Psyllid ID: psy13227

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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-------
Protein Sequence
MLVESTKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVEKPEEENLEKLKFISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ
Secondary Structure (PSIPRED)
ccEEEEEEEEEEEEEEEEEcHHHHHHcccccccccccccccccccccEEccEEEEEEccccHHHccccHHHHHHcccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHccccccEEEEcccccccccccEEEEEEccHHHHHHHHHHHccccccccEEEEEEcccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEEEEEEEEEEEEccHHHHHHHcHHHHcHccccccccccccEEEccEEEEEEcccHHHHHHHHHHHcccccEEEEEEcccccccccccccccHHcccHHcccHHHccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEEcccccccEEEEEEEccHHHHHHHHHHHcccccccEEEEEEEcccccc
Coil and Loop (DISEMBL)
MLVESTKVVRTLKVEKKLVSKGIALRKHLAKygksandkpgpqsnttiigEEVHIQFISnkeevekpeeenleklkfiscrtckgahftnncpfkdsaLFLAdankkpfntvpgtnimaassddkksggpggapggpaiyvppslregpggkrvegynarrnddttairisnlsvntsenDLEDLVKqfgptskmylsrdktnglckgFAYIHFKNKADAAKAIQYLNGYGYDHLILSVdwskstnq
Flexible Loop (DISEMBL)
mlvestkvvrtlkvekklvskgiaLRKHLakygksandkpgpqsNTTIIGEEVHIQFISNKEEVEKPEEENLEKLKFISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVegynarrnddttairisnlsvntsendlEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ
Low Complexity Region (SEG)
MLVESTKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISnkeevekpeeenleklkFISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAassddkksggpggapggpaIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ
Disordered region (IsUnstruct)
********VRTLKVEKKLVSKGIALRKHL******************IIGEEVHIQFI**************EKLKFISCRTCKGAHFTNNCPFKDSALFLADANK*******************************************************************************VKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW******
Disordered Region (DISOPRED)
*LVESTKVVRTLKVEKKLVSKGIALRKHLAKYGKS*********NTTIIGEEVH*************************CRTCKGAHFTNNCPFKDS**********************************************************************IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV*WS*****
Disordered Region (DISEMBL)
MLVESTKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVEKPEEENLEKLKFISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAAS***********APGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ
Disordered Region (DISPRO)
MLVESTKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVEKPEEENLEKLKFISCRTCKGAHFTNNCPFKDSALFLADANK*********************************************************DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLVESTKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVEKPEEENLEKLKFISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ
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	247	2.2.26 [Sep-21-2011]
Q7QJV0	271	Eukaryotic translation in	yes	N/A	0.890	0.811	0.506	2e-60
Q1HQN4	272	Eukaryotic translation in	N/A	N/A	0.890	0.808	0.516	2e-59
B0VZS1	272	Eukaryotic translation in	N/A	N/A	0.898	0.816	0.5	6e-58
B4J4G8	269	Eukaryotic translation in	N/A	N/A	0.890	0.817	0.491	5e-56
B4N1L0	269	Eukaryotic translation in	N/A	N/A	0.890	0.817	0.487	8e-56
B4L710	269	Eukaryotic translation in	N/A	N/A	0.890	0.817	0.487	8e-56
B3MYX2	270	Eukaryotic translation in	N/A	N/A	0.894	0.818	0.483	1e-55
B4MA85	269	Eukaryotic translation in	N/A	N/A	0.890	0.817	0.487	1e-55
B4NTY9	269	Eukaryotic translation in	N/A	N/A	0.890	0.817	0.479	1e-55
B4I9X1	269	Eukaryotic translation in	N/A	N/A	0.890	0.817	0.479	1e-55

>sp|Q7QJV0|EIF3G_ANOGA Eukaryotic translation initiation factor 3 subunit G OS=Anopheles gambiae GN=eIF3-S4 PE=3 SV=3

 Score =  232 bits (591), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 122/241 (50%), Positives = 161/241 (66%), Gaps = 21/241 (8%)

Query: 7   KVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVEK 66
           KVVRT K+ + +V K +A RK LAK+G SA D+PGP   TT++ E+V +QFI+NKEE +K
Sbjct: 49  KVVRTYKISRVVVPKCVARRKSLAKFGDSATDRPGPNPQTTMVSEDVFMQFITNKEEEQK 108

Query: 67  PEEENLEKLK-FISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDDK 125
             E  L+ +K  + CRTC+G H++ +CP+K+SA    D   KP  T P     ++S    
Sbjct: 109 -NENALDSMKNIVKCRTCEGEHWSFHCPYKNSAY---DKPTKP-TTAPVPETTSSSK--- 160

Query: 126 KSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDL 185
                      P  YVPP ++E  G   + G   R  DDT+AIRISNLS   +E DLE+L
Sbjct: 161 -----------PGKYVPPHMKESQGKPGIGG-AMRGRDDTSAIRISNLSEAMTEADLEEL 208

Query: 186 VKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST 245
           VK+FGP +KM+LSRDK+ GLCKGFAY+HF+++ DAA AI+ LNGYGYDHLILSV+WSK  
Sbjct: 209 VKKFGPHTKMFLSRDKSTGLCKGFAYVHFRSRRDAATAIEVLNGYGYDHLILSVEWSKPQ 268

Query: 246 N 246
           N
Sbjct: 269 N 269

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. This subunit can bind 18S rRNA.
Anopheles gambiae (taxid: 7165)

>sp|Q1HQN4|EIF3G_AEDAE Eukaryotic translation initiation factor 3 subunit G OS=Aedes aegypti GN=eIF3-S4-1 PE=2 SV=1

 Score =  228 bits (582), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 126/244 (51%), Positives = 166/244 (68%), Gaps = 24/244 (9%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
            KVVRT K+ + +V K IA+RK+ +K+G S+NDKPGP   TT++ E+V++QF+SNKEE E
Sbjct: 48  VKVVRTYKITRLVVPKSIAMRKNWSKFGDSSNDKPGPNPQTTMVSEDVYMQFVSNKEE-E 106

Query: 66  KPEEENLEKLKFIS-CRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDD 124
           +  +  L+ LK I+ CR C+G H++ +CP+K +A     A  KP   VP    MA ++  
Sbjct: 107 QKSDNALDSLKNIAKCRICEGEHWSLSCPYKGTAYEAGKA--KP--VVPVQQEMAPTT-- 160

Query: 125 KKSGGPGGAPGGPAIYVPPSLREG--PGGKRVEGYNARRNDDTTAIRISNLSVNTSENDL 182
            KSG           YVPPS+R+   PG     G N R  DDTTAIRISNLS   +E DL
Sbjct: 161 AKSGK----------YVPPSMRDSQKPGM----GGNPRGRDDTTAIRISNLSEAMTEADL 206

Query: 183 EDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS 242
           E+LVK+ GP SKM+L+RDK  GLCKGFAY+HFK++ DAA AI+ LNG+GYDHLIL+V+WS
Sbjct: 207 EELVKKIGPHSKMFLARDKNTGLCKGFAYVHFKSRRDAATAIELLNGHGYDHLILNVEWS 266

Query: 243 KSTN 246
           K  N
Sbjct: 267 KPQN 270

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. This subunit can bind 18S rRNA.

Aedes aegypti (taxid: 7159)

>sp|B0VZS1|EIF3G_CULQU Eukaryotic translation initiation factor 3 subunit G OS=Culex quinquefasciatus GN=eIF3-S4 PE=3 SV=1

 Score =  224 bits (570), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 121/242 (50%), Positives = 159/242 (65%), Gaps = 20/242 (8%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
            KVVRT K+ + +V K +A RK+ AK+G SA DKPGP   TT + E++++QF+SNKEE E
Sbjct: 48  VKVVRTYKITRLVVPKSVAKRKNWAKFGDSAGDKPGPNPQTTFVSEDIYMQFVSNKEE-E 106

Query: 66  KPEEENLEKLKFIS-CRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDD 124
           +  +  L+ LK I+ CR C+G H++  CP+K ++     A  KP   VP     ++S   
Sbjct: 107 QKSDNALDSLKNIAKCRICEGEHWSVQCPYKGTSYEAGKA--KP---VPAAQPESSS--- 158

Query: 125 KKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLED 184
                   AP     YVPPS+R+    K   G N R  DDTTAIRISNLS   +E DLE+
Sbjct: 159 --------APIKSGKYVPPSMRDS--QKAALGANPRGRDDTTAIRISNLSEAMTEADLEE 208

Query: 185 LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
           LVK+ GP SKM+L+RDK  GLCKGFAY+HFK++ DAA AI+ LNG+GYDHLIL+V+WSK 
Sbjct: 209 LVKKIGPHSKMFLARDKNTGLCKGFAYVHFKSRRDAATAIELLNGHGYDHLILNVEWSKP 268

Query: 245 TN 246
            N
Sbjct: 269 QN 270

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. This subunit can bind 18S rRNA.

Culex quinquefasciatus (taxid: 7176)

>sp|B4J4G8|EI3G1_DROGR Eukaryotic translation initiation factor 3 subunit G-1 OS=Drosophila grimshawi GN=eIF3-S4-1 PE=3 SV=1

 Score =  217 bits (553), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 119/242 (49%), Positives = 156/242 (64%), Gaps = 22/242 (9%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
           TKVVRT K+ K++V K +A R+  AK+G+S NDKPGP S TT++ E++ +QFI++KE+ E
Sbjct: 48  TKVVRTYKITKQVVPKTVAKRRTWAKFGESKNDKPGPNSQTTMVSEDIIMQFINSKED-E 106

Query: 66  KPEEENLEKLKFIS-CRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDD 124
           K  +  L+  K I+ CR C G H++ NCP+K +A+               TN+M   +  
Sbjct: 107 KANDPLLDPSKNIAKCRICNGEHWSVNCPYKGTAM--------------DTNLMEKKAAA 152

Query: 125 KKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLED 184
             S        G   YVPP L++   G    G   R  DDT AIRISNLS + +E DLE+
Sbjct: 153 AASAAVDAPKSGK--YVPPFLKDSQKG----GMGIRGRDDTAAIRISNLSESMTEADLEE 206

Query: 185 LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
           LVK+ GP SKMYL+RDK  GLCKGFAY+HFK + DAA AI+ LNG+GYDHLILSV+WSK 
Sbjct: 207 LVKKIGPQSKMYLARDKNTGLCKGFAYVHFKQRKDAAAAIEILNGHGYDHLILSVEWSKP 266

Query: 245 TN 246
            N
Sbjct: 267 QN 268

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. This subunit can bind 18S rRNA.

Drosophila grimshawi (taxid: 7222)

>sp|B4N1L0|EI3G1_DROWI Eukaryotic translation initiation factor 3 subunit G-1 OS=Drosophila willistoni GN=eIF3-S4-1 PE=3 SV=1

 Score =  217 bits (552), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 118/242 (48%), Positives = 155/242 (64%), Gaps = 22/242 (9%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
           TKVVRT K+ K++V K +A R+   K+G+S NDKPGP S TT++ EE+ +QF+++KE+ E
Sbjct: 48  TKVVRTYKISKQVVPKTVAKRRTWTKFGESKNDKPGPNSQTTMVSEEIIMQFLNSKED-E 106

Query: 66  KPEEENLEKLKFIS-CRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDD 124
           K  +  L+  K I+ CR C G H++ NCP+K +A+               TN+M   +  
Sbjct: 107 KANDPLLDPSKNIAKCRICNGEHWSVNCPYKGTAM--------------DTNLMEKKAAA 152

Query: 125 KKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLED 184
             S        G   YVPP L++   G    G   R  DDT AIRISNLS + +E DLE+
Sbjct: 153 AASAAVDAPKSGK--YVPPFLKDSQKG----GMGMRGRDDTAAIRISNLSESMTEADLEE 206

Query: 185 LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
           LVK+ GP SKMYL+RDK  GLCKGFAY+HFK + DAA AI+ LNG+GYDHLILSV+WSK 
Sbjct: 207 LVKKIGPQSKMYLARDKNTGLCKGFAYVHFKQRKDAAAAIEILNGHGYDHLILSVEWSKP 266

Query: 245 TN 246
            N
Sbjct: 267 QN 268

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. This subunit can bind 18S rRNA.

Drosophila willistoni (taxid: 7260)

>sp|B4L710|EI3G1_DROMO Eukaryotic translation initiation factor 3 subunit G-1 OS=Drosophila mojavensis GN=eIF3-S4-1 PE=3 SV=1

 Score =  216 bits (551), Expect = 8e-56,   Method: Compositional matrix adjust.
 Identities = 118/242 (48%), Positives = 154/242 (63%), Gaps = 22/242 (9%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
           TKVVRT K+ K++V K +A R+   K+G S NDKPGP S TT++ EE+ +QF+++KE+ E
Sbjct: 48  TKVVRTYKISKQVVPKTVAKRRTWTKFGDSKNDKPGPNSQTTMVSEEIIMQFLNSKED-E 106

Query: 66  KPEEENLEKLKFIS-CRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDD 124
           K  +  L+  K I+ CR C G H++ NCP+K +A+               TN+M   +  
Sbjct: 107 KANDPLLDPTKNIAKCRICNGEHWSVNCPYKGTAM--------------DTNLMEKKAAA 152

Query: 125 KKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLED 184
             S        G   YVPP L++   G    G   R  DDT AIRISNLS + +E DLE+
Sbjct: 153 AASAAVDAPKSGK--YVPPFLKDSQKG----GMGMRGRDDTAAIRISNLSESMTEADLEE 206

Query: 185 LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
           LVK+ GP SKMYL+RDK  GLCKGFAY+HFK + DAA AI+ LNG+GYDHLILSV+WSK 
Sbjct: 207 LVKKIGPQSKMYLARDKNTGLCKGFAYVHFKQRKDAAAAIEILNGHGYDHLILSVEWSKP 266

Query: 245 TN 246
            N
Sbjct: 267 QN 268

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. This subunit can bind 18S rRNA.

Drosophila mojavensis (taxid: 7230)

>sp|B3MYX2|EI3G1_DROAN Eukaryotic translation initiation factor 3 subunit G-1 OS=Drosophila ananassae GN=eIF3-S4-1 PE=3 SV=1

 Score =  216 bits (550), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 117/242 (48%), Positives = 155/242 (64%), Gaps = 21/242 (8%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
           TKVVRT K+ K++V K +A R+   K+G+S NDKPGP S TT++ EE+ +QF+++KE+ E
Sbjct: 48  TKVVRTYKISKQVVPKTVAKRRTWTKFGESKNDKPGPNSQTTMVSEEIIMQFLNSKED-E 106

Query: 66  KPEEENLEKLKFIS-CRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDD 124
           K  +  L+  K I+ CR C G H++ NCP+K +A+               TN+M   +  
Sbjct: 107 KANDPLLDPTKNIAKCRICNGEHWSVNCPYKGTAM--------------DTNMMEKKATA 152

Query: 125 KKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLED 184
             +        G   YVPP L++  G     G   R  DDT AIRISNLS + +E DLE+
Sbjct: 153 AAAAAVDAPKSGK--YVPPFLKDSVGK---VGMGMRGRDDTAAIRISNLSESMTEADLEE 207

Query: 185 LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
           LVK+ GP SKMYL+RDK  GLCKGFAY+HFK + DAA AI+ LNG+GYDHLILSV+WSK 
Sbjct: 208 LVKKIGPQSKMYLARDKNTGLCKGFAYVHFKQRKDAAAAIEILNGHGYDHLILSVEWSKP 267

Query: 245 TN 246
            N
Sbjct: 268 QN 269

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. This subunit can bind 18S rRNA.

Drosophila ananassae (taxid: 7217)

>sp|B4MA85|EI3G1_DROVI Eukaryotic translation initiation factor 3 subunit G-1 OS=Drosophila virilis GN=eIF3-S4-1 PE=3 SV=1

 Score =  216 bits (550), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 118/242 (48%), Positives = 154/242 (63%), Gaps = 22/242 (9%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
           TKVVRT K+ K++V K +A R+   K+G S NDKPGP S TT++ EE+ +QF+++KE+ E
Sbjct: 48  TKVVRTYKISKQVVPKTVAKRRTWTKFGDSKNDKPGPNSQTTMVSEEIIMQFLNSKED-E 106

Query: 66  KPEEENLEKLKFIS-CRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDD 124
           K  +  L+  K I+ CR C G H++ NCP+K +A+               TN+M   +  
Sbjct: 107 KANDPLLDPSKNIAKCRICNGEHWSVNCPYKGTAM--------------DTNLMEKKAAA 152

Query: 125 KKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLED 184
             S        G   YVPP L++   G    G   R  DDT AIRISNLS + +E DLE+
Sbjct: 153 AASAAVDAPKSGK--YVPPFLKDSQKG----GMGMRGRDDTAAIRISNLSESMTEADLEE 206

Query: 185 LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
           LVK+ GP SKMYL+RDK  GLCKGFAY+HFK + DAA AI+ LNG+GYDHLILSV+WSK 
Sbjct: 207 LVKKIGPQSKMYLARDKNTGLCKGFAYVHFKQRKDAAAAIEILNGHGYDHLILSVEWSKP 266

Query: 245 TN 246
            N
Sbjct: 267 QN 268

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. This subunit can bind 18S rRNA.

Drosophila virilis (taxid: 7244)

>sp|B4NTY9|EI3G1_DROSI Eukaryotic translation initiation factor 3 subunit G-1 OS=Drosophila simulans GN=eIF3-S4-1 PE=3 SV=1

 Score =  216 bits (550), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 116/242 (47%), Positives = 154/242 (63%), Gaps = 22/242 (9%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
           TKVVRT K+ K++V K +A R+   K+G+S NDKPGP S TT++ EE+ +QF+++KE+ E
Sbjct: 48  TKVVRTYKISKQVVPKTVAKRRTWTKFGESKNDKPGPNSQTTMVSEEIFMQFLNSKED-E 106

Query: 66  KPEEENLEKLKFIS-CRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDD 124
           K  +  L+  K I+ CR C G H++ NCP+K +A+               TN+M   +  
Sbjct: 107 KANDPLLDPTKNIAKCRICNGEHWSVNCPYKGTAM--------------DTNMMEKKASA 152

Query: 125 KKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLED 184
             +        G   YVPP L++   G        R  DDT AIRISNLS + +E DLE+
Sbjct: 153 AAAAAVDAPKSGK--YVPPFLKDSQKG----ALGMRGRDDTAAIRISNLSESMTEADLEE 206

Query: 185 LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
           LVK+ GP SKMYL+RDK  GLCKGFAY+HFK + DAA AI+ LNG+GYDHLILSV+WSK 
Sbjct: 207 LVKKIGPQSKMYLARDKNTGLCKGFAYVHFKQRKDAAAAIEILNGHGYDHLILSVEWSKP 266

Query: 245 TN 246
            N
Sbjct: 267 QN 268

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. This subunit can bind 18S rRNA.

Drosophila simulans (taxid: 7240)

>sp|B4I9X1|EI3G1_DROSE Eukaryotic translation initiation factor 3 subunit G-1 OS=Drosophila sechellia GN=eIF3-S4-1 PE=3 SV=1

 Score =  216 bits (550), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 116/242 (47%), Positives = 154/242 (63%), Gaps = 22/242 (9%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
           TKVVRT K+ K++V K +A R+   K+G+S NDKPGP S TT++ EE+ +QF+++KE+ E
Sbjct: 48  TKVVRTYKISKQVVPKTVAKRRTWTKFGESKNDKPGPNSQTTMVSEEIFMQFLNSKED-E 106

Query: 66  KPEEENLEKLKFIS-CRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDD 124
           K  +  L+  K I+ CR C G H++ NCP+K +A+               TN+M   +  
Sbjct: 107 KANDPLLDPTKNIAKCRICNGEHWSVNCPYKGTAM--------------DTNMMEKKASA 152

Query: 125 KKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLED 184
             +        G   YVPP L++   G        R  DDT AIRISNLS + +E DLE+
Sbjct: 153 AAAAAVDAPKSGK--YVPPFLKDSQKG----ALGMRGRDDTAAIRISNLSESMTEADLEE 206

Query: 185 LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
           LVK+ GP SKMYL+RDK  GLCKGFAY+HFK + DAA AI+ LNG+GYDHLILSV+WSK 
Sbjct: 207 LVKKIGPQSKMYLARDKNTGLCKGFAYVHFKQRKDAAAAIEILNGHGYDHLILSVEWSKP 266

Query: 245 TN 246
            N
Sbjct: 267 QN 268

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome. This subunit can bind 18S rRNA.

Drosophila sechellia (taxid: 7238)

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	247
332376328	287	unknown [Dendroctonus ponderosae]	0.910	0.783	0.552	4e-65
242019535	288	eukaryotic translation initiation factor	0.906	0.777	0.538	5e-64
270013801	281	hypothetical protein TcasGA2_TC012449 [T	0.890	0.782	0.532	4e-63
383849126	285	PREDICTED: eukaryotic translation initia	0.927	0.803	0.524	2e-62
307179319	287	Eukaryotic translation initiation factor	0.919	0.790	0.511	1e-61
110761892	285	PREDICTED: eukaryotic translation initia	0.919	0.796	0.511	5e-61
340722601	285	PREDICTED: eukaryotic translation initia	0.919	0.796	0.511	9e-61
340722603	283	PREDICTED: eukaryotic translation initia	0.919	0.802	0.511	1e-60
350418617	285	PREDICTED: eukaryotic translation initia	0.919	0.796	0.507	2e-60
332022427	287	Eukaryotic translation initiation factor	0.919	0.790	0.507	2e-60

>gi|332376328|gb|AEE63304.1| unknown [Dendroctonus ponderosae]

 Score =  253 bits (647), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 137/248 (55%), Positives = 172/248 (69%), Gaps = 23/248 (9%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
            K++RT K+EK++VSK IALRK   K+G+SA DK GP   TTI+GE+V++QFIS+KEE  
Sbjct: 54  VKIIRTYKIEKRIVSKSIALRKTWKKFGESAGDKFGPNPATTIVGEDVYMQFISSKEEDM 113

Query: 66  KPEEENLEKLK------FISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMA 119
           KPE+E +EKLK       + CRTC   H+T  CP+KD+ L  AD  K P         MA
Sbjct: 114 KPEDEGIEKLKGLGDKNVVKCRTCGNDHWTTKCPWKDTVL--ADDKKPP---------MA 162

Query: 120 ASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYN-ARRNDDTTAIRISNLSVNTS 178
           A +    +GG   +  G + YVPPSLR+G G KR +G N  +R+D+  AIRI+NLS +T+
Sbjct: 163 AGA----AGGSEPSKPGGSKYVPPSLRDG-GAKRSDGANMGKRDDNYCAIRIANLSGSTT 217

Query: 179 ENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS 238
           + DLE+LVK FGP  K+YL++DK  GLCKGFAYIHFK KADAA AI  LNGYGYDHLIL 
Sbjct: 218 DIDLEELVKPFGPIHKLYLAKDKQTGLCKGFAYIHFKFKADAANAITLLNGYGYDHLILQ 277

Query: 239 VDWSKSTN 246
           VDWSK  N
Sbjct: 278 VDWSKPVN 285

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242019535|ref|XP_002430216.1| eukaryotic translation initiation factor 3 subunit, putative [Pediculus humanus corporis] gi|212515312|gb|EEB17478.1| eukaryotic translation initiation factor 3 subunit, putative [Pediculus humanus corporis]

 Score =  249 bits (637), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 132/245 (53%), Positives = 165/245 (67%), Gaps = 21/245 (8%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
            KVVRT K+EK++VSK IA RK   K+G SA+DKPGP   TT++ E++ +QF+SNKEE +
Sbjct: 51  VKVVRTYKIEKRIVSKTIAARKTWPKFGASADDKPGPNPATTVVSEDIFMQFVSNKEEQD 110

Query: 66  KPEEENLEKLK------FISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMA 119
           K EE++L+KLK       + CRTC G H+T  CPFKD+       NK+       T+IM 
Sbjct: 111 KLEEDSLDKLKSLGEKGVVKCRTCSGEHWTTKCPFKDTGYI--PGNKQDM----VTSIMG 164

Query: 120 ASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSE 179
              DDKK  G        + YVPPSLREG G KR +    +  D   AIRISNLS +T E
Sbjct: 165 NQMDDKKPSG--------SKYVPPSLREG-GNKRGDSMQTQHKDINFAIRISNLSESTQE 215

Query: 180 NDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV 239
           +DLEDL+K FGP  K++L++DK   LCKGFAYIHFKNK DAA AI+ LNG+GYDHLIL+V
Sbjct: 216 SDLEDLIKYFGPVQKIFLAKDKQTQLCKGFAYIHFKNKEDAASAIKGLNGHGYDHLILNV 275

Query: 240 DWSKS 244
           DWS S
Sbjct: 276 DWSTS 280

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270013801|gb|EFA10249.1| hypothetical protein TcasGA2_TC012449 [Tribolium castaneum]

