++..+.++.+.|.++.+..
T Consensus        56 ~kG~afV~F~~-------~e~a~~a~-~~~~~~i~gR~i~V~~~~~~~   95 (104)
T d1wg5a_          56 STGEAFVQFAS-------QEIAEKAL-KKHKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             BCSEEEEEESS-------HHHHHHHH-TTTTCCSSSSCCEEEEECTTT
T ss_pred             cceEEEEEeCC-------HHHHHHHH-hhCCCEEcceEEEEEECCHHH
Confidence            33456777766       78898888 478889999999998876543

>d1wfxa_ d.166.1.5 (A:) Probable RNA 2'-phosphotransferase KptA {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a+b)
fold: ADP-ribosylation
superfamily: ADP-ribosylation
family: Tpt1/KptA
domain: Probable RNA 2'-phosphotransferase KptA
species: Aeropyrum pernix [TaxId: 56636]

Probab=81.10  E-value=0.29  Score=37.67  Aligned_cols=49  Identities=12%  Similarity=0.074  Sum_probs=36.4

Q ss_pred             hhccCCCEEeeeeecchhhhhcc-CCHHHHHHHHhcCc--ceeeccCcceeecc
Q psy3930          19 LLQESPEIEVSVFLKCNKLARLT-HDPDDVVKALRKSK--LLEVTEDGTKVKGN   69 (299)
Q Consensus        19 ~~~~~~~v~~~~~~~f~~~~~~~-~~~~~i~~a~~~s~--~~~v~~~~~~vrr~   69 (299)
                      .|+.+|||+|..|+...+.+.+. .+.+.|.+.+...+  -.+++++  +||-+
T Consensus        21 ~~d~~G~v~v~dLl~~~~~~~~~~~~~~~i~~iV~~d~K~Rfel~~~--~IRA~   72 (180)
T d1wfxa_          21 RLTREGWARVSEVVEGLRKAGWSWVEEWHIVGVALHDPKGRYELRNG--EIRAR   72 (180)
T ss_dssp             CCCTTCCEEHHHHHHHHHHTTCTTCCHHHHHHHHHHCSSCCEEEETT--EEEES
T ss_pred             CcCCCCCEEHHHHHHHHHHcCCCcCcHHHHHHHHhcCCcccceecCC--EEEee
Confidence            47889999999999777666554 46777888887655  5677765  68765

>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=80.01  E-value=0.066  Score=37.27  Aligned_cols=20  Identities=15%  Similarity=0.144  Sum_probs=16.8

Q ss_pred             CCHHHHHHHHHhcCcccccc
Q psy3930         158 HDPDDVVKALRKSKLLEVTE  177 (299)
Q Consensus       158 ~~~~~a~~Al~~~~~~~~~~  177 (299)
                      .+.++|.+|+..+++..+.+
T Consensus        64 ~~~e~A~~A~~~lng~~i~~   83 (101)
T d2cq2a1          64 RTTEESKRAYVTLNGKEVVD   83 (101)
T ss_dssp             SSHHHHHHHHHHTTTCEEEC
T ss_pred             CCHHHHHHHHHHhCCCCCCC
Confidence            45899999999999987754