 Score =  247 bits (630), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 131/246 (53%), Positives = 166/246 (67%), Gaps = 26/246 (10%)

Query: 7   KVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVEK 66
           K+VRT K+EK++VSK IA RK   K+G+ ANDKPGP   TTI+ E+V++Q+I++KEE  K
Sbjct: 49  KIVRTYKIEKRVVSKSIAFRKTWKKFGECANDKPGPNPATTIVAEDVYMQYITSKEEDNK 108

Query: 67  PEEENLEKLK------FISCRTCKGAHFTNNCPFKDSALF---LADANKKPFNTVPGTNI 117
            E++ LEKLK       + CRTC G H+T+ CP+KD+ L    + D  K P   VP    
Sbjct: 109 QEDDALEKLKALGDKNVVKCRTCSGDHWTSKCPWKDTMLAGGKVPDDKKGP--AVP---- 162

Query: 118 MAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNT 177
                    SG   G  GG + Y+PPSLR+G   ++ +  N  R DD TAIRI+NLS +T
Sbjct: 163 ---------SGSDAGKAGG-SKYIPPSLRDG-AVRKSDNLNMARRDDATAIRITNLSEST 211

Query: 178 SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLIL 237
           +E DLEDLVK FGP  K+YL++DK  G CKGFAYIHFK K DAAKAI  LNG+GYDHLIL
Sbjct: 212 TETDLEDLVKPFGPIQKLYLAKDKQAGYCKGFAYIHFKFKNDAAKAISMLNGHGYDHLIL 271

Query: 238 SVDWSK 243
           +VDWSK
Sbjct: 272 TVDWSK 277

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383849126|ref|XP_003700197.1| PREDICTED: eukaryotic translation initiation factor 3 subunit G-like [Megachile rotundata]

 Score =  244 bits (624), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 131/250 (52%), Positives = 166/250 (66%), Gaps = 21/250 (8%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
            KVVRT K+E+++VSK IA RK+ AK+G SA+D+PGP   TT+ GE+V +QFIS+KEE  
Sbjct: 47  VKVVRTYKIERRVVSKTIAARKNWAKFGDSADDRPGPNPATTVGGEDVFMQFISSKEEEN 106

Query: 66  KPEEENLEKLK------FISCRTCKGAHFTNNCPFKDSALFLADA--NKKPFNTVPGTNI 117
           K EE+NL+KLK       + CR C G H+T+ CP+KD+ L       +KKP  T   T  
Sbjct: 107 KVEEDNLDKLKNMGDKGVVKCRNCNGDHWTSKCPYKDTVLAGGKVPDDKKPLTT---TGA 163

Query: 118 MAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNT 177
             A +D K  G         + YVPP +R+G   KR +    +R DDTTAIRISNLS +T
Sbjct: 164 PGAMTDLKPQG---------SKYVPPGMRDG-ANKRGDSMQMQRRDDTTAIRISNLSEST 213

Query: 178 SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLIL 237
           ++ DL++LVK FG   K YL++DK   LCKGFAY+HFK KADA KAI  LNGYGYDHLIL
Sbjct: 214 TDADLDELVKPFGSVLKFYLAKDKQTNLCKGFAYVHFKYKADAGKAISRLNGYGYDHLIL 273

Query: 238 SVDWSKSTNQ 247
           +VDWSK   Q
Sbjct: 274 NVDWSKPQQQ 283

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307179319|gb|EFN67683.1| Eukaryotic translation initiation factor 3 subunit G [Camponotus floridanus]

 Score =  242 bits (617), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 129/252 (51%), Positives = 172/252 (68%), Gaps = 25/252 (9%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
            KVVRT K+E+++VSK IA RK+ AK+G S +D+PGP   TT+IGE+V +QFIS+KEE  
Sbjct: 49  VKVVRTYKIERRIVSKTIAARKNWAKFGDSVDDRPGPNPATTVIGEDVFMQFISSKEEEN 108

Query: 66  KPEEENLEKLK------FISCRTCKGAHFTNNCPFKDSALF---LADANKKPFNT-VPGT 115
           K EE++L+KLK       + CR C G H+T+ CP+KD+ L    + D  K   NT VPG 
Sbjct: 109 KVEEDSLDKLKSMGDKGVVKCRNCNGDHWTSKCPYKDTVLAGGKVPDDKKPLVNTGVPG- 167

Query: 116 NIMAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSV 175
               A ++ K  GG          YVPP +R+G G KR +    +R DDTTAIRISNLS 
Sbjct: 168 ----AMAELKPQGGK---------YVPPGMRDG-GNKRGDSMQMQRRDDTTAIRISNLSQ 213

Query: 176 NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHL 235
           +T++ DL++LVK FG   K +L+++K + LCKGFAY+HFK++ADAA+AI  L+GYGYDHL
Sbjct: 214 STTDADLDELVKPFGSVVKQFLAKEKLSNLCKGFAYVHFKHRADAARAIATLDGYGYDHL 273

Query: 236 ILSVDWSKSTNQ 247
           ILSV+WSK   Q
Sbjct: 274 ILSVEWSKPQAQ 285

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110761892|ref|XP_391934.3| PREDICTED: eukaryotic translation initiation factor 3 subunit G-like [Apis mellifera] gi|380027326|ref|XP_003697378.1| PREDICTED: eukaryotic translation initiation factor 3 subunit G-like [Apis florea]

 Score =  240 bits (612), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 129/252 (51%), Positives = 166/252 (65%), Gaps = 25/252 (9%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
            KVVRT K+E+++VSK IA RK+ AK+G SA+D+PGP   TT+ GE+V +QFIS+KEE  
Sbjct: 47  VKVVRTYKIERRVVSKTIAARKNWAKFGDSADDRPGPNPATTVGGEDVFMQFISSKEEEN 106

Query: 66  KPEEENLEKLK------FISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMA 119
           K EE+ LEKLK       + CR C G H+T+ CP+KD+ L      K P +  P  N   
Sbjct: 107 KVEEDTLEKLKNMGDKGVVKCRNCNGDHWTSKCPYKDTVLA---GGKVPDDKKPLVN--- 160

Query: 120 ASSDDKKSGGPGGA----PGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSV 175
                  +G PG      P G + Y+PP +R+G G KR +    +R DDTTAIRISNLS 
Sbjct: 161 -------TGAPGTMTELKPQG-SKYIPPGMRDG-GSKRGDSMQMQRRDDTTAIRISNLSE 211

Query: 176 NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHL 235
           +T++ DL++LVK FG   K YL++DK   LCKGFAY+HFK + +AAKAI  LNGYGYDHL
Sbjct: 212 STTDADLDELVKPFGSVLKFYLAKDKQTNLCKGFAYVHFKYRMEAAKAIATLNGYGYDHL 271

Query: 236 ILSVDWSKSTNQ 247
           IL+VDWSK   Q
Sbjct: 272 ILNVDWSKPQQQ 283

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340722601|ref|XP_003399692.1| PREDICTED: eukaryotic translation initiation factor 3 subunit G-like isoform 1 [Bombus terrestris]

 Score =  239 bits (609), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 129/252 (51%), Positives = 166/252 (65%), Gaps = 25/252 (9%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
            KVVRT K+E+++VSK IA RK+ AK+G SA+D+PGP   TT+ GE+V +QFIS+KEE  
Sbjct: 47  VKVVRTYKIERRVVSKTIAARKNWAKFGDSADDRPGPNPATTVGGEDVFMQFISSKEEEN 106

Query: 66  KPEEENLEKLK------FISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMA 119
           K EE++L+KLK       + CR C G H+T+ CP+KD+ L      K P +  P  N  A
Sbjct: 107 KVEEDSLDKLKSMGDKGVVKCRNCNGDHWTSKCPYKDTVLA---GGKVPDDKKPLINTSA 163

Query: 120 ASSDDKKSGGPGGA----PGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSV 175
                     PG      P G + Y+PP +R+G G KR +    +R DDTTAIRISNLS 
Sbjct: 164 ----------PGAMTELKPQG-SKYIPPGMRDG-GSKRGDSMQMQRRDDTTAIRISNLSE 211

Query: 176 NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHL 235
           +T++ DL++LVK FG   K YL++DK   LCKGFAY+HFK K +AAKAI  LNGYGYDHL
Sbjct: 212 STTDADLDELVKPFGSVLKFYLAKDKQTNLCKGFAYVHFKYKMEAAKAIATLNGYGYDHL 271

Query: 236 ILSVDWSKSTNQ 247
           IL+VDWSK   Q
Sbjct: 272 ILNVDWSKPQQQ 283

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340722603|ref|XP_003399693.1| PREDICTED: eukaryotic translation initiation factor 3 subunit G-like isoform 2 [Bombus terrestris]

 Score =  238 bits (608), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 129/252 (51%), Positives = 166/252 (65%), Gaps = 25/252 (9%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
            KVVRT K+E+++VSK IA RK+ AK+G SA+D+PGP   TT+ GE+V +QFIS+KEE  
Sbjct: 45  VKVVRTYKIERRVVSKTIAARKNWAKFGDSADDRPGPNPATTVGGEDVFMQFISSKEEEN 104

Query: 66  KPEEENLEKLK------FISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMA 119
           K EE++L+KLK       + CR C G H+T+ CP+KD+ L      K P +  P  N  A
Sbjct: 105 KVEEDSLDKLKSMGDKGVVKCRNCNGDHWTSKCPYKDTVLA---GGKVPDDKKPLINTSA 161

Query: 120 ASSDDKKSGGPGGA----PGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSV 175
                     PG      P G + Y+PP +R+G G KR +    +R DDTTAIRISNLS 
Sbjct: 162 ----------PGAMTELKPQG-SKYIPPGMRDG-GSKRGDSMQMQRRDDTTAIRISNLSE 209

Query: 176 NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHL 235
           +T++ DL++LVK FG   K YL++DK   LCKGFAY+HFK K +AAKAI  LNGYGYDHL
Sbjct: 210 STTDADLDELVKPFGSVLKFYLAKDKQTNLCKGFAYVHFKYKMEAAKAIATLNGYGYDHL 269

Query: 236 ILSVDWSKSTNQ 247
           IL+VDWSK   Q
Sbjct: 270 ILNVDWSKPQQQ 281

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350418617|ref|XP_003491916.1| PREDICTED: eukaryotic translation initiation factor 3 subunit G-like isoform 1 [Bombus impatiens]

 Score =  238 bits (607), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 128/252 (50%), Positives = 166/252 (65%), Gaps = 25/252 (9%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
            KVVRT K+E+++VSK IA RK+ AK+G SA+D+PGP   TT+ GE+V +QFIS+KEE  
Sbjct: 47  VKVVRTYKIERRVVSKTIAARKNWAKFGDSADDRPGPNPATTVGGEDVFMQFISSKEEEN 106

Query: 66  KPEEENLEKLK------FISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMA 119
           K EE++L+KLK       + CR C G H+T+ CP+KD+ L      K P +  P  N  A
Sbjct: 107 KVEEDSLDKLKSMGDKGVVKCRNCNGDHWTSKCPYKDTVLA---GGKVPDDKKPLINTSA 163

Query: 120 ASSDDKKSGGPGGA----PGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSV 175
                     PG      P G + Y+PP +R+G G KR +    +R DDTTAIRISNLS 
Sbjct: 164 ----------PGAMTELKPQG-SKYIPPGMRDG-GSKRGDSMQMQRRDDTTAIRISNLSE 211

Query: 176 NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHL 235
           +T++ DL++LVK FG   K YL++DK   LCKGFAY+HFK + +AAKAI  LNGYGYDHL
Sbjct: 212 STTDADLDELVKPFGSVLKFYLAKDKQTNLCKGFAYVHFKYRVEAAKAIATLNGYGYDHL 271

Query: 236 ILSVDWSKSTNQ 247
           IL+VDWSK   Q
Sbjct: 272 ILNVDWSKPQQQ 283

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332022427|gb|EGI62735.1| Eukaryotic translation initiation factor 3 subunit G [Acromyrmex echinatior]

 Score =  238 bits (607), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 128/252 (50%), Positives = 171/252 (67%), Gaps = 25/252 (9%)

Query: 6   TKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVE 65
            KVVR  K+E+++VSK IA RK+ AK+G SA+D+PGP   TT+ GE+V +QFIS+KEE  
Sbjct: 49  VKVVRAYKIERRIVSKTIAARKNWAKFGDSADDRPGPNPATTVGGEDVFMQFISSKEEEN 108

Query: 66  KPEEENLEKLK------FISCRTCKGAHFTNNCPFKDSALF---LADANKKPFNT-VPGT 115
           K EE++L+KLK       + CR C G H+T+ CP+KD+ L    + D  K   NT VPG 
Sbjct: 109 KVEEDSLDKLKSMGDKGVVKCRNCNGDHWTSKCPYKDTVLAGGKVPDDKKPLVNTGVPG- 167

Query: 116 NIMAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSV 175
               A ++ K  GG          YVPP +R+G G KR +    +R DDTTAIRISNLS 
Sbjct: 168 ----AMAELKPQGGK---------YVPPGMRDG-GNKRGDSMQMQRRDDTTAIRISNLSQ 213

Query: 176 NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHL 235
           +T++ DL++LVK FG   K +L+++K + LCKGFAY+HFK++ADAA+AI  L+GYGYDHL
Sbjct: 214 STTDADLDELVKPFGSVVKQFLAKEKLSNLCKGFAYVHFKHRADAARAIATLDGYGYDHL 273

Query: 236 ILSVDWSKSTNQ 247
           ILSV+WSK   Q
Sbjct: 274 ILSVEWSKPQAQ 285

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	247
FB|FBgn0029629	269	CG8636 [Drosophila melanogaste	0.417	0.382	0.626	4.2e-51
FB|FBgn0038796	273	CG10881 [Drosophila melanogast	0.910	0.824	0.433	1.2e-47
ZFIN|ZDB-GENE-040426-1076	293	eif3g "eukaryotic translation	0.429	0.361	0.518	2.2e-42
UNIPROTKB|Q6DJI8	308	eif3g-a "Eukaryotic translatio	0.429	0.344	0.541	3.6e-42
UNIPROTKB|Q28CY2	310	eif3g "Eukaryotic translation	0.429	0.341	0.541	5.9e-42
UNIPROTKB|Q641B2	308	eif3g-b "Eukaryotic translatio	0.429	0.344	0.541	7.5e-42
UNIPROTKB|F2Z4J5	320	EIF3G "Eukaryotic translation	0.429	0.331	0.532	7.5e-42
UNIPROTKB|Q3ZC12	320	EIF3G "Eukaryotic translation	0.429	0.331	0.532	7.5e-42
UNIPROTKB|E2RGG6	320	EIF3G "Eukaryotic translation	0.429	0.331	0.532	7.5e-42
UNIPROTKB|O75821	320	EIF3G "Eukaryotic translation	0.429	0.331	0.532	7.5e-42

FB|FBgn0029629 CG8636 [Drosophila melanogaster (taxid:7227)]

 Score = 342 (125.4 bits), Expect = 4.2e-51, Sum P(2) = 4.2e-51
 Identities = 67/107 (62%), Positives = 79/107 (73%)

Query:   140 YVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSR 199
             YVPP L++   G        R  DDT AIRISNLS + +E DLE+LVK+ GP SKMYL+R
Sbjct:   166 YVPPFLKDSQKG----ALGMRGRDDTAAIRISNLSESMTEADLEELVKKIGPQSKMYLAR 221

Query:   200 DKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTN 246
             DK  GLCKGFAY+HFK + DAA AI+ LNG+GYDHLILSV+WSK  N
Sbjct:   222 DKNTGLCKGFAYVHFKQRKDAAAAIEILNGHGYDHLILSVEWSKPQN 268

GO:0006413 "translational initiation" evidence=ISS

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0003729 "mRNA binding" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0000022 "mitotic spindle elongation" evidence=IMP

GO:0007067 "mitosis" evidence=IMP

FB|FBgn0038796 CG10881 [Drosophila melanogaster (taxid:7227)]

 Score = 498 (180.4 bits), Expect = 1.2e-47, P = 1.2e-47
 Identities = 105/242 (43%), Positives = 144/242 (59%)

Query:     4 ESTKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISXXXX 63
             +  KVVRT K+EK++V K +A R++  K+G S +DKPGP S TT+  EE+ +QFI     
Sbjct:    44 KKVKVVRTFKIEKQIVPKAVARRRNWVKFGDSRSDKPGPNSQTTMASEEIFMQFIGSKDF 103

Query:    64 XXXXXXXXXXXXXFISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAXXXX 123
                             CR C G H++ NCP+K +++   D+      TV  T   A    
Sbjct:   104 DQTHETQLDPGKNIAKCRICNGEHWSVNCPYKGTSM---DSK-----TVMETKANAAAAA 155

Query:   124 XXXXXXXXXXXXXXXIYVPPSLREGPG--GKRVEGYNARRNDDTTAIRISNLSVNTSEND 181
                             YVPP +++G G  G +  G   R  DD++A+RISNLS + +E D
Sbjct:   156 AISDPSKTGK------YVPPFMKDGGGISGSKNWG-RGRDRDDSSAVRISNLSESMTETD 208

Query:   182 LEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW 241
             LE+LVK+ GP +KMYL+R+K +GLCKGFAY+HFK + DAA AI+ LNG+GYDHLIL V+W
Sbjct:   209 LEELVKKIGPHTKMYLAREKNSGLCKGFAYVHFKFRQDAAAAIEVLNGHGYDHLILCVEW 268

Query:   242 SK 243
             SK
Sbjct:   269 SK 270

GO:0003729 "mRNA binding" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0006413 "translational initiation" evidence=ISS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ZFIN|ZDB-GENE-040426-1076 eif3g "eukaryotic translation initiation factor 3, subunit G" [Danio rerio (taxid:7955)]

 Score = 290 (107.1 bits), Expect = 2.2e-42, Sum P(2) = 2.2e-42
 Identities = 56/108 (51%), Positives = 78/108 (72%)

Query:   140 YVPPSLREGPGGKRVEGYNA-RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLS 198
             YVPPSLR+G G +R E     RR DD   IR++NLS +T E DL++L + FG  S++YL+
Sbjct:   186 YVPPSLRDG-GTRRGESMQPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLA 244

Query:   199 RDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTN 246
             +DK  G  KGFA+I F  + DAA+AI  ++G+GYDHLIL+V+W+K +N
Sbjct:   245 KDKNTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSN 292

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006413 "translational initiation" evidence=IEA;ISS

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=IEA;ISS

GO:0005737 "cytoplasm" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006412 "translation" evidence=IEA

UNIPROTKB|Q6DJI8 eif3g-a "Eukaryotic translation initiation factor 3 subunit G-A" [Xenopus laevis (taxid:8355)]

 Score = 297 (109.6 bits), Expect = 3.6e-42, Sum P(2) = 3.6e-42
 Identities = 59/109 (54%), Positives = 80/109 (73%)

Query:   140 YVPPSLREGPGGKRVEGYNA-RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLS 198
             YVPPSLR+G G +R E     RR DD   IR++NLS +T E DL++L + FG  S++YL+
Sbjct:   201 YVPPSLRDG-GSRRGESMQPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLA 259

Query:   199 RDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK-STN 246
             +DKT G  KGFA+I F  + DAA+AI  ++G+GYDHLIL+V+W+K STN
Sbjct:   260 KDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTN 308

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0006413 "translational initiation" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

UNIPROTKB|Q28CY2 eif3g "Eukaryotic translation initiation factor 3 subunit G" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 297 (109.6 bits), Expect = 5.9e-42, Sum P(2) = 5.9e-42
 Identities = 59/109 (54%), Positives = 80/109 (73%)

Query:   140 YVPPSLREGPGGKRVEGYNA-RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLS 198
             YVPPSLR+G G +R E     RR DD   IR++NLS +T E DL++L + FG  S++YL+
Sbjct:   203 YVPPSLRDG-GSRRGESMQPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLA 261

Query:   199 RDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK-STN 246
             +DKT G  KGFA+I F  + DAA+AI  ++G+GYDHLIL+V+W+K STN
Sbjct:   262 KDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTN 310

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0006413 "translational initiation" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

UNIPROTKB|Q641B2 eif3g-b "Eukaryotic translation initiation factor 3 subunit G-B" [Xenopus laevis (taxid:8355)]

 Score = 297 (109.6 bits), Expect = 7.5e-42, Sum P(2) = 7.5e-42
 Identities = 59/109 (54%), Positives = 80/109 (73%)

Query:   140 YVPPSLREGPGGKRVEGYNA-RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLS 198
             YVPPSLR+G G +R E     RR DD   IR++NLS +T E DL++L + FG  S++YL+
Sbjct:   201 YVPPSLRDG-GSRRGESMQPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLA 259

Query:   199 RDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK-STN 246
             +DKT G  KGFA+I F  + DAA+AI  ++G+GYDHLIL+V+W+K STN
Sbjct:   260 KDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTN 308

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0006413 "translational initiation" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

UNIPROTKB|F2Z4J5 EIF3G "Eukaryotic translation initiation factor 3 subunit G" [Bos taurus (taxid:9913)]

 Score = 291 (107.5 bits), Expect = 7.5e-42, Sum P(2) = 7.5e-42
 Identities = 58/109 (53%), Positives = 79/109 (72%)

Query:   140 YVPPSLREGPGGKRVEGYNA-RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLS 198
             YVPPSLR+G   +R E     RR DD   IR++NLS +T E DL++L + FG  S++YL+
Sbjct:   213 YVPPSLRDG-ASRRGESMQPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLA 271

Query:   199 RDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK-STN 246
             +DKT G  KGFA+I F  + DAA+AI  ++G+GYDHLIL+V+W+K STN
Sbjct:   272 KDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTN 320

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q3ZC12 EIF3G "Eukaryotic translation initiation factor 3 subunit G" [Bos taurus (taxid:9913)]

 Score = 291 (107.5 bits), Expect = 7.5e-42, Sum P(2) = 7.5e-42
 Identities = 58/109 (53%), Positives = 79/109 (72%)

Query:   140 YVPPSLREGPGGKRVEGYNA-RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLS 198
             YVPPSLR+G   +R E     RR DD   IR++NLS +T E DL++L + FG  S++YL+
Sbjct:   213 YVPPSLRDG-ASRRGESMQPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLA 271

Query:   199 RDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK-STN 246
             +DKT G  KGFA+I F  + DAA+AI  ++G+GYDHLIL+V+W+K STN
Sbjct:   272 KDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTN 320

GO:0006413 "translational initiation" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0048471 "perinuclear region of cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2RGG6 EIF3G "Eukaryotic translation initiation factor 3 subunit G" [Canis lupus familiaris (taxid:9615)]

 Score = 291 (107.5 bits), Expect = 7.5e-42, Sum P(2) = 7.5e-42
 Identities = 58/109 (53%), Positives = 79/109 (72%)

Query:   140 YVPPSLREGPGGKRVEGYNA-RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLS 198
             YVPPSLR+G   +R E     RR DD   IR++NLS +T E DL++L + FG  S++YL+
Sbjct:   213 YVPPSLRDG-ASRRGESMQPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLA 271

Query:   199 RDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK-STN 246
             +DKT G  KGFA+I F  + DAA+AI  ++G+GYDHLIL+V+W+K STN
Sbjct:   272 KDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTN 320

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|O75821 EIF3G "Eukaryotic translation initiation factor 3 subunit G" [Homo sapiens (taxid:9606)]

 Score = 291 (107.5 bits), Expect = 7.5e-42, Sum P(2) = 7.5e-42
 Identities = 58/109 (53%), Positives = 79/109 (72%)

Query:   140 YVPPSLREGPGGKRVEGYNA-RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLS 198
             YVPPSLR+G   +R E     RR DD   IR++NLS +T E DL++L + FG  S++YL+
Sbjct:   213 YVPPSLRDG-ASRRGESMQPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLA 271

Query:   199 RDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK-STN 246
             +DKT G  KGFA+I F  + DAA+AI  ++G+GYDHLIL+V+W+K STN
Sbjct:   272 KDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTN 320

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0048471 "perinuclear region of cytoplasm" evidence=IEA

GO:0006413 "translational initiation" evidence=IC;IDA;TAS

GO:0003743 "translation initiation factor activity" evidence=IC;IDA

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005829 "cytosol" evidence=TAS

GO:0006412 "translation" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q2U002	EIF3G_ASPOR	No assigned EC number	0.3517	0.9109	0.7839	yes	N/A
Q5RK09	EIF3G_RAT	No assigned EC number	0.4078	0.9149	0.7062	yes	N/A
Q4X1I3	EIF3G_ASPFU	No assigned EC number	0.3426	0.9109	0.7758	yes	N/A
Q9Z1D1	EIF3G_MOUSE	No assigned EC number	0.4085	0.9068	0.7	yes	N/A
Q7QJV0	EIF3G_ANOGA	No assigned EC number	0.5062	0.8906	0.8118	yes	N/A
P78795	EIF3G_SCHPO	No assigned EC number	0.3227	0.9068	0.7943	yes	N/A
O75821	EIF3G_HUMAN	No assigned EC number	0.4078	0.9149	0.7062	yes	N/A
Q9W4X7	EI3G1_DROME	No assigned EC number	0.4793	0.8906	0.8178	yes	N/A
Q1HQN4	EIF3G_AEDAE	No assigned EC number	0.5163	0.8906	0.8088	N/A	N/A
Q28CY2	EIF3G_XENTR	No assigned EC number	0.4223	0.9352	0.7451	yes	N/A
A2R7Z2	EIF3G_ASPNC	No assigned EC number	0.3466	0.9068	0.7777	yes	N/A
Q6DRC4	EIF3G_DANRE	No assigned EC number	0.4063	0.9271	0.7815	yes	N/A
Q3ZC12	EIF3G_BOVIN	No assigned EC number	0.4078	0.9149	0.7062	yes	N/A
Q29GU0	EI3G1_DROPS	No assigned EC number	0.4834	0.8906	0.8178	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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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	247
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	6e-36
cd12933	114	cd12933, eIF3G, eIF3G domain found in eukaryotic t	3e-33
pfam12353	126	pfam12353, eIF3g, Eukaryotic translation initiatio	3e-33
smart00360	73	smart00360, RRM, RNA recognition motif	3e-17
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-13
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-11
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-11
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-11
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-11
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-11
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	8e-11
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	9e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-10
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-10
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-10
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	4e-10
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-10
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	6e-10
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-09
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-09
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	5e-09
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	8e-09
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	9e-09
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-08
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-08
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-08
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-08
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-08
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	5e-08
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	9e-08
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	1e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-07
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-07
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-07
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-07
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	3e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-07
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-07
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	4e-07
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	4e-07
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	5e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	6e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	8e-07
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	9e-07
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	9e-07
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	1e-06
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-06
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-06
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-06
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-06
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-06
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	2e-06
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	3e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-06
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	3e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-06
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	3e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	5e-06
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	5e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	6e-06
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	6e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	7e-06
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	8e-06
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	8e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	9e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	9e-06
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	1e-05
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-05
cd12253	79	cd12253, RRM_PIN4_like, RNA recognition motif in y	2e-05
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	2e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-05
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	2e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	3e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	3e-05
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	3e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	3e-05
cd12234	72	cd12234, RRM1_AtRSp31_like, RNA recognition motif	3e-05
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	3e-05
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	4e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	4e-05
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	5e-05
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	5e-05
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	5e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	6e-05
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	7e-05
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	7e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	7e-05
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	7e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	7e-05
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	8e-05
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	8e-05
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	8e-05
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	8e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	8e-05
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-04
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	1e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	1e-04
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	1e-04
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	2e-04
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	2e-04
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-04
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-04
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	2e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	2e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-04
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	3e-04
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	3e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-04
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	3e-04
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	3e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	4e-04
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	4e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	4e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	4e-04
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	4e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	4e-04
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	4e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	4e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	5e-04
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	5e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	5e-04
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	5e-04
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	6e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	6e-04
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	6e-04
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	7e-04
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	7e-04
cd12681	69	cd12681, RRM_SKAR, RNA recognition motif in S6K1 A	7e-04
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	8e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	8e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	8e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	8e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	8e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	8e-04
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	9e-04
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	9e-04
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	0.001
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	0.001
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.001
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	0.001
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	0.001
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	0.001
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.002
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	0.002
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.002
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	0.002
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.002
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	0.002
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	0.002
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	0.002
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	0.002
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	0.002
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	0.002
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	0.003
cd12295	74	cd12295, RRM_YRA2, RNA recognition motif in yeast	0.003
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	0.003
cd12687	75	cd12687, RRM1_PTBPH3, RNA recognition motif 1 in p	0.003
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	0.003
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.003
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.004
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.004
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	0.004
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	0.004
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.004
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	0.004

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

 Score =  121 bits (307), Expect = 6e-36
 Identities = 39/77 (50%), Positives = 59/77 (76%)

Query: 167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
            IR++NLS +  E+DL +L + FGP S++YL++DK  G  +GFA++ F  + DA +AI+ 
Sbjct: 1   TIRVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK 60

Query: 227 LNGYGYDHLILSVDWSK 243
           LNG+GYD+LILSV+W+K
Sbjct: 61  LNGFGYDNLILSVEWAK 77

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

>gnl|CDD|240597 cd12933, eIF3G, eIF3G domain found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score =  116 bits (292), Expect = 3e-33
 Identities = 48/96 (50%), Positives = 60/96 (62%), Gaps = 6/96 (6%)

Query: 7   KVVRTLKVE--KKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEV 64
           K+ RT K E  K+ VSK +A RK   K+G    D PGP   TTI+GEEV +Q I NKEE+
Sbjct: 19  KITRTYKEEKVKRKVSKAVAERKKWKKFGDEKGDPPGPNPATTIVGEEVFLQLIRNKEEL 78

Query: 65  EKPEEENLEKL----KFISCRTCKGAHFTNNCPFKD 96
           E+ EEE  +K     K + CR CKG H+T  CP+KD
Sbjct: 79  EEEEEEAKKKKKKGKKLVVCRICKGDHWTTKCPYKD 114

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. eIF3 is a large multi-subunit 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. Besides, eIF-3G is one of the cytosolic targets; it interacts with mature apoptosis-inducing factor (AIF). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G; it plays an important role in the initiation phase of protein synthesis in yeast. It binds both mRNA and rRNA fragments due to an RNA recognition motif near its C-terminus. Length = 114

>gnl|CDD|221544 pfam12353, eIF3g, Eukaryotic translation initiation factor 3 subunit G

 Score =  116 bits (293), Expect = 3e-33
 Identities = 47/98 (47%), Positives = 60/98 (61%), Gaps = 5/98 (5%)

Query: 6   TKVVRTLK--VEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEE 63
            KV RT K     + VSK +A RK  AK+G   ND PGP S+TT++GEEV +Q I N +E
Sbjct: 28  VKVTRTYKETKVTEKVSKAVAERKKWAKFGDEKNDPPGPNSSTTVVGEEVFLQLIRNWKE 87

Query: 64  VEKPEEENLEKL---KFISCRTCKGAHFTNNCPFKDSA 98
            E+ EEE   K    K + CR CKG H+T  CP+KD+ 
Sbjct: 88  EEEEEEEEKAKKSGKKLVKCRICKGDHWTTKCPYKDTL 125

This domain family is found in eukaryotes, and is approximately 130 amino acids in length. The family is found in association with pfam00076. This family is subunit G of the eukaryotic translation initiation factor 3. Subunit G is required for eIF3 integrity. Length = 126

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

 Score = 73.4 bits (181), Expect = 3e-17
 Identities = 28/72 (38%), Positives = 43/72 (59%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + NL  +T+E +L +L  +FG    + L RDK  G  KGFA++ F+++ DA KA++ L
Sbjct: 2   LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61

Query: 228 NGYGYDHLILSV 239
           NG   D   L V
Sbjct: 62  NGKELDGRPLKV 73

Length = 73

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

 Score = 68.5 bits (168), Expect = 2e-15
 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + NL  +T+E DL +L  +FG    + + RDK +G  KGFA++ F++  DA KA++ L
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 228 NGYGYDHLILSVD 240
           NG   D   L V 
Sbjct: 60  NGKELDGRKLKVS 72

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

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

 Score = 62.6 bits (153), Expect = 3e-13
 Identities = 27/63 (42%), Positives = 43/63 (68%), Gaps = 1/63 (1%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + NL  +T+E DL+DL  +FGP   + + RD+T G  KGFA++ F+++ DA KA++ L
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDET-GRSKGFAFVEFEDEEDAEKALEAL 59

Query: 228 NGY 230
           NG 
Sbjct: 60  NGK 62

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

 Score = 58.0 bits (141), Expect = 2e-11
 Identities = 24/71 (33%), Positives = 43/71 (60%)

Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG 231
            LS+ T+E DL ++  ++GP  K+ +  D+  G  +GF +++F++  DA +A + LNG  
Sbjct: 6   GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGME 65

Query: 232 YDHLILSVDWS 242
            D   + VD+S
Sbjct: 66  IDGRRIRVDYS 76

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

>gnl|CDD|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 = 58.0 bits (141), Expect = 2e-11
 Identities = 25/74 (33%), Positives = 43/74 (58%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +S LS  T+E +LE L  +FG   ++ L +D   G  +GF ++ F++  DA  AI+ LNG
Sbjct: 6   VSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNG 65

Query: 230 YGYDHLILSVDWSK 243
              +  ++ V+ +K
Sbjct: 66  KELEGRVIKVEKAK 79

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

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

 Score = 57.7 bits (140), Expect = 3e-11
 Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL    +E DL+ L   FG   ++ + R    G  KGFA++ F +KADA KAI+ +NG
Sbjct: 4   VRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPD-GKKKGFAFVQFTSKADAEKAIKGVNG 62

Query: 230 YGYDHLILSVDWS 242
                  ++VDW+
Sbjct: 63  KKIKGRPVAVDWA 75

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

>gnl|CDD|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 = 57.3 bits (139), Expect = 3e-11
 Identities = 22/60 (36%), Positives = 33/60 (55%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL   T+E +L +L + FG  S+++L  DK     KGFA++ F     A KA   L+G
Sbjct: 4   VRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDG 63

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

 Score = 56.9 bits (138), Expect = 4e-11
 Identities = 21/73 (28%), Positives = 37/73 (50%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL +  ++    +LV  FG   + +L   ++ G  KG+ ++ + +KA A KA   L+G
Sbjct: 4   VGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLDG 63

Query: 230 YGYDHLILSVDWS 242
                  L VDW+
Sbjct: 64  KQIGGRKLQVDWA 76

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

 Score = 60.3 bits (145), Expect = 8e-11
 Identities = 28/90 (31%), Positives = 51/90 (56%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
             +  ++   + + NL  + +E DL +L K+FGP  ++ L RD+  G  +GFA++ F+++
Sbjct: 108 RQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESE 167

Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
             A KAI+ LNG   +   L V  ++  +Q
Sbjct: 168 ESAEKAIEELNGKELEGRPLRVQKAQPASQ 197

Length = 306

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

 Score = 56.2 bits (136), Expect = 9e-11
 Identities = 24/72 (33%), Positives = 35/72 (48%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I + NL  +  E+ L  L   FG  + + + RD T   CKG+ ++   N  +A  AI  L
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 228 NGYGYDHLILSV 239
           NGY     +L V
Sbjct: 64  NGYRLGGRVLQV 75

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

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

 Score = 55.7 bits (135), Expect = 1e-10
 Identities = 23/61 (37%), Positives = 35/61 (57%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL  N +E+DL  + + FG    + L RD   G  KG+ +I F +  DA KA++ LNG
Sbjct: 3   VGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNG 62

Query: 230 Y 230
           +
Sbjct: 63  F 63

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

 Score = 55.3 bits (134), Expect = 2e-10
 Identities = 21/66 (31%), Positives = 35/66 (53%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + NL  N +E DL+DL  QFG  +   +  D+  G  +GF ++  +   +A  AI+ L
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 228 NGYGYD 233
           NG  + 
Sbjct: 62  NGTDFG 67

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

 Score = 54.5 bits (132), Expect = 3e-10
 Identities = 17/62 (27%), Positives = 38/62 (61%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + +  L+ N +++ L+++   +G    + L  D+   L +G+AY+ F++  DA KAI+++
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 228 NG 229
           +G
Sbjct: 61  DG 62

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

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

 Score = 54.5 bits (132), Expect = 4e-10
 Identities = 22/74 (29%), Positives = 39/74 (52%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + NLS  T+E  + +L  + G   ++ +  D+      GF ++ +  + DA  A++YL
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 228 NGYGYDHLILSVDW 241
           NG   D  I+ VDW
Sbjct: 61  NGTKLDDRIIRVDW 74

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

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

 Score = 54.3 bits (131), Expect = 4e-10
 Identities = 26/67 (38%), Positives = 42/67 (62%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
           +T  + + NL  +  E+DLE L  +FG  S+++++ DK +G  KGFAY+ F +  DA KA
Sbjct: 1   ETGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60

Query: 224 IQYLNGY 230
            + L+G 
Sbjct: 61  YKELDGK 67

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

 Score = 53.8 bits (130), Expect = 6e-10
 Identities = 26/66 (39%), Positives = 36/66 (54%), Gaps = 4/66 (6%)

Query: 170 ISNLSVNTSENDLEDLVKQFGP--TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I  L  NT++ DLE L + FG   ++K  L  DK    CKG+ ++ F +   A KAI+ L
Sbjct: 5   IRGLPPNTTDEDLEKLCQPFGKIISTKAIL--DKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 228 NGYGYD 233
           NG G  
Sbjct: 63  NGRGVQ 68

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

 Score = 53.0 bits (128), Expect = 1e-09
 Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 8/74 (10%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL ++T+E  L +L  ++G   ++   +D        +A++HF+ + DA KA++ +NG
Sbjct: 6   VRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEMNG 57

Query: 230 YGYDHLILSVDWSK 243
              +   + V  +K
Sbjct: 58  KELEGSPIEVSLAK 71

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

 Score = 53.1 bits (128), Expect = 1e-09
 Identities = 19/66 (28%), Positives = 39/66 (59%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           +++ NL+  T+ +DL  + +++G    +Y+ RD+     +GFA++ F +K DA  A+  +
Sbjct: 1   LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 228 NGYGYD 233
           +G   D
Sbjct: 61  DGKELD 66

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|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 = 52.5 bits (126), Expect = 2e-09
 Identities = 22/71 (30%), Positives = 39/71 (54%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I  LS +T+E  LE +  ++G  S++ + +D+     +GF ++ F+N  DA  A+  +NG
Sbjct: 5   IGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNG 64

Query: 230 YGYDHLILSVD 240
              D   + VD
Sbjct: 65  KSVDGRQIRVD 75

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

 Score = 51.4 bits (124), Expect = 5e-09
 Identities = 22/68 (32%), Positives = 34/68 (50%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I NL  + +E +L++L  QFG      + +DK  G  KG A++ FK K  A K ++  + 
Sbjct: 5   IRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADN 64

Query: 230 YGYDHLIL 237
                L L
Sbjct: 65  AEDSGLSL 72

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 50.6 bits (122), Expect = 8e-09
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + NL  + +E DL +    +G    + L R+K     +GFA++ F +  DA  A++ L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRP--RGFAFVEFASPEDAEAALKKL 58

Query: 228 NG 229
           NG
Sbjct: 59  NG 60

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

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

 Score = 51.1 bits (123), Expect = 9e-09
 Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 9/90 (10%)

Query: 152 KRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAY 211
           + VEG+          I ++ +     E D+ D   +FG    ++L+ D+  G  KG+A 
Sbjct: 2   RSVEGW---------IIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYAL 52

Query: 212 IHFKNKADAAKAIQYLNGYGYDHLILSVDW 241
           I ++ K +A  AI+ LNG       +SVDW
Sbjct: 53  IEYETKKEAQAAIEGLNGKELLGQTISVDW 82

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

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

 Score = 50.3 bits (121), Expect = 1e-08
 Identities = 19/74 (25%), Positives = 41/74 (55%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL  +T++  LE+   + GP  + ++ +DK +  C+GF Y+ F  + DA +A++    
Sbjct: 4   VRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEKKK 63

Query: 230 YGYDHLILSVDWSK 243
             +    + V+++K
Sbjct: 64  TKFGGRKIHVEFAK 77

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|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 = 49.9 bits (120), Expect = 2e-08
 Identities = 22/73 (30%), Positives = 39/73 (53%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + N+  + +E  L ++  + GP     L  D+  G  KG+ +  F++   AA AI+ LNG
Sbjct: 3   VGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNG 62

Query: 230 YGYDHLILSVDWS 242
           Y ++   L VD++
Sbjct: 63  YEFNGRALRVDFA 75

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

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

 Score = 50.0 bits (119), Expect = 2e-08
 Identities = 22/75 (29%), Positives = 46/75 (61%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + +  LS+ T+E DL ++  ++GP + + +  D+  G  +GFA+++F+   D+ +A+++ 
Sbjct: 2   LGVFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHA 61

Query: 228 NGYGYDHLILSVDWS 242
           NG   D   + VD+S
Sbjct: 62  NGMELDGRRIRVDYS 76

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

>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 = 49.7 bits (119), Expect = 2e-08
 Identities = 19/70 (27%), Positives = 40/70 (57%), Gaps = 1/70 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +S L  + ++ +LE L K+ G    + L  ++ +G  KG AY+ ++N++ A++A+  ++G
Sbjct: 7   VSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVLKMDG 65

Query: 230 YGYDHLILSV 239
                  +SV
Sbjct: 66  TEIKEKTISV 75

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

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

 Score = 50.0 bits (119), Expect = 2e-08
 Identities = 24/80 (30%), Positives = 46/80 (57%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           D    + +  LS+ T+E DL ++  ++GP + + +  D+ +   +GFA+++F+N  DA +
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 223 AIQYLNGYGYDHLILSVDWS 242
           A +  NG   D   + VD+S
Sbjct: 67  AKERANGMELDGRRIRVDFS 86

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

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

 Score = 49.6 bits (119), Expect = 2e-08
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 4/65 (6%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYL---SRDKTNGLCKGFAYIHFKNKADAAKAI 224
           I + NL     E+DL  +  +FG    + +     +K   L  GFA++ FK+ + A  A+
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 225 QYLNG 229
           Q LNG
Sbjct: 63  Q-LNG 66

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

 Score = 53.0 bits (127), Expect = 3e-08
 Identities = 27/79 (34%), Positives = 39/79 (49%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I + NLS +T E  L  L   FG    + + RD T   CKG+ ++   N  +AA AI  L
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 228 NGYGYDHLILSVDWSKSTN 246
           NGY   + +L V +  +  
Sbjct: 332 NGYTLGNRVLQVSFKTNKA 350

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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 48.9 bits (116), Expect = 5e-08
 Identities = 28/77 (36%), Positives = 38/77 (49%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I + NLS    E+ L  L   FG  + + + RD T   CKGF ++   N  +AA AI  L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 228 NGYGYDHLILSVDWSKS 244
           NGY     +L V +  S
Sbjct: 64  NGYRLGDRVLQVSFKTS 80

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

 Score = 48.1 bits (115), Expect = 9e-08
 Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 5/67 (7%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTS---KMYLSRDKTNGLCK--GFAYIHFKNKADAAK 222
           + ISNLS ++SE DLE+ +K F P S        R   +   +  G AY  F +   A K
Sbjct: 2   VYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEK 61

Query: 223 AIQYLNG 229
            ++ LNG
Sbjct: 62  VVKDLNG 68

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

>gnl|CDD|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 = 47.7 bits (114), Expect = 1e-07
 Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 2/65 (3%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKM--YLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           + + NL+  T++ DLE  + + G            K NG  KGFAY+ F ++A AA   +
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 226 YLNGY 230
            L G 
Sbjct: 61  KLEGR 65

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

 Score = 47.9 bits (114), Expect = 1e-07
 Identities = 17/74 (22%), Positives = 32/74 (43%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL+ + ++ DL D      P     +  D   G  +G+ ++ F    DA +A+  L  
Sbjct: 4   VRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKLKN 63

Query: 230 YGYDHLILSVDWSK 243
                 IL +D ++
Sbjct: 64  KKLHGRILRLDIAE 77

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

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 5/65 (7%)

Query: 171 SNLSVN-----TSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           +NL VN      ++ +L  L +  GP     + RD+  G   G+ ++ + ++ DA KAI 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 226 YLNGY 230
            LNG+
Sbjct: 61  TLNGF 65

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|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 = 47.5 bits (114), Expect = 1e-07
 Identities = 19/60 (31%), Positives = 35/60 (58%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +  L    +E D+  L +++G   ++ + RDK  G  KG A++ F ++ +A KAI+ L+G
Sbjct: 4   VGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHG 63

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

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 16/62 (25%), Positives = 33/62 (53%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + NL    +E  L +L  Q GP   +++ +D+     +G+ ++ F ++ DA  AI+ +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 228 NG 229
           N 
Sbjct: 61  NM 62

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

 Score = 46.4 bits (111), Expect = 3e-07
 Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +  LS+   E DL +   + G    + + RD+ +   KG AY+ F ++     A+  L G
Sbjct: 4   VMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-LTG 62

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

 Score = 46.4 bits (111), Expect = 3e-07
 Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + + NL  +  +  L++L  ++G  +   + +D   G  KGF +++F+N   A KA++
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVE 60

Query: 226 YLNGYGYD 233
            LNG   +
Sbjct: 61  ELNGKEVN 68

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

 Score = 46.4 bits (111), Expect = 4e-07
 Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 2/60 (3%)

Query: 172 NLSVNTSENDLEDLVKQFG--PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
            L + T+E D+   +      P   + L RDK  G  +GFA++ F +  DA + +  LN 
Sbjct: 9   GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68

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

 Score = 46.1 bits (110), Expect = 4e-07
 Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I + N+   T+  +L++  K  G  +++ +  DK  G  KGFAYI F +K+    A+  L
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-L 60

Query: 228 NG 229
           N 
Sbjct: 61  NE 62

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

 Score = 46.2 bits (110), Expect = 4e-07
 Identities = 23/66 (34%), Positives = 37/66 (56%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
           ++  + I NL+   +E DLE L  ++GP S+++L  DK     KGFA++ +     A KA
Sbjct: 1   ESGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKA 60

Query: 224 IQYLNG 229
              L+G
Sbjct: 61  FAELDG 66

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

 Score = 45.7 bits (109), Expect = 5e-07
 Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           +R+SNL  + +E DLE+L  + G   K+ ++ D++ G  +G A + F+ + DA +AI+  
Sbjct: 3   LRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRS-GRSEGTADVVFEKREDAERAIKQF 61

Query: 228 NGYGYDHLILSV 239
           NG   D   + V
Sbjct: 62  NGVLLDGQPMQV 73

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

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

 Score = 46.1 bits (110), Expect = 6e-07
 Identities = 16/54 (29%), Positives = 33/54 (61%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
           +  LS+ T+E  L ++  ++G   ++ L RD   G  KG+A++ ++++ DA +A
Sbjct: 8   VGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRA 61

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

 Score = 49.4 bits (118), Expect = 7e-07
 Identities = 21/64 (32%), Positives = 40/64 (62%), Gaps = 1/64 (1%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + + NL  + +E+ L +L  +FG  +   + +D  +G  +GFA+++F+   DAAKA++
Sbjct: 179 TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVE 237

Query: 226 YLNG 229
            +NG
Sbjct: 238 EMNG 241

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

 Score = 45.2 bits (108), Expect = 8e-07
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
           ++ + NL  +  E +L    +  G    + + RD+  G+ KGF Y+ FK K   A A++ 
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALK- 59

Query: 227 LNG 229
           LNG
Sbjct: 60  LNG 62

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

 Score = 45.5 bits (107), Expect = 9e-07
 Identities = 26/74 (35%), Positives = 38/74 (51%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I + NLS ++ E+ L  L   FG  + + + RD     CKGF ++   N  +AA AI  L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 228 NGYGYDHLILSVDW 241
           NGY     +L V +
Sbjct: 66  NGYRLGDRVLQVSF 79

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

 Score = 48.7 bits (116), Expect = 9e-07
 Identities = 22/67 (32%), Positives = 35/67 (52%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           D    I I NL +   E+ +++L++ FG      L +D   GL KG+A+  +K+ +    
Sbjct: 293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDV 352

Query: 223 AIQYLNG 229
           AI  LNG
Sbjct: 353 AIAALNG 359

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

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

 Score = 44.9 bits (107), Expect = 1e-06
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +SNL    S++D+++L  +FG   K  +  D+ +G   G A + F+ +ADA KA++  NG
Sbjct: 5   VSNLDFGVSDDDIKELFAEFGALKKAAVHYDR-SGRSLGTADVVFERRADALKAMKQYNG 63

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

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

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 170 ISNLSVNTSENDLEDLVKQFGP--TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           +S L    ++ +LE L   +G   TS++    D   GL +G  +I F  + +A +AI+ L
Sbjct: 5   VSGLPKTMTQQELEALFSPYGRIITSRILC--DNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 228 NGY 230
           NG 
Sbjct: 63  NGT 65

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

 Score = 45.1 bits (106), Expect = 1e-06
 Identities = 24/77 (31%), Positives = 38/77 (49%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I + NL+ +  E+ L  +   FG  + + + RD     CKGF ++   N  +AA AI  L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 228 NGYGYDHLILSVDWSKS 244
           NGY     +L V +  +
Sbjct: 66  NGYRLGDRVLQVSFKTN 82

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

 Score = 44.4 bits (106), Expect = 2e-06
 Identities = 18/59 (30%), Positives = 32/59 (54%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
           + +L  + +E  L ++    GP   + + RD       G+AY++F+N ADA +A+  LN
Sbjct: 4   VGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

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|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 = 44.5 bits (106), Expect = 2e-06
 Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + + NL    +E +L+     FG   ++ + +DK      G+A++ F     AA AI 
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIV 54

Query: 226 YLNGYGYDHLILSVDWSK 243
            +NG   +   +   W K
Sbjct: 55  AVNGTSINGQTVKCSWGK 72

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 19/63 (30%), Positives = 32/63 (50%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + I +L     E +L     QFG  +++ LSR K  G  KG+A++ F++   A    + +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 228 NGY 230
           N Y
Sbjct: 62  NNY 64

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 43.7 bits (104), Expect = 2e-06
 Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 5/59 (8%)

Query: 184 DLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS 242
            L   FG   K+ L + K      GFA++ F  +  A KA+QYLNG  +    L VD+S
Sbjct: 3   KLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 56

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

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

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 27/80 (33%), Positives = 37/80 (46%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I I NL  +  E  L  +   FG  + + + RD     CKGF ++   N  +AA AI  L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 228 NGYGYDHLILSVDWSKSTNQ 247
           NGY     IL V +  S + 
Sbjct: 64  NGYRLGDKILQVSFKTSKSH 83

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

 Score = 44.0 bits (104), Expect = 2e-06
 Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I + NL  +  E DLEDL  ++G    + L   K       FA++ F++  DA  A+   
Sbjct: 2   IYVGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFEDPRDAEDAVFGR 58

Query: 228 NGYGYDHLILSVDW 241
           NGY +    L V++
Sbjct: 59  NGYDFGQCRLRVEF 72

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

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

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 20/62 (32%), Positives = 33/62 (53%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I I  L    SE+ +++L++ FG      L +D   GL KG+A+  + + +   +AI  L
Sbjct: 3   IFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGL 62

Query: 228 NG 229
           NG
Sbjct: 63  NG 64

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

 Score = 43.4 bits (103), Expect = 3e-06
 Identities = 17/61 (27%), Positives = 36/61 (59%), Gaps = 5/61 (8%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL    ++ +LED  +++GP   ++++R+       GFA++ F++  DA  A++ L+G
Sbjct: 4   VGNLGPRATKRELEDEFEKYGPLRSVWVARNPP-----GFAFVEFEDPRDAEDAVRALDG 58

Query: 230 Y 230
            
Sbjct: 59  R 59

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|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 43.5 bits (103), Expect = 3e-06
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 10/82 (12%)

Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTS--KMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           +T + I +LS   +E DL++L +++G      M   R        G AY+  + + DA +
Sbjct: 2   STTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPPR--------GCAYVCMETRQDAHR 53

Query: 223 AIQYLNGYGYDHLILSVDWSKS 244
           A+Q L         + V W+ +
Sbjct: 54  ALQKLRNVKLAGKKIKVAWAPN 75

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

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

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 22/71 (30%), Positives = 42/71 (59%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           ++ L+ +T+E+ L    +++GP  ++ L RDK  G  +G+A+I F+++ D   A +Y +G
Sbjct: 6   VARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYADG 65

Query: 230 YGYDHLILSVD 240
              D   + VD
Sbjct: 66  KKIDGRRVLVD 76

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

 Score = 43.5 bits (103), Expect = 3e-06
 Identities = 20/62 (32%), Positives = 28/62 (45%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I + +LS       L      FG  S   + +D   G  KG+ ++ F  K DA  AIQ +
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 228 NG 229
           NG
Sbjct: 62  NG 63

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

 Score = 43.0 bits (102), Expect = 5e-06
 Identities = 17/63 (26%), Positives = 34/63 (53%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I ++++  + SE+D++ + + FG      L+ D   G  KG+ +I ++N   A  AI  +
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 228 NGY 230
           N +
Sbjct: 63  NLF 65

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|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 42.9 bits (102), Expect = 5e-06
 Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 2/64 (3%)

Query: 168 IRISNLSVNTSENDLEDLVKQFG-PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
           +R+  L  + +E D+ D       P   +++  D  +G   G AY+ F +  DA +A++ 
Sbjct: 2   VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDD-DGRPTGEAYVEFASPEDARRALRK 60

Query: 227 LNGY 230
            N  
Sbjct: 61  HNNK 64

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 46.4 bits (110), Expect = 6e-06
 Identities = 20/61 (32%), Positives = 34/61 (55%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL  N +E +L  + + FG    + L RD   G  KGF +I F +  +A +A++ +NG
Sbjct: 191 VGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNG 250

Query: 230 Y 230
           +
Sbjct: 251 F 251

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|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 43.0 bits (101), Expect = 6e-06
 Identities = 22/73 (30%), Positives = 36/73 (49%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I+NL    ++   E+LV+ FG   + +L   +T G  KG+ ++ +  K  AA+A   L G
Sbjct: 4   IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 230 YGYDHLILSVDWS 242
                  L V W+
Sbjct: 64  KQLGSRTLYVHWT 76

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

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

 Score = 42.8 bits (101), Expect = 7e-06
 Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 5/79 (6%)

Query: 171 SNLSVNTSENDLED-----LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           +NL +N     L D     L    GP     + RDK  G   GF ++ +++  DA +AI+
Sbjct: 1   TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 226 YLNGYGYDHLILSVDWSKS 244
            LNG    +  + V +++ 
Sbjct: 61  TLNGLQLQNKRIKVAYARP 79

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

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

 Score = 42.6 bits (101), Expect = 8e-06
 Identities = 28/89 (31%), Positives = 44/89 (49%), Gaps = 15/89 (16%)

Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTS--KMYLSRD----KTNGLCKGFAYIHFKNKA 218
           TT + + NL+   +E  L     +FGP +  K+   R     + N  C GF  + F N+A
Sbjct: 1   TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNC-GF--VAFMNRA 57

Query: 219 DAAKAIQYLNG---YGYDHLILSVDWSKS 244
           DA +A+  L+G    GY+   L + W K+
Sbjct: 58  DAERALDELDGKDVMGYE---LKLGWGKA 83

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

>gnl|CDD|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 42.7 bits (100), Expect = 8e-06
 Identities = 20/61 (32%), Positives = 34/61 (55%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           IS L    ++ D+ED+  +FG      +  D+  GL +G A+I F  +++A +AI   NG
Sbjct: 5   ISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSFNG 64

Query: 230 Y 230
           +
Sbjct: 65  H 65

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

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

 Score = 42.5 bits (101), Expect = 9e-06
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK-NKADAAKAIQYLN 228
           +  LS + +E+DLE+   +FG  S + + + K  G  +GFAYI  + ++A   K    LN
Sbjct: 4   VGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKSTLN 63

Query: 229 G 229
           G
Sbjct: 64  G 64

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

 Score = 42.3 bits (100), Expect = 9e-06
 Identities = 17/54 (31%), Positives = 31/54 (57%)

Query: 176 NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + +E+DL +    FG    +++ +DK     KG AY+ F   + AA+A++ +NG
Sbjct: 13  SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNG 66

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

 Score = 42.2 bits (99), Expect = 1e-05
 Identities = 20/64 (31%), Positives = 37/64 (57%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + ++NL    +E++L  + + +G   +  L RDK+ GL +G A++ +  + +A  AI 
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 226 YLNG 229
            LNG
Sbjct: 61  SLNG 64

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 17/63 (26%), Positives = 32/63 (50%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T I +  L  +T+++ L     QFG   +  +  D+  G  +G+ ++ FK+K  A +A +
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 226 YLN 228
             N
Sbjct: 61  DPN 63

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

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 23/77 (29%), Positives = 37/77 (48%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
           D+  I I  L    +E D+  +  Q+G    + L RDK  G  KGFA++ ++++     A
Sbjct: 8   DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILA 67

Query: 224 IQYLNGYGYDHLILSVD 240
           +  LNG       + VD
Sbjct: 68  VDNLNGIKLLGRTIRVD 84

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|240699 cd12253, RRM_PIN4_like, RNA recognition motif in yeast RNA-binding protein PIN4, fission yeast RNA-binding post-transcriptional regulators cip1, cip2 and similar proteins

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 20/78 (25%), Positives = 39/78 (50%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           TAI I N+  +  +  L D+++  G       +    NG+ +G A+ +F++  +A   ++
Sbjct: 2   TAIVIKNIPFSLRKEQLLDIIEDLGIPLPYAFNYHFDNGVFRGLAFANFRSPEEAQTVVE 61

Query: 226 YLNGYGYDHLILSVDWSK 243
            LNGY      L V++ +
Sbjct: 62  ALNGYEISGRRLRVEYKR 79

This subfamily corresponds to the RRM in PIN4, also termed psi inducibility protein 4 or modifier of damage tolerance Mdt1, a novel phosphothreonine (pThr)-containing protein that specifically interacts with the pThr-binding site of the Rad53 FHA1 domain. It is encoded by gene MDT1 (YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is involved in normal G2/M cell cycle progression in the absence of DNA damage and functions as a novel target of checkpoint-dependent cell cycle arrest pathways. It contains an N-terminal RRM, a nuclear localization signal, a coiled coil, and a total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein 1) and cip2 (Csx1-interacting protein 2) are novel cytoplasmic RRM-containing proteins that counteract Csx1 function during oxidative stress. They are not essential for viability in fission yeast Schizosaccharomyces pombe. Both cip1 and cip2 contain one RRM. Like PIN4, Cip2 also possesses an R3H motif that may function in sequence-specific binding to single-stranded nucleic acids. . Length = 79

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

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I + NL  +  E D+EDL  ++GP   + L   K       FA++ F++  DA  A++  
Sbjct: 2   IYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDPRDAEDAVRGR 58

Query: 228 NGYGYDHLILSVD 240
           +GY +D   L V+
Sbjct: 59  DGYDFDGYRLRVE 71

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

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 20/60 (33%), Positives = 34/60 (56%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +SNL  + + NDL  +  ++G   K+ + +DK     KG A+I F ++ DA K ++ LN 
Sbjct: 6   VSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNN 65

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

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 20/64 (31%), Positives = 36/64 (56%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T++ + N++  T  +DL  L  ++GP   +Y+  D      +GFAY+ F++  DA  A+ 
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 226 YLNG 229
           YL+ 
Sbjct: 61  YLDR 64

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|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 41.4 bits (97), Expect = 2e-05
 Identities = 18/72 (25%), Positives = 35/72 (48%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           ++NL ++ +  + E+LV+ +G   + +L   +  G  KG+ ++ +  K  A+KA   L G
Sbjct: 4   VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63

Query: 230 YGYDHLILSVDW 241
                  L   W
Sbjct: 64  KQLGESTLFAQW 75

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

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

 Score = 41.3 bits (97), Expect = 3e-05
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 5/64 (7%)

Query: 171 SNLSVN-----TSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           +NL VN      +++++  L    G      L RDK  G   G+ ++++ +  DA KAI 
Sbjct: 2   TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61

Query: 226 YLNG 229
            LNG
Sbjct: 62  TLNG 65

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

 Score = 40.8 bits (96), Expect = 3e-05
 Identities = 17/48 (35%), Positives = 27/48 (56%)

Query: 178 SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           +E DL +  K+FG    + + +DK  G  KGF Y+ F   + AA A++
Sbjct: 13  TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALE 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|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 21/68 (30%), Positives = 35/68 (51%)

Query: 177 TSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLI 236
           T++ DLE +  +FG      + RDK  G    +A+I F+ K D  +A   ++    D   
Sbjct: 15  TTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRR 74

Query: 237 LSVDWSKS 244
           + VD+S+S
Sbjct: 75  IHVDFSQS 82

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|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 = 40.7 bits (96), Expect = 3e-05
 Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 4/64 (6%)

Query: 178 SENDLEDLVKQFGP--TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHL 235
           ++ DL  L   FG   ++K++   DK  G  K F ++ + N   A  AI+ +NG+     
Sbjct: 11  TDQDLYQLFAPFGNVISAKVF--VDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGK 68

Query: 236 ILSV 239
            L V
Sbjct: 69  RLKV 72

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

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

 Score = 40.7 bits (96), Expect = 3e-05
 Identities = 15/56 (26%), Positives = 26/56 (46%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           + NL       +L++   QFG      +  DK  GL KG+ ++ F ++     A+Q
Sbjct: 4   VGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQ 59

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|240680 cd12234, RRM1_AtRSp31_like, RNA recognition motif in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants

 Score = 40.6 bits (95), Expect = 3e-05
 Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 10/74 (13%)

Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG-- 229
           N   +  ++++E L  ++G   ++ +   K+     GFA+++ +++ DA  AI+ L+   
Sbjct: 7   NFEYDARQSEIERLFGKYGRVDRVDM---KS-----GFAFVYMEDERDAEDAIRGLDNFE 58

Query: 230 YGYDHLILSVDWSK 243
           +G     L V+W+K
Sbjct: 59  FGRQRRRLRVEWAK 72

This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. Length = 72

>gnl|CDD|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 = 40.8 bits (96), Expect = 3e-05
 Identities = 19/63 (30%), Positives = 34/63 (53%)

Query: 161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADA 220
           ++DD   + +  +  N  E DL  L +QFG   ++ + +DK  G+ KG A++ +  +  A
Sbjct: 1   KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESA 60

Query: 221 AKA 223
            KA
Sbjct: 61  LKA 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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 40.6 bits (96), Expect = 4e-05
 Identities = 17/61 (27%), Positives = 36/61 (59%), Gaps = 1/61 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +  +  +  E++L  L ++ GP  ++ L  D  +GL +G+A++ + NK  A +A++ L+ 
Sbjct: 6   VGKIPRDLFEDELVPLFEKAGPIYELRLMMD-FSGLNRGYAFVTYTNKEAAQRAVKQLHN 64

Query: 230 Y 230
           Y
Sbjct: 65  Y 65

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

 Score = 40.5 bits (94), Expect = 4e-05
 Identities = 19/73 (26%), Positives = 34/73 (46%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + +LS   +  D++     FG  S   + +D   G  KG+ ++ F NK DA  AI ++ G
Sbjct: 6   VGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGG 65

Query: 230 YGYDHLILSVDWS 242
                  +  +W+
Sbjct: 66  QWLGGRQIRTNWA 78

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

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

 Score = 40.4 bits (95), Expect = 5e-05
 Identities = 19/61 (31%), Positives = 32/61 (52%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + +  L  N +   L+ +  ++G    + L R K  G  KGFA+I F+   +A KA ++L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 228 N 228
           N
Sbjct: 62  N 62

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

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

 Score = 43.5 bits (102), Expect = 5e-05
 Identities = 31/128 (24%), Positives = 54/128 (42%), Gaps = 10/128 (7%)

Query: 109 FNTVPGTNIMAASSDDKKSGGPGGAPGG-------PAIYVPPSLREGPGGKRVEGYNARR 161
           F++ P T        +   G  G +  G         +    SL     G   +  N   
Sbjct: 47  FSSYPSTGRQHRQGYNDFYGNGGSSACGLGSMGNMANMASTNSLNSLGSGGSDD--NDTN 104

Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
           N  T  I ++ L  + ++ +L  L +  GP +   + RD   G   G+A++ F ++AD+ 
Sbjct: 105 NSGTNLI-VNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQ 163

Query: 222 KAIQYLNG 229
           +AI+ LNG
Sbjct: 164 RAIKNLNG 171

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

 Score = 40.1 bits (94), Expect = 5e-05
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + NL  +  E ++EDL  ++GP   + L   K      G+A+I F++  DA  AI+  
Sbjct: 2   VYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAEDAIRGR 58

Query: 228 NGYGYDHLILSVD 240
           +GY +D   L V+
Sbjct: 59  DGYDFDGQRLRVE 71

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

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

 Score = 40.0 bits (94), Expect = 6e-05
 Identities = 18/60 (30%), Positives = 31/60 (51%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NLS +  E+ + +   ++G  S + L  D  +G  KGF Y+ F ++  A  A+  L G
Sbjct: 3   VGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALGG 62

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 39.9 bits (93), Expect = 7e-05
 Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL     E  L +L  Q GP +K+ + +DK  G  K F ++ FK+      AI  LNG
Sbjct: 6   VGNLECRVREEILYELFLQAGPLTKVTICKDK-EGKPKSFGFVCFKHSESVPYAIALLNG 64

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 40.1 bits (94), Expect = 7e-05
 Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 168 IRISNLSVNTSENDLEDL-VKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
           + +SNL  + +E  + +  V Q GP  ++ LS ++  G   G A I FK   DA KA   
Sbjct: 2   VIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNE-GGKSTGIANITFKRAGDATKAYDK 60

Query: 227 LNG 229
            NG
Sbjct: 61  FNG 63

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

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

 Score = 39.9 bits (93), Expect = 7e-05
 Identities = 19/64 (29%), Positives = 34/64 (53%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
             + +S L    ++ +LE L  Q+G      + RD+  G+ +G  +I F  + +A +AI+
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 226 YLNG 229
            LNG
Sbjct: 61  GLNG 64

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

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

 Score = 39.6 bits (93), Expect = 7e-05
 Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 3/73 (4%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTN-GLCKGFAYIHFKNKADAAKAIQY 226
           I + NL  + +  DL+DL ++ G  + +       N G  KGF  + F++  DA +AI+ 
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECG--NVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEM 58

Query: 227 LNGYGYDHLILSV 239
            NGY  +   L V
Sbjct: 59  FNGYDLEGRELEV 71

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

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

 Score = 40.0 bits (94), Expect = 7e-05
 Identities = 17/54 (31%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           NLS +  ++DLE+  K+ G    + +++D  +G  KGF ++ F  +  A KA++
Sbjct: 6   NLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALE 58

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

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

 Score = 39.5 bits (92), Expect = 8e-05
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 8/64 (12%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
             I + N+S   + ++L  L ++FG      +  DK     K +A++H + + +A  AI+
Sbjct: 1   WKIFVGNVSATCTSDELRGLFEEFGRV----VECDKV----KDYAFVHMEREEEALAAIE 52

Query: 226 YLNG 229
            LNG
Sbjct: 53  ALNG 56

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

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

 Score = 39.8 bits (93), Expect = 8e-05
 Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +  L+   +E ++E++   +G    +Y+ RD+     +G A++ + +K  A  AI+ LNG
Sbjct: 4   VGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKALNG 62

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 39.7 bits (93), Expect = 8e-05
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 6/59 (10%)

Query: 172 NLSVNTSENDLEDLVKQFGPTSKM-YLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
               +   +D++ L +  GP  K+  LSR          A+I F+N   A  AI+ LNG
Sbjct: 6   PFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQ-----PHAFITFENLEAAQLAIETLNG 59

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

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

 Score = 39.9 bits (93), Expect = 8e-05
 Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 182 LEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW 241
           L+ +  ++G   +  + R +   LC GFA++  K + +A  A++  NG   D   ++VDW
Sbjct: 18  LKKIFGRYGKVREATIPRKRGGKLC-GFAFVTMKKRKNAEIALENTNGLEIDGRPVAVDW 76

Query: 242 SKSTN 246
           +   N
Sbjct: 77  AVQKN 81

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|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 39.7 bits (92), Expect = 8e-05
 Identities = 21/80 (26%), Positives = 39/80 (48%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + ++ L  N ++++L  L    G      L RDK  G   G+ ++++ N  DA +AI 
Sbjct: 2   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAIN 61

Query: 226 YLNGYGYDHLILSVDWSKST 245
            LNG       + V +++ +
Sbjct: 62  TLNGLRLQSKTIKVSYARPS 81

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

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

 Score = 42.5 bits (100), Expect = 1e-04
 Identities = 20/62 (32%), Positives = 36/62 (58%)

Query: 167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
           ++ + +L  + +E  L DL K FGP   + + RD       G+ Y++F+N ADA +A++ 
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 227 LN 228
           +N
Sbjct: 62  MN 63

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

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 15/56 (26%), Positives = 28/56 (50%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           +  LS +T++ DL++   +FG      +  D   G  +GF ++ FK+ A   K + 
Sbjct: 3   VGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLD 58

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 21/84 (25%), Positives = 40/84 (47%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           D  T + ++ L  N ++ + + L    G      L RDK  G   G+ ++++ +  DA K
Sbjct: 1   DSKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADK 60

Query: 223 AIQYLNGYGYDHLILSVDWSKSTN 246
           AI  LNG       + V +++ ++
Sbjct: 61  AINTLNGLKLQTKTIKVSYARPSS 84

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 38.7 bits (91), Expect = 1e-04
 Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 8/76 (10%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +  L   TS  +LE    +FG   ++     +       +AYI +++   A  A + L G
Sbjct: 3   VGGLGPWTSLAELEREFDRFGAIRRIDYDPGRN------YAYIEYESIEAAQAAKEALRG 56

Query: 230 Y--GYDHLILSVDWSK 243
           +  G     L VD++ 
Sbjct: 57  FPLGGPGRRLRVDFAD 72

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

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

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL    +E+ L +L  Q GP     L R+  N     +A++ + +   AA A+Q +NG
Sbjct: 3   VGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGN---DPYAFVEYYDHRSAAAALQTMNG 59

Query: 230 YGYDHLILSVDWS 242
                  + V+W+
Sbjct: 60  RLILGQEIKVNWA 72

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

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 8/70 (11%)

Query: 168 IRISNLSVNTSENDLEDLVKQFG--------PTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           + +SNL  NT+E DL +     G           K++L +DK  G  KG A + + +   
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 220 AAKAIQYLNG 229
           A+ AI++ N 
Sbjct: 61  ASAAIEWFNN 70

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 170 ISNLSVNTSENDLEDLVKQFGP--TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           +S LS  T   DL+ L  ++G    +K+  +       C  F ++   +  +AAK IQ+L
Sbjct: 4   VSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARC--FGFVTMASVEEAAKCIQHL 61

Query: 228 NGYGYDHLILSVD 240
           +       ++SV+
Sbjct: 62  HRTELHGRVISVE 74

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

>gnl|CDD|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 = 21/71 (29%), Positives = 36/71 (50%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + N+    +E  L+D+  + GP     L  D+  G  KG+ +  +K++  A  A++ LNG
Sbjct: 3   VGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNG 62

Query: 230 YGYDHLILSVD 240
           Y  +   L VD
Sbjct: 63  YELNGRQLRVD 73

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|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 = 38.4 bits (90), Expect = 2e-04
 Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 6/65 (9%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + +  L    +E++L  L   FG    + +      G  KG  ++ F ++A A  AIQ
Sbjct: 2   TTVFVGGLDPAVTEDELRSLFGPFGEIVYVKIP----PG--KGCGFVQFVHRAAAEAAIQ 55

Query: 226 YLNGY 230
            L G 
Sbjct: 56  QLQGT 60

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

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 20/63 (31%), Positives = 30/63 (47%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I I +L     E +L+    QFG    + ++R K  G  K + +I F N   AA A + +
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 228 NGY 230
           N Y
Sbjct: 62  NNY 64

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 22/63 (34%), Positives = 29/63 (46%), Gaps = 5/63 (7%)

Query: 170 ISNLSVNTSENDLEDLVKQFG---PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
           I NL     E  L D    FG    T K  + RD   G  KGFA+I + +   +  AI+ 
Sbjct: 6   IGNLDPEVDEKLLYDTFSAFGVILQTPK--IMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 227 LNG 229
           +NG
Sbjct: 64  MNG 66

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

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

 Score = 38.5 bits (89), Expect = 2e-04
 Identities = 19/60 (31%), Positives = 31/60 (51%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + +LS   + +D++     FG  S   + +D   G  KG+ ++ F NK DA  AIQ + G
Sbjct: 6   VGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGG 65

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

 Score = 41.6 bits (97), Expect = 2e-04
 Identities = 17/61 (27%), Positives = 33/61 (54%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I ++++  + SE D++ + + FG   K  L+R  T    KG+ +I + N    ++AI  +
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM 266

Query: 228 N 228
           N
Sbjct: 267 N 267

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

 Score = 41.1 bits (96), Expect = 3e-04
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 7/76 (9%)

Query: 159 ARRNDDTTAIRISNLSV-----NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIH 213
           AR + D  +I+ +NL V       ++++LE +   FG      +  D   GL KG  +I 
Sbjct: 80  ARPSSD--SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIR 137

Query: 214 FKNKADAAKAIQYLNG 229
           F  + +A +AI+ LNG
Sbjct: 138 FDKRDEADRAIKTLNG 153

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

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

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 4/76 (5%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I + NL  +    D+EDL  ++G    +    D  N     FA++ F++  DA  A+   
Sbjct: 2   IYVGNLPPDIRTKDIEDLFYKYGAIRDI----DLKNRRGPPFAFVEFEDPRDAEDAVYGR 57

Query: 228 NGYGYDHLILSVDWSK 243
           +GY YD   L V++ +
Sbjct: 58  DGYDYDGYRLRVEFPR 73

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

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 19/57 (33%), Positives = 29/57 (50%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
           + +  L  +  E DL +   QFGP  K  +  DK  G  +GF +++F+N   A KA 
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAA 58

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA--IQ 225
           I +  LS NT+E+D++    QFG      L  DK     +GF ++ F+++    K   I 
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIH 61

Query: 226 Y 226
           +
Sbjct: 62  F 62

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

 Score = 38.3 bits (90), Expect = 3e-04
 Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 3/54 (5%)

Query: 182 LEDLVKQFGPTS--KMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD 233
           L  +  +FG      +Y+  D+T G  KG+A++ F    +A +A++ LNGY  D
Sbjct: 24  LRKIFSKFGVGKIVGIYMPVDET-GKTKGYAFVEFATPEEAKEAVKALNGYKLD 76

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

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

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I I  L  +  E++L  L ++ G   +M +  D  NG  +G+A++ F NK +A  AI+ L
Sbjct: 4   IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQL 62

Query: 228 NGY 230
           N Y
Sbjct: 63  NNY 65

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

 Score = 38.2 bits (88), Expect = 4e-04
 Identities = 22/81 (27%), Positives = 39/81 (48%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           D  T + ++ L  N ++ +L+ L    G      L RDK  G   G+ ++++ +  DA K
Sbjct: 2   DSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 61

Query: 223 AIQYLNGYGYDHLILSVDWSK 243
           AI  LNG       + V +++
Sbjct: 62  AINTLNGLRLQTKTIKVSYAR 82

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSK---MYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
           + I NL    +E  L  L  ++G   K   ++       G  +G+ ++ F+ K +A KA+
Sbjct: 2   LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKAL 61

Query: 225 QYLNGYGYDHLILSVDWSK 243
           + LNG       L V W+ 
Sbjct: 62  KSLNGKTALGKKLVVRWAH 80

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

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

 Score = 38.2 bits (88), Expect = 4e-04
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + ISNL V+  E +LE+++K FG      + RD  NG+ +G  +   ++       IQ
Sbjct: 2   TNLYISNLPVSMDEQELENMLKPFGHVISTRILRD-ANGVSRGVGFARMESTEKCEVVIQ 60

Query: 226 YLNG 229
           + NG
Sbjct: 61  HFNG 64

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

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

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
           D  +I +  LS + ++ +L +   + G   ++ L   K       FA+I F+ +  AA+A
Sbjct: 2   DKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARA 59

Query: 224 IQYLNGY 230
           ++  N  
Sbjct: 60  VESENHS 66

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

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 16/60 (26%), Positives = 34/60 (56%), Gaps = 6/60 (10%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL  + +E + ++L  ++G  S+++L+++      KGF +I    + +A KA   L+G
Sbjct: 6   VGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAELDG 59

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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 37.9 bits (87), Expect = 4e-04
 Identities = 22/66 (33%), Positives = 32/66 (48%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + I  L  NT++ DL  L + +G         DKT   CKG+ ++ F + A A KA+ 
Sbjct: 8   TNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVS 67

Query: 226 YLNGYG 231
            L   G
Sbjct: 68  ALKASG 73

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

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSK-MYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           I +  L ++ +E D+ + +   G   K + L R KT G  +GFA++ F +  +A +
Sbjct: 5   IMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEATR 60

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

 Score = 38.0 bits (88), Expect = 4e-04
 Identities = 17/63 (26%), Positives = 34/63 (53%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           +++ + N++ +T   DL     ++GP   +Y+  D      +GFAY+ F++  DA  A+ 
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 226 YLN 228
            L+
Sbjct: 61  NLD 63

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

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

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 3/51 (5%)

Query: 178 SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
           SE+D EDL+K FG +S   +SR          A+  F N+  A++A+  L+
Sbjct: 12  SEDDKEDLLKHFGASSVRVMSRRGKLKNT---AFATFDNEQAASQALSRLH 59

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

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL    S  +L DL  ++G   ++ +   K     +G A++ +++  DA  A  +L+G
Sbjct: 7   VRNLPFKISSEELYDLFGKYGAIRQIRIGNTKE---TRGTAFVVYEDIYDAKNACDHLSG 63

Query: 230 YGYDHLILSV 239
           +   +  L V
Sbjct: 64  FNVANRYLVV 73

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNG-----LCKGFAYIHFKNKADA 220
           T + + NL+  T+E  L+   ++ G    + +++ K        L  G+ ++ FK+K  A
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 221 AKAIQYLNG 229
            KA++ L G
Sbjct: 61  QKALKRLQG 69

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

 Score = 37.4 bits (87), Expect = 5e-04
 Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 5/67 (7%)

Query: 167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI-- 224
            + I NL+ + +E+D+ +  K     + + L+ DK  G  KGF ++ F ++     A+  
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALKL 59

Query: 225 --QYLNG 229
               L G
Sbjct: 60  DGTVLCG 66

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

 Score = 37.2 bits (87), Expect = 5e-04
 Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
           +SNL  +  E++L  L  + G  + + L ++   G  KG+AY+ F+N+    +A
Sbjct: 4   VSNLDYSVPEDELRKLFSKCGEITDVRLVKNY-KGKSKGYAYVEFENEESVQEA 56

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

>gnl|CDD|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 = 37.2 bits (87), Expect = 5e-04
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T I + NL   T+E +L +L ++FG   ++ L   +T       A + F   +DA KA +
Sbjct: 1   TVILVKNLPFGTTEEELRELFEKFGSLGRLLLPPSRT------IALVEFLEPSDARKAFK 54

Query: 226 YLNGYGYDHLILSVDW 241
            L    + H+ L ++W
Sbjct: 55  SLAYKRFKHVPLYLEW 70

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|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 37.4 bits (86), Expect = 6e-04
 Identities = 20/67 (29%), Positives = 31/67 (46%)

Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
            T + I  L   T++ DL  L + +G         DKT   CKG+ ++ F + + A KA+
Sbjct: 1   KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60

Query: 225 QYLNGYG 231
             L   G
Sbjct: 61  TALKASG 67

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

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

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + + N+    ++ +L +L   FG    + L + K +G  +GFA++ F  K +A  A++
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAME 59

Query: 226 YLNG---YGYDHLIL 237
            L     YG  HL+L
Sbjct: 60  ALKSTHLYG-RHLVL 73

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

 Score = 37.4 bits (86), Expect = 6e-04
 Identities = 18/60 (30%), Positives = 32/60 (53%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +S L    ++ +LE L  Q+G      +  D+  G+ +G  +I F  + +A +AI+ LNG
Sbjct: 7   VSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 66

This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 37.3 bits (86), Expect = 7e-04
 Identities = 17/50 (34%), Positives = 28/50 (56%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
           I +  LSVNT+  D++   +QFG      L  DKT    +GF ++ F+++
Sbjct: 2   IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 37.1 bits (86), Expect = 7e-04
 Identities = 16/62 (25%), Positives = 30/62 (48%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I + +LS   ++  L      F   S   +  D  +G  +G+ ++ F+++ DA  AI  +
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 228 NG 229
           NG
Sbjct: 62  NG 63

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|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like target (SKAR) and similar proteins

 Score = 36.9 bits (86), Expect = 7e-04
 Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 7/64 (10%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + +SNL  + +E+D+ +L   F     +  +R    G+    A + +  K DA  AI 
Sbjct: 1   TRLVVSNLHPSVTEDDIVEL---FSAIGALKRARLVRPGV----AEVVYVRKDDALTAID 53

Query: 226 YLNG 229
             N 
Sbjct: 54  KYNN 57

This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Length = 69

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

 Score = 37.3 bits (86), Expect = 8e-04
 Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 5/62 (8%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + NL  N ++ +LE     +GP   ++++R+       GFA++ F++  DAA A++ L
Sbjct: 7   VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVREL 61

Query: 228 NG 229
           +G
Sbjct: 62  DG 63

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

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

 Score = 36.9 bits (86), Expect = 8e-04
 Identities = 16/62 (25%), Positives = 29/62 (46%), Gaps = 9/62 (14%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK--GFAYIHFKNKADAAKAIQYL 227
           + N++ N  + +L  L +QFG    +Y +       CK  GF  + + +   A +A + L
Sbjct: 6   VRNINSNVEDEELRALFEQFGDIRTLYTA-------CKHRGFIMVSYYDIRAARRAKRAL 58

Query: 228 NG 229
            G
Sbjct: 59  QG 60

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

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 37.3 bits (86), Expect = 8e-04
 Identities = 20/63 (31%), Positives = 33/63 (52%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T++ + N++  T   DL     ++GP   +Y+  D      +GFAYI F++  DA  A+ 
Sbjct: 1   TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60

Query: 226 YLN 228
            LN
Sbjct: 61  NLN 63

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 36.9 bits (85), Expect = 8e-04
 Identities = 18/60 (30%), Positives = 32/60 (53%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +S L    S+ ++E L  Q+G      +  D+  G+ +G  +I F  + +A +AI+ LNG
Sbjct: 6   VSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGLNG 65

This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 36.9 bits (85), Expect = 8e-04
 Identities = 17/56 (30%), Positives = 30/56 (53%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           +  LS +TS+ DL+D   +FG  +   +  D   G  +GF +I FK+ +   K ++
Sbjct: 4   VGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLE 59

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

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

 Score = 36.7 bits (85), Expect = 8e-04
 Identities = 16/57 (28%), Positives = 31/57 (54%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
           + + NLS  T+E++L     + G   ++ +   + +G CKGFA++ F+    A  A+
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

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

 Score = 36.8 bits (86), Expect = 9e-04
 Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL  +  +  L +    FG  +   +  D   G  KGF ++ F +  +A KA+  +NG
Sbjct: 6   VKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAVTEMNG 64

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

 Score = 37.0 bits (86), Expect = 9e-04
 Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 11/69 (15%)

Query: 159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
           A RN     + I NL  + SE +L + +++FGP  ++ + ++K        A++HF + A
Sbjct: 2   ASRN-----VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEK------NIAFVHFLSIA 50

Query: 219 DAAKAIQYL 227
           +A K +  L
Sbjct: 51  NAIKVVTTL 59

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

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

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 13/60 (21%), Positives = 25/60 (41%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
             + + NL  + +E  L     +FG         DK+ G  KG  ++ FK++      ++
Sbjct: 2   FTLFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLK 61

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

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 20/81 (24%), Positives = 38/81 (46%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + ++ L  N ++ +   L    G      L RDK  G   G+ ++++ +  DA KAI 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 226 YLNGYGYDHLILSVDWSKSTN 246
            LNG       + V +++ ++
Sbjct: 63  TLNGLRLQTKTIKVSYARPSS 83

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 37.1 bits (85), Expect = 0.001
 Identities = 18/60 (30%), Positives = 32/60 (53%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +S L    ++ +LE L  Q+G      +  D+  G+ +G  +I F  + +A +AI+ LNG
Sbjct: 10  VSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 69

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 6/59 (10%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
           + + NL  + +E+DL  LV  FG  + + L R K   L      +   +   A   + Y
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQAL------VEMDSVESAKSMVDY 54

This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. . Length = 74

>gnl|CDD|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 = 20/62 (32%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I I NL  +     L D    FG      ++ D+ NG  KG+ ++HF+ +  A +AI+ +
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 228 NG 229
           NG
Sbjct: 64  NG 65

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

 Score = 36.0 bits (83), Expect = 0.001
 Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 8/62 (12%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I + N+  +TS+ +L  L + +G              + + FA++H + +A A +AI+ L
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSC--------AVMRQFAFVHLRGEAAADRAIEEL 54

Query: 228 NG 229
           NG
Sbjct: 55  NG 56

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

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

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 14/60 (23%), Positives = 31/60 (51%), Gaps = 1/60 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL    ++  L +L  + G  +   +  D+  G+ +GF ++ F N  +A +A+  ++G
Sbjct: 290 VKNLDDTVTDEKLRELFSECGEITSAKVMLDEK-GVSRGFGFVCFSNPEEANRAVTEMHG 348

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 14/66 (21%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLC---KGFAYIHFKNKADAAKAI 224
           + + NL   T+  +L  L +++G  ++           C   K + ++H + + DA  AI
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTE-----------CDVVKNYGFVHMEEEEDAEDAI 50

Query: 225 QYLNGY 230
           + LNGY
Sbjct: 51  KALNGY 56

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

 Score = 35.6 bits (82), Expect = 0.002
 Identities = 15/73 (20%), Positives = 35/73 (47%), Gaps = 8/73 (10%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + NL    +E ++  L +Q+G   +          + K + ++H  +K  A +AI+ L
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLEC--------DIIKNYGFVHMDDKTAADEAIRNL 54

Query: 228 NGYGYDHLILSVD 240
           + Y    + ++V+
Sbjct: 55  HHYKLHGVAINVE 67

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|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 = 36.1 bits (84), Expect = 0.002
 Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 6/76 (7%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPT---SKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
           + NL  + +E +L++   + G      K+  + D   G  +  A+I +K + +A KA  Y
Sbjct: 5   VKNLPASLTEAELKEHFSKHGGEITDVKLLRTED---GKSRRIAFIGYKTEEEAQKAKDY 61

Query: 227 LNGYGYDHLILSVDWS 242
            N    +   +SV+++
Sbjct: 62  FNNTYINTSKISVEFA 77

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

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

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 7/77 (9%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKM---YLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
           ++N   +  ++D+ DL +Q+G    +    L  +KT    + F Y+ F +   AA A+  
Sbjct: 5   VTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKT----RRFCYVQFTSPESAAAAVAL 60

Query: 227 LNGYGYDHLILSVDWSK 243
           LNG   +   L V  S 
Sbjct: 61  LNGKLGEGYKLVVKISD 77

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 22/73 (30%), Positives = 40/73 (54%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NLS +  +  L+   ++FG      +  D+  G  +GF Y+ F++  DA KAI+ ++G
Sbjct: 4   VGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDG 63

Query: 230 YGYDHLILSVDWS 242
              D   ++VD+S
Sbjct: 64  KELDGRPINVDFS 76

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

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 35.7 bits (82), Expect = 0.002
 Identities = 17/56 (30%), Positives = 29/56 (51%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           I  LS +TS+ DL + + +FG      +  D   G  +GF ++ FK+ A   K ++
Sbjct: 4   IGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLE 59

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

>gnl|CDD|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 = 35.5 bits (82), Expect = 0.002
 Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 8/67 (11%)

Query: 177 TSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLI 236
           T E D+E L + FGP  +  + +         FA++ F++  DA KA++ L+G   D  +
Sbjct: 12  TREEDIEKLFEPFGPLVRCDIRKT--------FAFVEFEDSEDATKALEALHGSRIDGSV 63

Query: 237 LSVDWSK 243
           L+V++ K
Sbjct: 64  LTVEFVK 70

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

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 16/53 (30%), Positives = 25/53 (47%)

Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
            L   T+E DL+D    FG    + + +D   G  KGF ++ F +  D  K +
Sbjct: 6   GLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 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|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 4/51 (7%)

Query: 179 ENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + D+ +   +FGP   + +  DK +   +G  Y+ FK    A K IQ LNG
Sbjct: 25  KEDVLEECSKFGPVEHIKV--DKNS--PEGVVYVKFKTVEAAQKCIQALNG 71

This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

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

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 13/51 (25%), Positives = 24/51 (47%)

Query: 176 NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
           + +E DL +   Q+G    + +  DK  G  +GFA++ F +     K +  
Sbjct: 10  DVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 14/47 (29%), Positives = 24/47 (51%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
           I  L+  T+++ L +   QFG  +   + RD   G  +GF ++ FK 
Sbjct: 3   IGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKK 49

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

>gnl|CDD|240741 cd12295, RRM_YRA2, RNA recognition motif in yeast RNA annealing protein YRA2 (Yra2p) and similar proteins

 Score = 35.0 bits (81), Expect = 0.003
 Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 8/65 (12%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPT--SKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           +RI+N+ ++ S+  +EDL+K+FG    SK Y  +D         A   F++ +   K ++
Sbjct: 3   LRITNIPLDVSDYTIEDLIKEFGEPVYSKFYDHKDSRT------AVFEFEDPSILEKVVE 56

Query: 226 YLNGY 230
             NG 
Sbjct: 57  KYNGK 61

This subfamily corresponds to the RRM of Yra2p, a nonessential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA2 gene. It may share some overlapping functions with Yra1p, and is able to complement an YRA1 deletion when overexpressed in yeast. Yra2p belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. It is a major component of endogenous Yra1p complexes. It interacts with Yra1p and functions as a negative regulator of Yra1p. Yra2p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
            + + NL    +E  + +L  Q GP  K+ + +DK +G  K FA+++FK++     A+  
Sbjct: 3   TLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFKHEVSVPYAMNL 61

Query: 227 LNG 229
           LNG
Sbjct: 62  LNG 64

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|241131 cd12687, RRM1_PTBPH3, RNA recognition motif 1 in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3)

 Score = 35.3 bits (81), Expect = 0.003
 Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 6/59 (10%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
           + + N+    SENDL  LV+ FG  +K+ + R K   L      +  ++ + A  A+QY
Sbjct: 3   LHVRNVGHEISENDLLQLVQPFGVVTKLVMLRAKNQAL------LQMQDVSSAISALQY 55

This subfamily corresponds to the RRM1 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 = 75

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

 Score = 35.0 bits (81), Expect = 0.003
 Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL    +E  L +L  Q GP   + + +D  NG  K FA++ FK++     AIQ LNG
Sbjct: 6   VGNLDARVTEEILYELFLQAGPLEGVKIPKDP-NGKPKSFAFVTFKHEVSVPYAIQLLNG 64

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

 Score = 34.7 bits (80), Expect = 0.003
 Identities = 12/70 (17%), Positives = 31/70 (44%), Gaps = 8/70 (11%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +     +TSE+ + ++   +G   ++ +           FA++ F++   A +A   ++G
Sbjct: 4   VRPFPPDTSESAIREIFSPYGAVKEVKM--------ISNFAFVEFESLESAIRAKDSVHG 55

Query: 230 YGYDHLILSV 239
              ++  L V
Sbjct: 56  KVLNNNPLYV 65

This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. . Length = 67

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 35.2 bits (80), Expect = 0.004
 Identities = 20/66 (30%), Positives = 30/66 (45%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + I  L   T++ DL  L + +G         DK    CKG+ ++ F + A A KA+ 
Sbjct: 5   TNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVA 64

Query: 226 YLNGYG 231
            L   G
Sbjct: 65  SLKANG 70

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

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

 Score = 35.0 bits (81), Expect = 0.004
 Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 8/60 (13%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I  L     E D+E   K +G   ++ L          GF ++ F++  DA  A+  LNG
Sbjct: 4   IGRLPYRARERDVERFFKGYGRIREINLKN--------GFGFVEFEDPRDADDAVYELNG 55

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

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + ISNL ++  E +LE ++K FG      + RD  +G  +G  +   ++       I 
Sbjct: 1   TNLYISNLPLSMDEQELESMLKPFGQVISTRILRD-ASGTSRGVGFARMESTEKCEAIIT 59

Query: 226 YLNG 229
           + NG
Sbjct: 60  HFNG 63

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

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

 Score = 34.8 bits (80), Expect = 0.004
 Identities = 21/79 (26%), Positives = 42/79 (53%), Gaps = 4/79 (5%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
           D   + + NL  N + ++L+++ +      ++   +D ++   KG AYI FK +A+A KA
Sbjct: 2   DARTLFVKNLPYNITVDELKEVFED-AVDIRLPSGKDGSS---KGIAYIEFKTEAEAEKA 57

Query: 224 IQYLNGYGYDHLILSVDWS 242
           ++   G   D   + VD++
Sbjct: 58  LEEKQGAEVDGRSIVVDYT 76

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

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

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 15/72 (20%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN-----K 217
            D+  + + NL  + +E++L++  K+FG   ++ ++     G    F ++ F +     K
Sbjct: 1   PDSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQK 60

Query: 218 ADAAKAIQYLNG 229
             A K I +   
Sbjct: 61  ILANKPIYFRGD 72

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 34.9 bits (80), Expect = 0.004
 Identities = 17/65 (26%), Positives = 34/65 (52%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + +  +  +  E++L  L ++ GP   + L  D  +G  +G+A+I F  K  A +A++
Sbjct: 2   TEVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVK 61

Query: 226 YLNGY 230
             + Y
Sbjct: 62  LCDNY 66

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	247
KOG0122|consensus	270		100.0
PF12353	128	eIF3g: Eukaryotic translation initiation factor 3	100.0
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.78
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.71
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.68
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.65
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.65
KOG0121|consensus	153		99.62
KOG4207|consensus	256		99.6
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.56
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.56
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.54
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.53
KOG0148|consensus	321		99.51
KOG0107|consensus	195		99.51
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.51
PLN03120	260	nucleic acid binding protein; Provisional	99.49
KOG0149|consensus	247		99.49
KOG0113|consensus	335		99.49
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.48
PLN03213	759	repressor of silencing 3; Provisional	99.48
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.47
KOG0130|consensus	170		99.47
KOG0145|consensus	360		99.47
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.46
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.46
smart00362	72	RRM_2 RNA recognition motif.	99.45
KOG0125|consensus	376		99.45
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.45
KOG0126|consensus	219		99.44
smart00360	71	RRM RNA recognition motif.	99.43
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.43
KOG0111|consensus	298		99.43
KOG0145|consensus	360		99.42
PLN03121	243	nucleic acid binding protein; Provisional	99.38
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.38
KOG0131|consensus	203		99.37
KOG0148|consensus	321		99.36
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.36
KOG0108|consensus	435		99.35
KOG0117|consensus	506		99.34
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.33
KOG0146|consensus	371		99.31
smart00361	70	RRM_1 RNA recognition motif.	99.3
KOG0114|consensus	124		99.29
KOG0127|consensus	678		99.28
KOG0105|consensus	241		99.27
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.26
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.26
KOG0144|consensus	510		99.25
KOG0117|consensus	506		99.24
KOG0127|consensus	678		99.23
KOG0124|consensus	544		99.16
KOG0147|consensus	549		99.16
KOG0144|consensus	510		99.15
KOG4208|consensus	214		99.11
KOG0415|consensus	479		99.1
KOG0131|consensus	203		99.08
KOG0109|consensus	346		99.04
KOG0153|consensus	377		98.98
KOG0123|consensus	369		98.97
KOG0123|consensus	369		98.95
KOG4661|consensus	940		98.94
KOG4206|consensus	221		98.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.93
KOG4212|consensus	608		98.91
KOG0132|consensus	894		98.88
KOG0124|consensus	544		98.86
KOG0146|consensus	371		98.86
KOG0109|consensus	346		98.84
KOG0533|consensus	243		98.84
KOG0110|consensus	725		98.83
KOG0151|consensus	877		98.83
KOG0110|consensus	725		98.77
KOG1457|consensus	284		98.76
KOG4205|consensus	311		98.76
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.65
KOG0226|consensus	290		98.59
KOG4212|consensus	608		98.57
KOG4209|consensus	231		98.57
KOG4205|consensus	311		98.56
KOG1548|consensus	382		98.55
KOG0116|consensus	419		98.47
KOG0106|consensus	216		98.41
KOG4660|consensus	549		98.32
KOG4454|consensus	267		98.28
KOG1190|consensus	492		98.2
KOG0120|consensus	500		98.17
KOG1995|consensus	351		98.07
KOG4211|consensus	510		98.04
KOG0147|consensus	549		97.91
KOG4210|consensus	285		97.85
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.7
KOG1457|consensus	284		97.7
KOG4211|consensus	510		97.69
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.57
KOG4206|consensus	221		97.55
KOG4849|consensus	498		97.53
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.5
KOG3152|consensus	278		97.45
KOG0106|consensus	216		97.36
KOG2314|consensus	698		97.31
KOG0105|consensus	241		97.29
KOG4307|consensus	944		97.27
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.24
KOG1456|consensus	494		97.21
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.04
KOG1365|consensus	508		97.03
KOG1190|consensus	492		96.92
KOG1548|consensus	382		96.87
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.76
KOG0120|consensus	500		96.5
KOG1456|consensus	494		96.47
KOG2193|consensus	584		96.36
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.35
KOG2202|consensus	260		96.03
KOG0128|consensus	881		96.01
KOG2416|consensus	718		96.0
KOG0129|consensus	520		95.8
KOG0128|consensus	881		95.75
KOG4307|consensus	944		95.55
KOG1365|consensus	508		95.49
KOG1855|consensus	484		95.47
KOG0129|consensus	520		95.41
KOG0112|consensus	975		95.25
KOG2068|consensus	327		95.19
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.83
KOG2135|consensus	526		94.71
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.71
KOG0115|consensus	275		94.7
KOG4676|consensus	479		93.82
KOG1996|consensus	378		93.78
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.25
KOG4660|consensus	549		92.92
KOG2253|consensus	668		92.43
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	92.3
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	91.97
PF13696	32	zf-CCHC_2: Zinc knuckle	91.9
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	91.88
KOG4285|consensus	350		91.59
KOG0112|consensus	975		90.95
KOG4210|consensus	285		89.47
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	89.02
PF13917	42	zf-CCHC_3: Zinc knuckle	88.58
KOG0804|consensus	493		84.65
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	84.53

>KOG0122|consensus

Probab=100.00  E-value=6.6e-69  Score=460.86  Aligned_cols=224  Identities=43%  Similarity=0.775  Sum_probs=189.8

Q ss_pred             ceeeEEEEEEEEEEEeChhHHhhcCCcccccccCCCCCCCCCCeeecceEEEEeecCccccccch--hHhhhccc--eee
Q psy13227          4 ESTKVVRTLKVEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVEKPE--EENLEKLK--FIS   79 (247)
Q Consensus         4 ~k~k~~~~~~~~~~~v~~~va~Rk~w~kfg~~~~~~~g~~~~tt~~~e~v~~~~~~~~~~~~~~~--~~~~~~~~--~~~   79 (247)
                      +||||||+|||+|+.|+|+||+||+|.|||++++++|||+..||.++|||.|+|+++|+.+++++  ++...++.  +++
T Consensus        42 kK~Kvt~~~kv~k~~v~K~vaeRknW~KFG~~~~~~~Gp~~~Tt~v~EeI~l~~~~~~~~~~~~~~~~d~~s~~g~~~~~  121 (270)
T KOG0122|consen   42 KKVKVTRTFKVEKRAVPKAVAERKNWVKFGDSKGEPAGPSVATTRVTEEIELRFIRSPTFEEEQDIQEDKASKLGKSIVA  121 (270)
T ss_pred             cEEEEEEEEEEEEEeccHHHHhhccchhhccccCCCCCCceeeEecccceeEEeccCcccchhhhhhhcchhhcccceee
Confidence            79999999999999999999999999999999999999999999999999999999996544332  22333332  899


Q ss_pred             eeeccCCccccCCCCccchhh-hhhcCCCCCCCCCCccccccCCCCCCCCCCCCCCCCCccccCCCCCCCCCCCCcCCCc
Q psy13227         80 CRTCKGAHFTNNCPFKDSALF-LADANKKPFNTVPGTNIMAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYN  158 (247)
Q Consensus        80 Cr~C~g~h~t~~CP~k~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~yvpp~~r~~~~~~~~~~~~  158 (247)
                      ||+|+|||||++||||+++.+ ++         +|+...       .++... ..++..|.||||++|.++.+.+| ++ 
T Consensus       122 CR~C~gdHwt~~CPyK~~~~~~ld---------e~~~~e-------~~~~~~-ap~~~~g~yvpP~mR~ga~~~~g-~~-  182 (270)
T KOG0122|consen  122 CRICKGDHWTTNCPYKDTLSPALD---------EPATAE-------SPAESA-APGTKKGKYVPPSMRAGADRASG-SD-  182 (270)
T ss_pred             eeecCCCeeeecCCchhhcccccc---------CCcccc-------cchhhc-CcCCcCccccCccccCCcccccc-cc-
Confidence            999999999999999999875 22         111100       001111 11677899999999999333334 32 


Q ss_pred             ccCCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEE
Q psy13227        159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS  238 (247)
Q Consensus       159 ~~~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~  238 (247)
                      .|.|+|.++|+|+|||++++|++|++||.+||.|.+++|++|++||.++|||||+|.++++|++||..|||+.|++++|+
T Consensus       183 ~R~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILr  262 (270)
T KOG0122|consen  183 MRERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILR  262 (270)
T ss_pred             cccCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEE
Confidence            36788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCCCC
Q psy13227        239 VDWSKSTN  246 (247)
Q Consensus       239 V~~akp~~  246 (247)
                      |+|++|++
T Consensus       263 vEwskP~~  270 (270)
T KOG0122|consen  263 VEWSKPSN  270 (270)
T ss_pred             EEecCCCC
Confidence            99999975

>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes

Probab=100.00  E-value=1.6e-39  Score=260.01  Aligned_cols=95  Identities=43%  Similarity=0.754  Sum_probs=83.1

Q ss_pred             ceeeEEEEEE--EEEEEeChhHHhhcCCcccccccCCCCCCCCCCeeecceEEEEeecCccccccchhHh---hhccc--
Q psy13227          4 ESTKVVRTLK--VEKKLVSKGIALRKHLAKYGKSANDKPGPQSNTTIIGEEVHIQFISNKEEVEKPEEEN---LEKLK--   76 (247)
Q Consensus         4 ~k~k~~~~~~--~~~~~v~~~va~Rk~w~kfg~~~~~~~g~~~~tt~~~e~v~~~~~~~~~~~~~~~~~~---~~~~~--   76 (247)
                      +||||||+||  +++++|+++||+||+|+|||++++++|||+++||+++|||+|+|+++|+..++++++.   +....  
T Consensus        26 kkvKvtk~~k~~~~~~~V~k~VaeRk~W~KFG~~~~~~pGp~~~Tt~~~EeI~l~~~~~~~~~~~~~~~~~~~~~~~~~~  105 (128)
T PF12353_consen   26 KKVKVTKKIKVTVVKEKVNKAVAERKKWKKFGDEKNDPPGPDSSTTQVGEEIFLELSRNWESEEEEEEEEEAKKKKKGKS  105 (128)
T ss_pred             CEEEEEEEEEEEEEEEEeCHHHHHhhCccccCccccCCCCCCcccccccceEEEEecCCccccccccccchhhhcccCCc
Confidence            6999999999  6788999999999999999999999999999999999999999999998764443222   11111  


Q ss_pred             eeeeeeccCCccccCCCCccch
Q psy13227         77 FISCRTCKGAHFTNNCPFKDSA   98 (247)
Q Consensus        77 ~~~Cr~C~g~h~t~~CP~k~~~   98 (247)
                      +|+||+|+|||||++|||||+|
T Consensus       106 ~v~CR~CkGdH~T~~CPyKd~~  127 (128)
T PF12353_consen  106 KVKCRICKGDHWTSKCPYKDTL  127 (128)
T ss_pred             eEEeCCCCCCcccccCCccccc
Confidence            8999999999999999999987

Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.

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

Probab=99.78  E-value=1.9e-18  Score=141.20  Aligned_cols=85  Identities=22%  Similarity=0.368  Sum_probs=81.1

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      +...++|||+||++++++++|+++|.+||.|.++.|+.|+.|++++|||||+|.+.++|+.|++.||+..|+|+.|+|+|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            45668999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      +++++
T Consensus       111 a~~~~  115 (144)
T PLN03134        111 ANDRP  115 (144)
T ss_pred             CCcCC
Confidence            98764

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.71  E-value=1.6e-16  Score=145.44  Aligned_cols=83  Identities=33%  Similarity=0.501  Sum_probs=79.3

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ...+|||+|||+++++++|+++|++||.|.+++|++|+.||.++|||||+|.+.++|..||..|||..|+|+.|+|.|+.
T Consensus       268 ~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~  347 (352)
T TIGR01661       268 AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKT  347 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcc
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q psy13227        244 STN  246 (247)
Q Consensus       244 p~~  246 (247)
                      ++.
T Consensus       348 ~~~  350 (352)
T TIGR01661       348 NKA  350 (352)
T ss_pred             CCC
Confidence            764

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.68  E-value=2e-16  Score=144.74  Aligned_cols=82  Identities=22%  Similarity=0.470  Sum_probs=79.0

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      .++|||+|||.++++++|+++|+.||+|.+|.|++++.+|+++|||||+|.+.++|+.||+.|||..+.|+.|.|+|++|
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q psy13227        245 TN  246 (247)
Q Consensus       245 ~~  246 (247)
                      ..
T Consensus        83 ~~   84 (352)
T TIGR01661        83 SS   84 (352)
T ss_pred             cc
Confidence            63

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.65  E-value=7.4e-16  Score=142.40  Aligned_cols=85  Identities=26%  Similarity=0.497  Sum_probs=80.8

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      .....++|||+|||+++++++|+++|..||.|.+|.|++|+.+++++|||||+|.+.++|++||..|||..+.++.|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      |++|.
T Consensus       183 ~a~p~  187 (346)
T TIGR01659       183 YARPG  187 (346)
T ss_pred             ccccc
Confidence            99874

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).

>PF00076 RRM_1: RNA recognition motif

Probab=99.65  E-value=1.9e-15  Score=106.18  Aligned_cols=70  Identities=30%  Similarity=0.589  Sum_probs=67.5

Q ss_pred             EEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEE
Q psy13227        168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS  238 (247)
Q Consensus       168 l~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~  238 (247)
                      |||+|||+++++++|+++|++||.|..+.+..+ .++..+|||||.|.+.++|+.|++.|||..++|+.|+
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-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999998 5899999999999999999999999999999999885

(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 ....

>KOG0121|consensus

Probab=99.62  E-value=8.6e-16  Score=121.56  Aligned_cols=81  Identities=22%  Similarity=0.501  Sum_probs=77.8

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      -..++||||+||+..++|++|.+||+++|.|.+|.+-.|+.+..+.|||||+|.+.++|+.|++.+||..++.++|+++|
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~  112 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDW  112 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeec
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             c
Q psy13227        242 S  242 (247)
Q Consensus       242 a  242 (247)
                      .
T Consensus       113 D  113 (153)
T KOG0121|consen  113 D  113 (153)
T ss_pred             c
Confidence            5

>KOG4207|consensus

Probab=99.60  E-value=1.4e-15  Score=129.03  Aligned_cols=83  Identities=28%  Similarity=0.563  Sum_probs=79.9

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      +-+.+++|.|-||.+.++.++|+.+|.+||.|-.|+|++|+.|+.++|||||-|....+|+.|++.|+|..++|+.|+|+
T Consensus         9 dv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq   88 (256)
T KOG4207|consen    9 DVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQ   88 (256)
T ss_pred             CcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeeh
Confidence            45677899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q psy13227        241 WSK  243 (247)
Q Consensus       241 ~ak  243 (247)
                      +|+
T Consensus        89 ~ar   91 (256)
T KOG4207|consen   89 MAR   91 (256)
T ss_pred             hhh
Confidence            886

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

Probab=99.56  E-value=1.7e-14  Score=141.12  Aligned_cols=84  Identities=23%  Similarity=0.351  Sum_probs=79.8

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+||++++++++|+++|+.||.|.+++|++++.+|.++|||||+|.+.++|..||..|||+.++|+.|+|.++
T Consensus       202 ~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kA  281 (612)
T TIGR01645       202 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  281 (612)
T ss_pred             cccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEec
Confidence            34579999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      .+++
T Consensus       282 i~pP  285 (612)
T TIGR01645       282 VTPP  285 (612)
T ss_pred             CCCc
Confidence            8754

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.

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.56  E-value=3.7e-14  Score=100.60  Aligned_cols=70  Identities=39%  Similarity=0.688  Sum_probs=65.2

Q ss_pred             EEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEE
Q psy13227        168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS  238 (247)
Q Consensus       168 l~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~  238 (247)
                      |||+|||+++++++|+++|+.||.|..+.+..++. +.++|+|||+|.+.++|.+|+..++|..++|+.|+
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-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999976 99999999999999999999999999999999875

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 ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.54  E-value=3.4e-14  Score=131.39  Aligned_cols=82  Identities=23%  Similarity=0.424  Sum_probs=76.8

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC--eEEEEee
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH--LILSVDW  241 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g--~~L~V~~  241 (247)
                      ..++|||+|||+++++++|+++|++||.|..+.|++++.++.++|||||+|.+.++|++||+.||+..+.+  +.|.|.|
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            34689999999999999999999999999999999999999999999999999999999999999999876  7899999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      +...
T Consensus       272 a~~~  275 (346)
T TIGR01659       272 AEEH  275 (346)
T ss_pred             CCcc
Confidence            8864

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=99.53  E-value=3.6e-14  Score=138.82  Aligned_cols=81  Identities=21%  Similarity=0.369  Sum_probs=77.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+||++++++++|+++|.+||.|.+|+++.|+.||+++|||||+|.+.++|++|+..|||..++|+.|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             C
Q psy13227        243 K  243 (247)
Q Consensus       243 k  243 (247)
                      .
T Consensus       185 ~  185 (612)
T TIGR01645       185 S  185 (612)
T ss_pred             c
Confidence            4

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0148|consensus

Probab=99.51  E-value=3e-14  Score=125.09  Aligned_cols=82  Identities=27%  Similarity=0.483  Sum_probs=79.2

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      ...+||+-|+..++-++|++.|.+||.|+.++|++|..|+++|||+||.|.++++|+.||..|||..|++|.|+-.||..
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q psy13227        245 TN  246 (247)
Q Consensus       245 ~~  246 (247)
                      ++
T Consensus       142 Kp  143 (321)
T KOG0148|consen  142 KP  143 (321)
T ss_pred             Cc
Confidence            65

>KOG0107|consensus

Probab=99.51  E-value=5.5e-14  Score=116.60  Aligned_cols=79  Identities=25%  Similarity=0.555  Sum_probs=73.4

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      .+-.+.|||+||+..+++.||..+|..||+|..|.|.+++     .|||||+|.+..||+.|+..|+|..|.|..|+|++
T Consensus         7 ~~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~   81 (195)
T KOG0107|consen    7 RNGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVEL   81 (195)
T ss_pred             cCCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEe
Confidence            3557899999999999999999999999999999998865     78999999999999999999999999999999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      +.-+
T Consensus        82 S~G~   85 (195)
T KOG0107|consen   82 STGR   85 (195)
T ss_pred             ecCC
Confidence            8754

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

Probab=99.51  E-value=7.7e-14  Score=136.01  Aligned_cols=79  Identities=28%  Similarity=0.521  Sum_probs=76.1

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      .+|||+|||.+++|++|+++|+.||.|.+|+|.+|..|++++|||||+|.+.++|++|+..||+..+.|+.|+|.|+..
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~   79 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            3799999999999999999999999999999999999999999999999999999999999999999999999999864

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

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.49  E-value=1.3e-13  Score=121.80  Aligned_cols=75  Identities=19%  Similarity=0.351  Sum_probs=70.5

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      .++|||+|||+.+++++|+++|+.||.|.+|.|++++.   ++|||||+|.+.++|+.||. |||..|.|+.|+|.++.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEecc
Confidence            46999999999999999999999999999999999863   47899999999999999996 99999999999999986

>KOG0149|consensus

Probab=99.49  E-value=5.1e-14  Score=121.52  Aligned_cols=80  Identities=21%  Similarity=0.333  Sum_probs=73.2

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      +...++|||++|+|.+..++|++.|.+||+|....|+.|+.||++|||+||+|.+.+.|.+|++. ..-.|+||+.++.+
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnl   87 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNL   87 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccch
Confidence            34567999999999999999999999999999999999999999999999999999999999994 45579999988876


Q ss_pred             c
Q psy13227        242 S  242 (247)
Q Consensus       242 a  242 (247)
                      |
T Consensus        88 A   88 (247)
T KOG0149|consen   88 A   88 (247)
T ss_pred             h
Confidence            5

>KOG0113|consensus

Probab=99.49  E-value=1.2e-13  Score=122.62  Aligned_cols=83  Identities=28%  Similarity=0.490  Sum_probs=78.9

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      .|...||||+.|+.+++|..|+..|..||+|.+|.|++|..||+++|||||+|.+..+...|.+..+|..|+|+.|-|++
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            36778999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCC
Q psy13227        242 SKS  244 (247)
Q Consensus       242 akp  244 (247)
                      -.-
T Consensus       178 ERg  180 (335)
T KOG0113|consen  178 ERG  180 (335)
T ss_pred             ccc
Confidence            653

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

Probab=99.48  E-value=2e-13  Score=130.99  Aligned_cols=82  Identities=29%  Similarity=0.458  Sum_probs=78.1

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +..++|||+|||..+++++|+++|..||.|..+.|+.+..+|.++|||||+|.+.++|..||..|||..++|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            45579999999999999999999999999999999999989999999999999999999999999999999999999998


Q ss_pred             CC
Q psy13227        243 KS  244 (247)
Q Consensus       243 kp  244 (247)
                      ..
T Consensus       373 ~~  374 (509)
T TIGR01642       373 CV  374 (509)
T ss_pred             cc
Confidence            64

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

>PLN03213 repressor of silencing 3; Provisional

Probab=99.48  E-value=9.7e-14  Score=130.25  Aligned_cols=77  Identities=21%  Similarity=0.374  Sum_probs=72.0

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCH--HHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK--ADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~--e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ..+|||+||++.++++||+.+|+.||.|.++.|+  ++||  ||||||+|.+.  .++.+||..|||..|+|+.|+|+.|
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA   85 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA   85 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence            4689999999999999999999999999999999  4577  99999999987  7899999999999999999999999


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      +|.
T Consensus        86 KP~   88 (759)
T PLN03213         86 KEH   88 (759)
T ss_pred             cHH
Confidence            874

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

Probab=99.47  E-value=2.3e-13  Score=129.02  Aligned_cols=79  Identities=27%  Similarity=0.559  Sum_probs=76.7

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      .++|||+|||..+++++|+++|..||.|..|.++.+..+|.++|||||+|.+.++|..|+..|||..+.|+.|.|.|+.
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            5799999999999999999999999999999999999899999999999999999999999999999999999999976

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.

>KOG0130|consensus

Probab=99.47  E-value=1.2e-13  Score=110.43  Aligned_cols=84  Identities=26%  Similarity=0.453  Sum_probs=80.0

Q ss_pred             cCCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEE
Q psy13227        160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV  239 (247)
Q Consensus       160 ~~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V  239 (247)
                      .+.-+...|||+++.+.++|++|.+.|..||.|..|+|-.|+.||..+|||+|+|.+.+.|+.|+..|||..+.|+.|.|
T Consensus        67 qrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~V  146 (170)
T KOG0130|consen   67 QRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSV  146 (170)
T ss_pred             ccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeE
Confidence            35567789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecC
Q psy13227        240 DWSK  243 (247)
Q Consensus       240 ~~ak  243 (247)
                      +|+-
T Consensus       147 Dw~F  150 (170)
T KOG0130|consen  147 DWCF  150 (170)
T ss_pred             EEEE
Confidence            9975

>KOG0145|consensus

Probab=99.47  E-value=1.7e-13  Score=120.03  Aligned_cols=84  Identities=25%  Similarity=0.490  Sum_probs=80.5

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +..+.|.|.-||..+++++|+.||...|+|.++++++|+-+|++-||+||.|.+.+||++||..|||..+..+.|+|.||
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyA  118 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYA  118 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEec
Confidence            44578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +|..
T Consensus       119 RPSs  122 (360)
T KOG0145|consen  119 RPSS  122 (360)
T ss_pred             cCCh
Confidence            9974

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

Probab=99.46  E-value=3.4e-13  Score=115.05  Aligned_cols=79  Identities=34%  Similarity=0.628  Sum_probs=76.7

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      .++|||+|||..+++++|+++|..||.|.++.+..++.++.++|||||.|.+.++|..|+..|+|..|.|+.|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            5899999999999999999999999999999999998899999999999999999999999999999999999999965

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

Probab=99.46  E-value=3.1e-13  Score=131.76  Aligned_cols=83  Identities=19%  Similarity=0.382  Sum_probs=78.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+||++++++++|+++|+.||.|.++.++.+ .+|.++|||||.|.+.++|.+|+..|||..++|+.|.|.|
T Consensus       282 ~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~  360 (562)
T TIGR01628       282 KAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVAL  360 (562)
T ss_pred             ccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEe
Confidence            345678999999999999999999999999999999999 5899999999999999999999999999999999999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      +.++
T Consensus       361 a~~k  364 (562)
T TIGR01628       361 AQRK  364 (562)
T ss_pred             ccCc
Confidence            9865

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

>smart00362 RRM_2 RNA recognition motif

Probab=99.45  E-value=6e-13  Score=92.05  Aligned_cols=72  Identities=36%  Similarity=0.657  Sum_probs=67.6

Q ss_pred             EEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       167 tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      +|+|+|||..+++++|+++|..||.+..+.+..+.  +.++|+|||+|.+.++|+.|+..++|..+.|+.|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            48999999999999999999999999999998876  7889999999999999999999999999999998874

>KOG0125|consensus

Probab=99.45  E-value=4.5e-13  Score=120.41  Aligned_cols=81  Identities=22%  Similarity=0.372  Sum_probs=75.0

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +....|+|+|+|+...+.||+.+|.+||.|.+|.|+.+.  .-+|||+||+|.+.+||++|-.+|||..+.|++|.|..|
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            344579999999999999999999999999999999983  458999999999999999999999999999999999998


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      .++
T Consensus       172 Tar  174 (376)
T KOG0125|consen  172 TAR  174 (376)
T ss_pred             chh
Confidence            865

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

Probab=99.45  E-value=4e-13  Score=131.11  Aligned_cols=80  Identities=25%  Similarity=0.420  Sum_probs=74.1

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC-CeEEEEee
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD-HLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~-g~~L~V~~  241 (247)
                      ...++|||+|||.+++|++|+++|+.||.|..++|++| .+|+++|||||+|.+.++|+.||+.||+..+. ++.|.|.+
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccc
Confidence            44589999999999999999999999999999999999 79999999999999999999999999999985 77787777


Q ss_pred             cC
Q psy13227        242 SK  243 (247)
Q Consensus       242 ak  243 (247)
                      +.
T Consensus       135 S~  136 (578)
T TIGR01648       135 SV  136 (578)
T ss_pred             cc
Confidence            64

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.

>KOG0126|consensus

Probab=99.44  E-value=1.8e-14  Score=120.14  Aligned_cols=80  Identities=29%  Similarity=0.453  Sum_probs=76.9

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      -.|+.-|||+|||+..+|.||.-+|++||.|..|.|++|+.||+++||||+.|.+..+.--|+..|||..|.|+.|+|+.
T Consensus        32 YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDH  111 (219)
T KOG0126|consen   32 YKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDH  111 (219)
T ss_pred             cccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeee
Confidence            46778999999999999999999999999999999999999999999999999999999999999999999999999985

>smart00360 RRM RNA recognition motif

Probab=99.43  E-value=7.9e-13  Score=91.00  Aligned_cols=71  Identities=38%  Similarity=0.648  Sum_probs=67.2

Q ss_pred             EeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       170 V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      |+|||..+++++|+++|..||.|..+.+..++.++.++|||||+|.+.++|..|+..|++..++|+.|.|+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57999999999999999999999999999988789999999999999999999999999999999998874

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

Probab=99.43  E-value=7.2e-13  Score=125.66  Aligned_cols=81  Identities=22%  Similarity=0.338  Sum_probs=76.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+..+|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||. |||..+.|+.|.|.++
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSS  165 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeec
Confidence            346799999999999999999999999999999999999999999999999999999999997 8999999999999886


Q ss_pred             CC
Q psy13227        243 KS  244 (247)
Q Consensus       243 kp  244 (247)
                      ..
T Consensus       166 ~~  167 (457)
T TIGR01622       166 QA  167 (457)
T ss_pred             ch
Confidence            53

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.

>KOG0111|consensus

Probab=99.43  E-value=8.2e-14  Score=119.40  Aligned_cols=83  Identities=20%  Similarity=0.341  Sum_probs=79.9

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+-++|||++|.+.++|.-|...|-+||.|..|.++.|.+++++|||+||+|.-.+||..||..||+..+-|+.|+|.+|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      +|.
T Consensus        88 kP~   90 (298)
T KOG0111|consen   88 KPE   90 (298)
T ss_pred             CCc
Confidence            985

>KOG0145|consensus

Probab=99.42  E-value=1.2e-12  Score=114.82  Aligned_cols=82  Identities=33%  Similarity=0.497  Sum_probs=78.2

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      ..+|||-||+++++|.-|.++|.+||.|..+++++|..|.+++||+||++.+.++|..||..|||+.++++.|.|.|-..
T Consensus       278 g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  278 GWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTN  357 (360)
T ss_pred             eeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecC
Confidence            47999999999999999999999999999999999998899999999999999999999999999999999999999766


Q ss_pred             CC
Q psy13227        245 TN  246 (247)
Q Consensus       245 ~~  246 (247)
                      +.
T Consensus       358 k~  359 (360)
T KOG0145|consen  358 KA  359 (360)
T ss_pred             CC
Confidence            53

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.38  E-value=2.3e-12  Score=112.51  Aligned_cols=74  Identities=20%  Similarity=0.278  Sum_probs=67.9

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      +..+|||+||++.+++++|+++|+.||.|.+|.|+++.   ..+|||||+|.+.++++.|+. |||..|.++.|.|..
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~   77 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITR   77 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEe
Confidence            45799999999999999999999999999999999985   445799999999999999996 999999999998864

>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=99.38  E-value=5.6e-12  Score=87.57  Aligned_cols=74  Identities=34%  Similarity=0.609  Sum_probs=69.1

Q ss_pred             EEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       167 tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      +|+|+|||..+++++|+++|..||.|..+.+..+..+ .++|+|||+|.+.++|..|+..+++..++|+.|.|.|
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999988644 7799999999999999999999999999999999875

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).

>KOG0131|consensus

Probab=99.37  E-value=6.6e-13  Score=110.82  Aligned_cols=83  Identities=23%  Similarity=0.365  Sum_probs=78.7

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      .++...||||+||++.++++.|.+||-+.|+|.++++++|+.+...+||||++|.++++|+-|++.||...+.|+.|+|.
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~   84 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVN   84 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEE
Confidence            35667899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ecC
Q psy13227        241 WSK  243 (247)
Q Consensus       241 ~ak  243 (247)
                      -+.
T Consensus        85 kas   87 (203)
T KOG0131|consen   85 KAS   87 (203)
T ss_pred             ecc
Confidence            765

>KOG0148|consensus

Probab=99.36  E-value=2.7e-12  Score=112.96  Aligned_cols=79  Identities=24%  Similarity=0.511  Sum_probs=74.5

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ...+.|+|||+|++..++|++|++.|++||+|..|++.++      +||+||.|.+.|.|..||-.+|+..+.|..+++.
T Consensus       160 ssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCs  233 (321)
T KOG0148|consen  160 SSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCS  233 (321)
T ss_pred             CCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEe
Confidence            4578899999999999999999999999999999999988      5899999999999999999999999999999999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      |.+..
T Consensus       234 WGKe~  238 (321)
T KOG0148|consen  234 WGKEG  238 (321)
T ss_pred             ccccC
Confidence            98743

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

Probab=99.36  E-value=9.3e-12  Score=119.71  Aligned_cols=79  Identities=23%  Similarity=0.220  Sum_probs=72.7

Q ss_pred             CCCccEEEEeecCC-CCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        162 NDDTTAIRISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       162 ~~~~~tl~V~nLp~-~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ....++|||+||++ .+++++|+++|+.||.|.+|.+++++     +|||||+|.+.++|..|+..|||..|.|+.|+|.
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~  346 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVC  346 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEE
Confidence            34668999999998 69999999999999999999998874     6899999999999999999999999999999999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      +++..
T Consensus       347 ~s~~~  351 (481)
T TIGR01649       347 PSKQQ  351 (481)
T ss_pred             Ecccc
Confidence            98653

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).

>KOG0108|consensus

Probab=99.35  E-value=1.9e-12  Score=122.37  Aligned_cols=81  Identities=26%  Similarity=0.489  Sum_probs=78.3

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST  245 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp~  245 (247)
                      +.|||+|+|+++++++|..+|+..|.|.+++++.|++||+++||||++|.+.++|..|++.|||..+.|+.|+|.|+.-.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999998754


Q ss_pred             C
Q psy13227        246 N  246 (247)
Q Consensus       246 ~  246 (247)
                      +
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            3

>KOG0117|consensus

Probab=99.34  E-value=5.7e-12  Score=117.16  Aligned_cols=81  Identities=25%  Similarity=0.372  Sum_probs=75.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC-CeEEEEee
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD-HLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~-g~~L~V~~  241 (247)
                      ...+-|||+.||.++.|++|..||.+.|.|..++|+.|+.+|.+||||||+|.+.++|+.||+.||+++|. |+.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            45688999999999999999999999999999999999999999999999999999999999999999874 78888776


Q ss_pred             cC
Q psy13227        242 SK  243 (247)
Q Consensus       242 ak  243 (247)
                      +.
T Consensus       161 Sv  162 (506)
T KOG0117|consen  161 SV  162 (506)
T ss_pred             ee
Confidence            54

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

Probab=99.33  E-value=6.8e-12  Score=122.54  Aligned_cols=74  Identities=26%  Similarity=0.465  Sum_probs=69.1

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhcc--CCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQF--GPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~f--G~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ...+|||+||++++++++|+++|+.|  |.|.+|.++        ++||||+|.+.++|++|++.|||..|+|+.|+|.|
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35689999999999999999999999  999999765        35999999999999999999999999999999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      ++|+
T Consensus       304 Akp~  307 (578)
T TIGR01648       304 AKPV  307 (578)
T ss_pred             ccCC
Confidence            9985

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.

>KOG0146|consensus

Probab=99.31  E-value=2.1e-12  Score=113.59  Aligned_cols=87  Identities=23%  Similarity=0.362  Sum_probs=83.7

Q ss_pred             cCCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEE
Q psy13227        160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV  239 (247)
Q Consensus       160 ~~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V  239 (247)
                      ++.++.|+|||-+||....+.+|..+|-+||.|.+.++..|+.|..+|.|+||.|.+..+|+.||..|||+.|+-++|+|
T Consensus       280 reGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKV  359 (371)
T KOG0146|consen  280 REGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKV  359 (371)
T ss_pred             hcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhh
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy13227        240 DWSKSTN  246 (247)
Q Consensus       240 ~~akp~~  246 (247)
                      .+-+|+.
T Consensus       360 QLKRPkd  366 (371)
T KOG0146|consen  360 QLKRPKD  366 (371)
T ss_pred             hhcCccc
Confidence            9999875

>smart00361 RRM_1 RNA recognition motif

Probab=99.30  E-value=1.5e-11  Score=88.04  Aligned_cols=62  Identities=31%  Similarity=0.468  Sum_probs=56.4

Q ss_pred             HHHHHHHhh----ccCCeeEEE-EeecCCC--CceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        179 ENDLEDLVK----QFGPTSKMY-LSRDKTN--GLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       179 e~dL~~lF~----~fG~I~~i~-l~~d~~t--g~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      +++|+++|+    .||.|.++. ++.++.+  +.++||+||.|.+.++|..|+..|||..++|+.|.+.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            578999998    999999996 7777666  9999999999999999999999999999999999863

>KOG0114|consensus

Probab=99.29  E-value=1.5e-11  Score=94.31  Aligned_cols=79  Identities=24%  Similarity=0.430  Sum_probs=71.9

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .....|||.|||.+++.++..++|.+||.|..|+|-..+   ..+|-|||.|.+..+|.+|++.|+|+.++++.|.|-+-
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            345689999999999999999999999999999997654   45899999999999999999999999999999999886


Q ss_pred             CC
Q psy13227        243 KS  244 (247)
Q Consensus       243 kp  244 (247)
                      +|
T Consensus        93 q~   94 (124)
T KOG0114|consen   93 QP   94 (124)
T ss_pred             CH
Confidence            65

>KOG0127|consensus

Probab=99.28  E-value=1e-11  Score=117.90  Aligned_cols=81  Identities=33%  Similarity=0.666  Sum_probs=75.7

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      -..|.|.|||+.+...+|+.+|+.||.|..|.|++.+.++.+ |||||.|....+|..|++.+||..|+|+.|-|+||-+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklc-GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLC-GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCcc-ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            578999999999999999999999999999999988755555 9999999999999999999999999999999999987


Q ss_pred             CC
Q psy13227        245 TN  246 (247)
Q Consensus       245 ~~  246 (247)
                      ++
T Consensus       196 Kd  197 (678)
T KOG0127|consen  196 KD  197 (678)
T ss_pred             cc
Confidence            64

>KOG0105|consensus

Probab=99.27  E-value=5.9e-12  Score=105.59  Aligned_cols=77  Identities=29%  Similarity=0.499  Sum_probs=69.5

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ..++|||+|||.++.+.+|++||.+||.|..|.|-..+   ..-.||||+|.+..+|+.||..-+|+.|+|..|+|+|+.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            34789999999999999999999999999999874432   345799999999999999999999999999999999986

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

Probab=99.26  E-value=2.2e-11  Score=117.14  Aligned_cols=75  Identities=20%  Similarity=0.309  Sum_probs=68.6

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHh--cCceeCCeEEEEeec
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL--NGYGYDHLILSVDWS  242 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~L--nG~~i~g~~L~V~~a  242 (247)
                      +.+|||+|||+++++++|+++|++||.|.++.++++      +|||||+|.+.++|+.|+..|  |+..++|+.|.|+|+
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s   75 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYS   75 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEec
Confidence            468999999999999999999999999999998864      579999999999999999874  788999999999998


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      .++
T Consensus        76 ~~~   78 (481)
T TIGR01649        76 TSQ   78 (481)
T ss_pred             CCc
Confidence            753

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).

>PF13893 RRM_5: RNA recognition motif

Probab=99.26  E-value=3.4e-11  Score=82.18  Aligned_cols=56  Identities=36%  Similarity=0.632  Sum_probs=51.2

Q ss_pred             HHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        182 LEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       182 L~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      |.++|++||.|.++.+..+.     +++|||+|.+.++|..|+..|||..++|+.|+|+||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999987663     689999999999999999999999999999999997

(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 ....

>KOG0144|consensus

Probab=99.25  E-value=6.3e-12  Score=116.47  Aligned_cols=83  Identities=28%  Similarity=0.510  Sum_probs=76.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCce-eC--CeEEEE
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG-YD--HLILSV  239 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~-i~--g~~L~V  239 (247)
                      .+.+.|||+-|+..++|.+++++|++||.|..|+|++|. .+.+||||||.|.+++-|..||+.|||.. +.  ...|.|
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVV  200 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVV  200 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEE
Confidence            456899999999999999999999999999999999995 89999999999999999999999999986 33  467999


Q ss_pred             eecCCCC
Q psy13227        240 DWSKSTN  246 (247)
Q Consensus       240 ~~akp~~  246 (247)
                      .||.++.
T Consensus       201 kFADtqk  207 (510)
T KOG0144|consen  201 KFADTQK  207 (510)
T ss_pred             EecccCC
Confidence            9998764

>KOG0117|consensus

Probab=99.24  E-value=1.6e-11  Score=114.18  Aligned_cols=73  Identities=30%  Similarity=0.534  Sum_probs=69.6

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST  245 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp~  245 (247)
                      -.|||.||+.++|++.|+++|+.||.|.+|..++|        ||||.|.++++|.+|++.+||+.|+|..|.|.+|+|.
T Consensus       260 KvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~  331 (506)
T KOG0117|consen  260 KVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPV  331 (506)
T ss_pred             eeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCCh
Confidence            46999999999999999999999999999998876        9999999999999999999999999999999999986


Q ss_pred             C
Q psy13227        246 N  246 (247)
Q Consensus       246 ~  246 (247)
                      .
T Consensus       332 ~  332 (506)
T KOG0117|consen  332 D  332 (506)
T ss_pred             h
Confidence            3

>KOG0127|consensus

Probab=99.23  E-value=1.6e-11  Score=116.53  Aligned_cols=82  Identities=21%  Similarity=0.385  Sum_probs=79.1

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      ..||||++||++++.++|.++|+.+|+|..++++.++.++.+|||+||+|.-.+|+++|+..+++..+.|++|+|..+++
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~   84 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKK   84 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccc
Confidence            37999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q psy13227        245 TN  246 (247)
Q Consensus       245 ~~  246 (247)
                      +.
T Consensus        85 R~   86 (678)
T KOG0127|consen   85 RA   86 (678)
T ss_pred             cc
Confidence            74

>KOG0124|consensus

Probab=99.16  E-value=2.7e-11  Score=110.51  Aligned_cols=78  Identities=22%  Similarity=0.382  Sum_probs=75.0

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      -.+.|||+.+++...|+.|+..|.+||+|.+|.+..|+.|++++|||||+|.-.+.|+-|++.|||..++|+.|+|..
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            347899999999999999999999999999999999999999999999999999999999999999999999999874

>KOG0147|consensus

Probab=99.16  E-value=3.9e-11  Score=113.99  Aligned_cols=76  Identities=33%  Similarity=0.586  Sum_probs=73.0

Q ss_pred             EEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       168 l~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      |||+||..++++++|+.+|.+||.|..|.+.+|.+||+++||+||+|.+.++|..|+..|||+.+-|+.|+|..-.
T Consensus       281 l~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  281 LYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             hhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence            9999999999999999999999999999999998899999999999999999999999999999999999987543

>KOG0144|consensus

Probab=99.15  E-value=1.1e-10  Score=108.22  Aligned_cols=82  Identities=22%  Similarity=0.454  Sum_probs=74.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCce-e--CCeEEEE
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG-Y--DHLILSV  239 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~-i--~g~~L~V  239 (247)
                      .+.-.+||+.+|..++|.||+++|.+||.|..|.|++|+.|+.++|||||.|.++++|.+|+..|+... +  ++..|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            556689999999999999999999999999999999999999999999999999999999999998875 3  3567888


Q ss_pred             eecCC
Q psy13227        240 DWSKS  244 (247)
Q Consensus       240 ~~akp  244 (247)
                      .+|..
T Consensus       112 k~Ad~  116 (510)
T KOG0144|consen  112 KYADG  116 (510)
T ss_pred             cccch
Confidence            88753

>KOG4208|consensus

Probab=99.11  E-value=2.4e-10  Score=97.16  Aligned_cols=84  Identities=21%  Similarity=0.387  Sum_probs=76.6

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhcc-CCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQF-GPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~f-G~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ......+||..+|..+.+..|..+|.+| |.+.++++.+++.||.++|||||+|.+.+.|+-|.+.||++.++++.|.|.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            3445679999999999999999999988 778888999999999999999999999999999999999999999999998


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      +-.|.
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            86653

>KOG0415|consensus

Probab=99.10  E-value=1.6e-10  Score=105.04  Aligned_cols=83  Identities=25%  Similarity=0.390  Sum_probs=79.0

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      .+..+.|||-.|++-++.+||.-+|+.||.|.++.|++|+.||.+-.||||+|.+.+++++|.-.|+...|+++.|+|+|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            34557899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q psy13227        242 SKS  244 (247)
Q Consensus       242 akp  244 (247)
                      +++
T Consensus       316 SQS  318 (479)
T KOG0415|consen  316 SQS  318 (479)
T ss_pred             hhh
Confidence            874

>KOG0131|consensus

Probab=99.08  E-value=1.4e-10  Score=97.09  Aligned_cols=83  Identities=24%  Similarity=0.311  Sum_probs=76.9

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEE-EEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKM-YLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i-~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      +.+..|||+||.+.++|..|.+.|+.||.|.+. .++++..||.++||+||.|.+.+.+.+|+..|||..+.++++.|.+
T Consensus        94 ~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~y  173 (203)
T KOG0131|consen   94 DVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSY  173 (203)
T ss_pred             cccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEE
Confidence            455789999999999999999999999998764 7889999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      +..+
T Consensus       174 a~k~  177 (203)
T KOG0131|consen  174 AFKK  177 (203)
T ss_pred             EEec
Confidence            8754

>KOG0109|consensus

Probab=99.04  E-value=2.8e-10  Score=101.17  Aligned_cols=72  Identities=28%  Similarity=0.526  Sum_probs=69.1

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST  245 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp~  245 (247)
                      ..|||+|||..+++.+|+.||.+||.|..|.|+++        ||||...+...++.||..|+|+.|+|..|+|+-++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            47999999999999999999999999999999987        9999999999999999999999999999999999877

>KOG0153|consensus

Probab=98.98  E-value=1.6e-09  Score=98.31  Aligned_cols=82  Identities=21%  Similarity=0.404  Sum_probs=72.3

Q ss_pred             CcccCCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHH-hcCceeCCe
Q psy13227        157 YNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY-LNGYGYDHL  235 (247)
Q Consensus       157 ~~~~~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~-LnG~~i~g~  235 (247)
                      +.++.+....+|||++|...++|.+|+++|.+||+|.+|.+...      +++|||+|.+++.|+.|... +|...|+|.
T Consensus       220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~  293 (377)
T KOG0153|consen  220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGF  293 (377)
T ss_pred             cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecce
Confidence            33356667789999999999999999999999999999988765      35999999999999999876 776779999


Q ss_pred             EEEEeecCC
Q psy13227        236 ILSVDWSKS  244 (247)
Q Consensus       236 ~L~V~~akp  244 (247)
                      +|.|.|+.|
T Consensus       294 Rl~i~Wg~~  302 (377)
T KOG0153|consen  294 RLKIKWGRP  302 (377)
T ss_pred             EEEEEeCCC
Confidence            999999998

>KOG0123|consensus

Probab=98.97  E-value=1.8e-09  Score=100.87  Aligned_cols=75  Identities=28%  Similarity=0.444  Sum_probs=70.5

Q ss_pred             EEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       167 tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      .|||.||+++++..+|.++|+.||.|.+|++..+. .| ++|| ||.|.+.+.|.+||..|||..+.+..|.|....+
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~  152 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFER  152 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccc
Confidence            39999999999999999999999999999999996 56 9999 9999999999999999999999999999976654

>KOG0123|consensus

Probab=98.95  E-value=2.1e-09  Score=100.34  Aligned_cols=75  Identities=24%  Similarity=0.408  Sum_probs=71.0

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST  245 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp~  245 (247)
                      .+|||+   +++++.+|.++|+++|++.++++.+|. |  +-|||||+|.+..+|++||..||...+.|+.+++.|+...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            468999   999999999999999999999999997 6  9999999999999999999999999999999999999865


Q ss_pred             C
Q psy13227        246 N  246 (247)
Q Consensus       246 ~  246 (247)
                      +
T Consensus        76 ~   76 (369)
T KOG0123|consen   76 P   76 (369)
T ss_pred             C
Confidence            4

>KOG4661|consensus

Probab=98.94  E-value=5.6e-09  Score=99.97  Aligned_cols=84  Identities=19%  Similarity=0.309  Sum_probs=77.9

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..-.++|||++|+..+.-.||+.||++||.|.-..|+.+..+--.+.|+||++.+..+|.++|..|+...+.|++|.|+-
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEk  481 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEK  481 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeee
Confidence            34557899999999999999999999999999999999977888899999999999999999999999999999999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      ++..
T Consensus       482 aKNE  485 (940)
T KOG4661|consen  482 AKNE  485 (940)
T ss_pred             cccC
Confidence            8754

>KOG4206|consensus

Probab=98.94  E-value=3e-09  Score=91.61  Aligned_cols=77  Identities=23%  Similarity=0.427  Sum_probs=71.2

Q ss_pred             cEEEEeecCCCCCHHHHHH----HhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        166 TAIRISNLSVNTSENDLED----LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~----lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      .||||.||++.+..++|+.    ||++||.|..|...+   |.+.||=|||.|.+.+.|-.|+..|+|+.+-|..++|+|
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqy   86 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQY   86 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhheec
Confidence            3999999999999999887    999999999987654   678899999999999999999999999999999999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      |+.+
T Consensus        87 A~s~   90 (221)
T KOG4206|consen   87 AKSD   90 (221)
T ss_pred             ccCc
Confidence            9865

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

Probab=98.93  E-value=3.2e-09  Score=102.04  Aligned_cols=73  Identities=16%  Similarity=0.338  Sum_probs=61.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhcc------------CCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCc
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQF------------GPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGY  230 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~f------------G~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~  230 (247)
                      ...++|||+|||+.+++++|.++|..|            +.|..+.+      +..+|||||+|.+.++|..||. |||.
T Consensus       173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~-l~g~  245 (509)
T TIGR01642       173 RQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMA-LDSI  245 (509)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhc-CCCe
Confidence            455789999999999999999999975            23444443      3457999999999999999995 9999


Q ss_pred             eeCCeEEEEeec
Q psy13227        231 GYDHLILSVDWS  242 (247)
Q Consensus       231 ~i~g~~L~V~~a  242 (247)
                      .|.|..|.|...
T Consensus       246 ~~~g~~l~v~r~  257 (509)
T TIGR01642       246 IYSNVFLKIRRP  257 (509)
T ss_pred             EeeCceeEecCc
Confidence            999999999754

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

>KOG4212|consensus

Probab=98.91  E-value=5.3e-09  Score=97.52  Aligned_cols=76  Identities=29%  Similarity=0.420  Sum_probs=71.3

Q ss_pred             cEEEEeecCCCCCHHHHHHHhh-ccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        166 TAIRISNLSVNTSENDLEDLVK-QFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~-~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +.+||+|+|+++.+.||++||. +.|.|..|.|..|. +|++||+|.|+|.+++.+++|++.||.+.+.|+.|.|...
T Consensus        45 R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   45 RSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKED  121 (608)
T ss_pred             ceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEecc
Confidence            4699999999999999999997 67999999999995 8999999999999999999999999999999999998653

>KOG0132|consensus

Probab=98.88  E-value=4.3e-09  Score=103.57  Aligned_cols=74  Identities=24%  Similarity=0.489  Sum_probs=69.8

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST  245 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp~  245 (247)
                      +||||++|+.+++|.||..+|..||.|.+|.++-.      +|+|||.+.++++|++|+..|+.+.+.++.|+|.|+..+
T Consensus       422 rTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  422 RTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            78999999999999999999999999999988655      689999999999999999999999999999999999754

>KOG0124|consensus

Probab=98.86  E-value=5.7e-09  Score=95.51  Aligned_cols=81  Identities=23%  Similarity=0.361  Sum_probs=75.9

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...+.|||..+.++.+|+||+..|.-||+|..|.+.+++.++.++||+||+|.+......||..||-+.++|..|+|--+
T Consensus       208 k~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~  287 (544)
T KOG0124|consen  208 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  287 (544)
T ss_pred             HhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccc
Confidence            34578999999999999999999999999999999999988899999999999999999999999999999999999765


Q ss_pred             C
Q psy13227        243 K  243 (247)
Q Consensus       243 k  243 (247)
                      -
T Consensus       288 v  288 (544)
T KOG0124|consen  288 V  288 (544)
T ss_pred             c
Confidence            4

>KOG0146|consensus

Probab=98.86  E-value=4.7e-09  Score=92.67  Aligned_cols=79  Identities=28%  Similarity=0.431  Sum_probs=71.6

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC---CeEEEEe
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD---HLILSVD  240 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~---g~~L~V~  240 (247)
                      +.++|||+-|...-.|+|++.+|.+||.|.++.+.+.. .|.+||+|||.|.+.-+|+.||..|+|...+   ...|.|.
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            44689999999999999999999999999999999996 8999999999999999999999999998743   4568888


Q ss_pred             ecC
Q psy13227        241 WSK  243 (247)
Q Consensus       241 ~ak  243 (247)
                      |+.
T Consensus        97 ~AD   99 (371)
T KOG0146|consen   97 FAD   99 (371)
T ss_pred             ecc
Confidence            875

>KOG0109|consensus

Probab=98.84  E-value=3e-09  Score=94.75  Aligned_cols=75  Identities=24%  Similarity=0.483  Sum_probs=70.7

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .-+++|+|+||++.++.++|+..|.+||++..+.|++|        |+||.|.-.++|..|++.||+.+++|+.++|+++
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~s  147 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLS  147 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeeee
Confidence            45689999999999999999999999999999999876        9999999999999999999999999999999998


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      .++
T Consensus       148 tsr  150 (346)
T KOG0109|consen  148 TSR  150 (346)
T ss_pred             ccc
Confidence            865

>KOG0533|consensus

Probab=98.84  E-value=1e-08  Score=90.26  Aligned_cols=80  Identities=26%  Similarity=0.458  Sum_probs=74.4

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      .+.|+|.||+..+.++||++||..||.+.++.|..++ .|.+.|.|-|.|...+||.+|++.|||..++|..+.+....+
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            3789999999999999999999999999999999996 899999999999999999999999999999999998887654


Q ss_pred             C
Q psy13227        245 T  245 (247)
Q Consensus       245 ~  245 (247)
                      .
T Consensus       162 ~  162 (243)
T KOG0533|consen  162 P  162 (243)
T ss_pred             c
Confidence            3

>KOG0110|consensus

Probab=98.83  E-value=2.4e-09  Score=104.50  Aligned_cols=83  Identities=23%  Similarity=0.445  Sum_probs=77.0

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ..+.|.|.|||+..+-.+++.+|..||.|.+|+|+.....+.++|||||+|.+.++|.+|+..|...-|.|+.|.++||+
T Consensus       612 ~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~  691 (725)
T KOG0110|consen  612 KGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAK  691 (725)
T ss_pred             ccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhc
Confidence            35799999999999999999999999999999999886677889999999999999999999999888999999999998


Q ss_pred             CCC
Q psy13227        244 STN  246 (247)
Q Consensus       244 p~~  246 (247)
                      ..+
T Consensus       692 ~d~  694 (725)
T KOG0110|consen  692 SDN  694 (725)
T ss_pred             cch
Confidence            643

>KOG0151|consensus

Probab=98.83  E-value=1.2e-08  Score=99.71  Aligned_cols=83  Identities=24%  Similarity=0.410  Sum_probs=74.6

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecC---CCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDK---TNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS  238 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~---~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~  238 (247)
                      ++..++|||+||++.+++++|...|..||+|..+.++.-+   +..+.+-++||.|.++.||++|++.|+|..|.+..++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            4667899999999999999999999999999999887654   2355678999999999999999999999999999999


Q ss_pred             EeecCC
Q psy13227        239 VDWSKS  244 (247)
Q Consensus       239 V~~akp  244 (247)
                      +-|+++
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            999963

>KOG0110|consensus

Probab=98.77  E-value=1.7e-08  Score=98.66  Aligned_cols=79  Identities=29%  Similarity=0.429  Sum_probs=70.3

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCC---CceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTN---GLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~t---g~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      .++|||.||+++++.++|..+|...|.|.++.|...+..   -.|.|||||+|.+.++|+.|++.|+|+.++|+.|.|.+
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKI  594 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEe
Confidence            344999999999999999999999999999988766522   13459999999999999999999999999999999999


Q ss_pred             cC
Q psy13227        242 SK  243 (247)
Q Consensus       242 ak  243 (247)
                      +.
T Consensus       595 S~  596 (725)
T KOG0110|consen  595 SE  596 (725)
T ss_pred             cc
Confidence            87

>KOG1457|consensus

Probab=98.76  E-value=1e-07  Score=82.42  Aligned_cols=84  Identities=23%  Similarity=0.364  Sum_probs=69.6

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEee-cCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC---CeEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSR-DKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD---HLIL  237 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~-d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~---g~~L  237 (247)
                      ++..+||||++||.++..-+|..||..|-.-....|-. ++...-++-+||++|.+.++|..|+..|||..++   +..|
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            46678999999999999999999999986655554432 2323345689999999999999999999999998   7889


Q ss_pred             EEeecCCC
Q psy13227        238 SVDWSKST  245 (247)
Q Consensus       238 ~V~~akp~  245 (247)
                      ++++|+..
T Consensus       111 hiElAKSN  118 (284)
T KOG1457|consen  111 HIELAKSN  118 (284)
T ss_pred             EeeehhcC
Confidence            99999854

>KOG4205|consensus

Probab=98.76  E-value=7.1e-09  Score=94.46  Aligned_cols=82  Identities=21%  Similarity=0.360  Sum_probs=74.6

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||++|+++++++.|++.|..||.|..+.+++|+.+++++||+||+|.+.+....++. ..-+.|+|+.|.+.-+
T Consensus         4 ~~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~a   82 (311)
T KOG4205|consen    4 GESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRA   82 (311)
T ss_pred             cCCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceec
Confidence            367899999999999999999999999999999999999999999999999999888888877 4567789999988887


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      .|+
T Consensus        83 v~r   85 (311)
T KOG4205|consen   83 VSR   85 (311)
T ss_pred             cCc
Confidence            775

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

Probab=98.65  E-value=2.2e-07  Score=71.06  Aligned_cols=79  Identities=19%  Similarity=0.355  Sum_probs=70.4

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhc--cCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC----CeEEEE
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQ--FGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD----HLILSV  239 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~--fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~----g~~L~V  239 (247)
                      +||.|.|+|-..+.++|.+++..  .|....++|+.|..++.+.|||||.|.+.+.|.+-.+.++|..+.    .++..|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            79999999999999999988864  367788999999989999999999999999999999999999875    566788


Q ss_pred             eecCC
Q psy13227        240 DWSKS  244 (247)
Q Consensus       240 ~~akp  244 (247)
                      .||+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            88864

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

>KOG0226|consensus

Probab=98.59  E-value=7.4e-08  Score=84.49  Aligned_cols=80  Identities=24%  Similarity=0.393  Sum_probs=74.3

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ...+...||.+.|.-+++.+.|-..|.+|-......+++|+.||+++||+||.|.+..++.+|+..|||..++.++|.+.
T Consensus       186 w~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklR  265 (290)
T KOG0226|consen  186 WDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLR  265 (290)
T ss_pred             CccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhh
Confidence            34566789999999999999999999999998999999999999999999999999999999999999999999987654

>KOG4212|consensus

Probab=98.57  E-value=1.1e-07  Score=88.77  Aligned_cols=76  Identities=25%  Similarity=0.317  Sum_probs=69.0

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|+|.|||.++|+..|++-|..||.|....|+   +.|+++|  .|.|.+.++|++|+..|||..++|+.|.|.|
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadim---e~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIM---ENGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhh---ccCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            3456889999999999999999999999999988873   4688887  8999999999999999999999999999987


Q ss_pred             c
Q psy13227        242 S  242 (247)
Q Consensus       242 a  242 (247)
                      .
T Consensus       608 ~  608 (608)
T KOG4212|consen  608 F  608 (608)
T ss_pred             C
Confidence            4

>KOG4209|consensus

Probab=98.57  E-value=9.1e-08  Score=84.04  Aligned_cols=81  Identities=21%  Similarity=0.345  Sum_probs=76.0

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+...+||+|+...++.+++...|..||.|.++.++.|+.+|.++||+||+|.+.+..+.++. |||..+.++.+.|.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            4667899999999999999999999999999999999999999999999999999999999999 999999999999887


Q ss_pred             cC
Q psy13227        242 SK  243 (247)
Q Consensus       242 ak  243 (247)
                      .+
T Consensus       177 ~r  178 (231)
T KOG4209|consen  177 KR  178 (231)
T ss_pred             ee
Confidence            54

>KOG4205|consensus

Probab=98.56  E-value=1.1e-07  Score=86.70  Aligned_cols=82  Identities=22%  Similarity=0.351  Sum_probs=76.6

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .....|||++||.++++.+|++.|.+||.|..+.++.|..+.+++||+||.|.+++.+.+++. ..-+.|+++.+.|..|
T Consensus        95 ~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA  173 (311)
T KOG4205|consen   95 LRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRA  173 (311)
T ss_pred             cceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeec
Confidence            345689999999999999999999999999999999999999999999999999999999988 6888999999999999


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      .|+
T Consensus       174 ~pk  176 (311)
T KOG4205|consen  174 IPK  176 (311)
T ss_pred             cch
Confidence            886

>KOG1548|consensus

Probab=98.55  E-value=2e-07  Score=84.78  Aligned_cols=81  Identities=22%  Similarity=0.313  Sum_probs=73.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCee--------EEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTS--------KMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD  233 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~--------~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~  233 (247)
                      ....+.|||+|||.++|.+++.++|++||.|.        +|.|-++. .|..+|=|.+.|..+++..-|+..|++..+.
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            34557799999999999999999999999876        37788885 6999999999999999999999999999999


Q ss_pred             CeEEEEeecC
Q psy13227        234 HLILSVDWSK  243 (247)
Q Consensus       234 g~~L~V~~ak  243 (247)
                      |+.|+|+.|+
T Consensus       210 g~~~rVerAk  219 (382)
T KOG1548|consen  210 GKKLRVERAK  219 (382)
T ss_pred             CcEEEEehhh
Confidence            9999999876

>KOG0116|consensus

Probab=98.47  E-value=3.6e-07  Score=86.37  Aligned_cols=83  Identities=24%  Similarity=0.366  Sum_probs=69.5

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      +.+..+|||.|||.++++++|+++|..||.|....|..-...+...+||||+|.+...++.||.+ +-..+++++|.|+.
T Consensus       285 ~~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Vee  363 (419)
T KOG0116|consen  285 RADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEE  363 (419)
T ss_pred             eecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEe
Confidence            34455699999999999999999999999999887655432344449999999999999999996 57779999999998


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      -++.
T Consensus       364 k~~~  367 (419)
T KOG0116|consen  364 KRPG  367 (419)
T ss_pred             cccc
Confidence            7764

>KOG0106|consensus

Probab=98.41  E-value=2.5e-07  Score=80.08  Aligned_cols=71  Identities=24%  Similarity=0.446  Sum_probs=65.6

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      ..+||++|++.+.+.||..||..||.|..+.+.        .||+||+|.+..+|..|+..||+..|.+..+.|+|++.
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            469999999999999999999999999988763        35999999999999999999999999999999999985

>KOG4660|consensus

Probab=98.32  E-value=4.5e-07  Score=86.83  Aligned_cols=71  Identities=17%  Similarity=0.263  Sum_probs=64.1

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEE
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS  238 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~  238 (247)
                      ....+|+|.|||..+++++|..+|+.||+|..|+.     |-..+|..||+|.+..+|++|++.||+..+.|+.|.
T Consensus        73 ~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   73 MNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            45579999999999999999999999999998764     555689999999999999999999999999888776

>KOG4454|consensus

Probab=98.28  E-value=3.3e-07  Score=79.04  Aligned_cols=77  Identities=25%  Similarity=0.263  Sum_probs=69.5

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...||||.|+...++|+-|.++|-.-|+|.++.|..++ .+..+ ||||.|.++-...-|++.|||..+.+..|.|.+-
T Consensus         8 ~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    8 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            34689999999999999999999999999999999886 56667 9999999999999999999999988888777654

>KOG1190|consensus

Probab=98.20  E-value=1.7e-05  Score=73.80  Aligned_cols=76  Identities=25%  Similarity=0.281  Sum_probs=69.3

Q ss_pred             ccEEEEeecCCC-CCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        165 TTAIRISNLSVN-TSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       165 ~~tl~V~nLp~~-~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      .+.|.|+||.+. ++.+.|..+|+.||.|.+|.|..++     +--|+|.|.+...|+-|+..|+|+.+.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            678999999755 7999999999999999999999886     2479999999999999999999999999999999998


Q ss_pred             CC
Q psy13227        244 ST  245 (247)
Q Consensus       244 p~  245 (247)
                      -.
T Consensus       372 H~  373 (492)
T KOG1190|consen  372 HT  373 (492)
T ss_pred             Cc
Confidence            53

>KOG0120|consensus

Probab=98.17  E-value=1.3e-06  Score=83.85  Aligned_cols=83  Identities=27%  Similarity=0.445  Sum_probs=78.0

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .....++|++||...+++.+.+++..||++....++.|..+|.++||||.+|.+......|+..|||..+++..|.|..|
T Consensus       287 ~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A  366 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRA  366 (500)
T ss_pred             cccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehh
Confidence            45568999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      .+.
T Consensus       367 ~~g  369 (500)
T KOG0120|consen  367 IVG  369 (500)
T ss_pred             hcc
Confidence            653

>KOG1995|consensus

Probab=98.07  E-value=7.7e-06  Score=74.90  Aligned_cols=85  Identities=24%  Similarity=0.325  Sum_probs=77.5

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCee--------EEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTS--------KMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD  233 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~--------~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~  233 (247)
                      ..+..+|||.+|+..+++.+|.++|.++|.|.        .|.|-+|++|+.++|-|.|+|.+...|+.||.-+++..+.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            45667899999999999999999999999875        4778899999999999999999999999999999999999


Q ss_pred             CeEEEEeecCCCC
Q psy13227        234 HLILSVDWSKSTN  246 (247)
Q Consensus       234 g~~L~V~~akp~~  246 (247)
                      +..|.|.++..++
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999998887654

>KOG4211|consensus

Probab=98.04  E-value=1.5e-05  Score=75.63  Aligned_cols=77  Identities=22%  Similarity=0.377  Sum_probs=65.8

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .....|++.+|||++|++||.+||+-++ |.++.+.+  .+|+..|-|||+|.+.++++.|++ .+...+.++.|.|--+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Alk-kdR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALK-KDRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHH-hhHHHhCCceEEEEcc
Confidence            4556799999999999999999999995 66654444  589999999999999999999999 5888889999988665


Q ss_pred             C
Q psy13227        243 K  243 (247)
Q Consensus       243 k  243 (247)
                      .
T Consensus        84 ~   84 (510)
T KOG4211|consen   84 G   84 (510)
T ss_pred             C
Confidence            4

>KOG0147|consensus

Probab=97.91  E-value=4.4e-06  Score=80.04  Aligned_cols=79  Identities=23%  Similarity=0.337  Sum_probs=74.0

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+..++|+..|+-..++-||.+||+.+|.|..|.++.|+.++.++|.+||+|.+.+....||. |.|..+.|..|.|..+
T Consensus       177 Rd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~s  255 (549)
T KOG0147|consen  177 RDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQLS  255 (549)
T ss_pred             HhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEeccc
Confidence            456789999999999999999999999999999999999999999999999999999999996 9999999999998764

>KOG4210|consensus

Probab=97.85  E-value=9.1e-06  Score=73.57  Aligned_cols=81  Identities=20%  Similarity=0.313  Sum_probs=74.3

Q ss_pred             ccEEE-EeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        165 TTAIR-ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       165 ~~tl~-V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ..++| |++|+..+++++|+.+|..+|.|..+++..++.++.++|||||.|.+...+..++.. +...+.++.+.+.+..
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDE  262 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCC
Confidence            34555 999999999999999999999999999999999999999999999999999999887 7888999999999988


Q ss_pred             CCC
Q psy13227        244 STN  246 (247)
Q Consensus       244 p~~  246 (247)
                      |++
T Consensus       263 ~~~  265 (285)
T KOG4210|consen  263 PRP  265 (285)
T ss_pred             CCc
Confidence            874

>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=97.70  E-value=0.00015  Score=53.99  Aligned_cols=68  Identities=24%  Similarity=0.309  Sum_probs=47.3

Q ss_pred             cEEEEeecCCCCCHHHHH----HHhhccC-CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        166 TAIRISNLSVNTSENDLE----DLVKQFG-PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~----~lF~~fG-~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      +.|+|.|||.+.+...|+    .|+.-+| .|..|.          .+-|+|.|.+.+.|.+|.+.|+|-.+-|.+|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            579999999999887654    5666676 455442          2589999999999999999999999999999999


Q ss_pred             ecC
Q psy13227        241 WSK  243 (247)
Q Consensus       241 ~ak  243 (247)
                      |..
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            873

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

>KOG1457|consensus

Probab=97.70  E-value=3.6e-05  Score=66.81  Aligned_cols=66  Identities=21%  Similarity=0.398  Sum_probs=54.9

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD  233 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~  233 (247)
                      .-.||||-||..+++|++|+.+|+.|.....++|. .+ .|.  ..||++|.+.+.|..|+..|+|..+.
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~-~~-~g~--~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIR-AR-GGM--PVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEe-cC-CCc--ceEeecHHHHHHHHHHHHHhhcceec
Confidence            34689999999999999999999999876666552 22 444  38999999999999999999998763

>KOG4211|consensus

Probab=97.69  E-value=8.3e-05  Score=70.69  Aligned_cols=76  Identities=20%  Similarity=0.324  Sum_probs=64.4

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeE-EEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSK-MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~-i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...|++.+||+.++++||.+||+..-.+.. |.++.++ .+++.|-|||.|.+.+.|+.|+.. |...|+++-|.|.-+
T Consensus       103 d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  103 DGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            358999999999999999999998755544 6677775 678999999999999999999984 777889998888644

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.57  E-value=0.00019  Score=65.69  Aligned_cols=80  Identities=19%  Similarity=0.388  Sum_probs=62.2

Q ss_pred             CccEEEEeecCCCCCHHH----HH--HHhhccCCeeEEEEeecCCCC-ceeeEE--EEEecCHHHHHHHHHHhcCceeCC
Q psy13227        164 DTTAIRISNLSVNTSEND----LE--DLVKQFGPTSKMYLSRDKTNG-LCKGFA--YIHFKNKADAAKAIQYLNGYGYDH  234 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~d----L~--~lF~~fG~I~~i~l~~d~~tg-~skGfa--FV~F~s~e~A~~Ai~~LnG~~i~g  234 (247)
                      +-.-+||.+|++.+..++    |.  ++|.+||.|..|.|-+...+- ...+.+  ||+|.+.++|.++|...+|..++|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            345689999998876554    43  789999999998775543111 112333  999999999999999999999999


Q ss_pred             eEEEEeecC
Q psy13227        235 LILSVDWSK  243 (247)
Q Consensus       235 ~~L~V~~ak  243 (247)
                      +.|+..|..
T Consensus       193 r~lkatYGT  201 (480)
T COG5175         193 RVLKATYGT  201 (480)
T ss_pred             ceEeeecCc
Confidence            999988764

>KOG4206|consensus

Probab=97.55  E-value=0.00031  Score=60.88  Aligned_cols=76  Identities=21%  Similarity=0.388  Sum_probs=67.5

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC-CeEEEEee
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD-HLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~-g~~L~V~~  241 (247)
                      .....+++.|||..++.+.|..+|..|.....++++..+     .+.|||+|.+...|..|...|+|..+- ...+.|.+
T Consensus       144 ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~  218 (221)
T KOG4206|consen  144 PPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITF  218 (221)
T ss_pred             CCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEecc
Confidence            445689999999999999999999999999999988765     679999999999999999999999887 77788877


Q ss_pred             cC
Q psy13227        242 SK  243 (247)
Q Consensus       242 ak  243 (247)
                      ++
T Consensus       219 a~  220 (221)
T KOG4206|consen  219 AK  220 (221)
T ss_pred             cC
Confidence            65

>KOG4849|consensus

Probab=97.53  E-value=6.5e-05  Score=68.90  Aligned_cols=74  Identities=22%  Similarity=0.288  Sum_probs=65.9

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccC--CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEE
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFG--PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV  239 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG--~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V  239 (247)
                      -.+||+||-|+++++||.+.+...|  .+..+++..++.+|+++|||+|...+....++.++.|....|+|+.-.|
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            5799999999999999999888776  5778888899999999999999999999999999999999998875443

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

Probab=97.50  E-value=0.00032  Score=54.32  Aligned_cols=59  Identities=29%  Similarity=0.440  Sum_probs=39.3

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCc
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGY  230 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~  230 (247)
                      +.|+|.+++..++.++|+++|+.||.|..|.+....      --|||-|.+.+.|+.|+..+.-.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhc
Confidence            578999999999999999999999999998876542      27999999999999999876544

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

>KOG3152|consensus

Probab=97.45  E-value=9.6e-05  Score=65.18  Aligned_cols=73  Identities=19%  Similarity=0.297  Sum_probs=62.3

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCC--------Cceee----EEEEEecCHHHHHHHHHHhcCce
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTN--------GLCKG----FAYIHFKNKADAAKAIQYLNGYG  231 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~t--------g~skG----faFV~F~s~e~A~~Ai~~LnG~~  231 (247)
                      ....||++++|+.++..-|+++|+.||.|-+|+|.....+        |.+++    -|+|+|.+...|.+....||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            3458999999999999999999999999999999876544        33332    36799999999999999999999


Q ss_pred             eCCeE
Q psy13227        232 YDHLI  236 (247)
Q Consensus       232 i~g~~  236 (247)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99864

>KOG0106|consensus

Probab=97.36  E-value=0.00019  Score=62.32  Aligned_cols=70  Identities=26%  Similarity=0.396  Sum_probs=61.2

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.+.|.|++..+.+.+|.+.|.++|.+....+        .++++||.|...++|..|+..|+|..+.++.|.+..
T Consensus        98 s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen   98 THFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             ccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeecc
Confidence            3467999999999999999999999999843322        357999999999999999999999999999999843

>KOG2314|consensus

Probab=97.31  E-value=0.00047  Score=66.70  Aligned_cols=75  Identities=24%  Similarity=0.410  Sum_probs=60.0

Q ss_pred             ccEEEEeecCCCC--CH----HHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC-CeEE
Q psy13227        165 TTAIRISNLSVNT--SE----NDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD-HLIL  237 (247)
Q Consensus       165 ~~tl~V~nLp~~~--te----~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~-g~~L  237 (247)
                      .+.|.|.|.|---  .-    .-|..+|+++|.|..++++.+.++| ++||.|++|.+..+|+.|++.|||+.++ +..+
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            3578899988532  22    2355789999999999999996555 9999999999999999999999999987 4444


Q ss_pred             EEe
Q psy13227        238 SVD  240 (247)
Q Consensus       238 ~V~  240 (247)
                      .|.
T Consensus       137 ~v~  139 (698)
T KOG2314|consen  137 FVR  139 (698)
T ss_pred             Eee
Confidence            443

>KOG0105|consensus

Probab=97.29  E-value=0.0013  Score=55.93  Aligned_cols=61  Identities=23%  Similarity=0.346  Sum_probs=55.3

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD  233 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~  233 (247)
                      ..|.|++||++.+.+||+++...-|.+....+.+|       |++.|+|...++.+-|+..|+...+.
T Consensus       116 ~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  116 YRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             eeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            57899999999999999999999999999888777       38899999999999999999887654

>KOG4307|consensus

Probab=97.27  E-value=0.0015  Score=64.65  Aligned_cols=75  Identities=16%  Similarity=0.390  Sum_probs=66.1

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCee-EEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTS-KMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~-~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      +.|-+.|+|.+++-+||.+||..|-.+- +|.+-++ +.|...|-|.|.|.+.++|.+|...|++..|.++.+.+.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            4799999999999999999999997654 4555555 5899999999999999999999999999999999988864

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

Probab=97.24  E-value=0.00093  Score=45.37  Aligned_cols=52  Identities=25%  Similarity=0.528  Sum_probs=42.2

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHH
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI  224 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai  224 (247)
                      +.|-|++.+.+..+. +...|..||.|..+.+...      .-+.||.|.++.+|++|+
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            568899999876644 5558889999999988622      348999999999999985

>KOG1456|consensus

Probab=97.21  E-value=0.0095  Score=55.45  Aligned_cols=79  Identities=18%  Similarity=0.171  Sum_probs=70.2

Q ss_pred             CCCCccEEEEeecCCC-CCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEE
Q psy13227        161 RNDDTTAIRISNLSVN-TSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV  239 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~-~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V  239 (247)
                      ...+.+.+.|.+|... ++-+.|..+|-.||.|.+|.+++.+     .|-|.|++.+....++|+..||+..+-|.+|.|
T Consensus       283 g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v  357 (494)
T KOG1456|consen  283 GGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNV  357 (494)
T ss_pred             CCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEE
Confidence            3467789999999865 5668899999999999999998876     468999999999999999999999999999999


Q ss_pred             eecCC
Q psy13227        240 DWSKS  244 (247)
Q Consensus       240 ~~akp  244 (247)
                      .+++-
T Consensus       358 ~~SkQ  362 (494)
T KOG1456|consen  358 CVSKQ  362 (494)
T ss_pred             eeccc
Confidence            98873

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.04  E-value=0.0026  Score=48.96  Aligned_cols=78  Identities=17%  Similarity=0.228  Sum_probs=52.4

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEE-EeecC------CCCceeeEEEEEecCHHHHHHHHHHhcCceeCCe-
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMY-LSRDK------TNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHL-  235 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~-l~~d~------~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~-  235 (247)
                      +.+.|.|-+.|+. ....+.+.|++||.|.+.. +.++.      .......+-.|.|.++.+|.+||. .||..+.|. 
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~   82 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSL   82 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcE
Confidence            4467889999998 5567788899999998764 11110      001123588999999999999999 699999874 


Q ss_pred             EEEEeecC
Q psy13227        236 ILSVDWSK  243 (247)
Q Consensus       236 ~L~V~~ak  243 (247)
                      .+-|.+.+
T Consensus        83 mvGV~~~~   90 (100)
T PF05172_consen   83 MVGVKPCD   90 (100)
T ss_dssp             EEEEEE-H
T ss_pred             EEEEEEcH
Confidence            55677764

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.

>KOG1365|consensus

Probab=97.03  E-value=0.0013  Score=61.18  Aligned_cols=74  Identities=19%  Similarity=0.240  Sum_probs=63.6

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCC-eeE--EEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGP-TSK--MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~-I~~--i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ..|++.+||+..+.+||.++|..|.. |..  ++++.+. .|++.|-|||.|.+.++|..|....+.+....+.|.|-
T Consensus       281 dcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvf  357 (508)
T KOG1365|consen  281 DCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVF  357 (508)
T ss_pred             CeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEe
Confidence            47999999999999999999998864 433  7888884 79999999999999999999999887777778887774

>KOG1190|consensus

Probab=96.92  E-value=0.0018  Score=60.67  Aligned_cols=78  Identities=23%  Similarity=0.266  Sum_probs=65.6

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCe-EEEEee
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHL-ILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~-~L~V~~  241 (247)
                      +.+.+|..+|+|.+++|++|+.+|..-|...+.+..    -++.+-+|++.+.+.++|-.|+-.++.+.++.. .|+|.|
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkf----f~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSF  487 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKF----FQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSF  487 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeee----cCCCcceeecccCChhHhhhhccccccccCCCCceEEEEe
Confidence            455689999999999999999999988876655442    234456999999999999999999999988755 899999


Q ss_pred             cCC
Q psy13227        242 SKS  244 (247)
Q Consensus       242 akp  244 (247)
                      ++.
T Consensus       488 Sks  490 (492)
T KOG1190|consen  488 SKS  490 (492)
T ss_pred             ecc
Confidence            986

>KOG1548|consensus

Probab=96.87  E-value=0.0038  Score=57.35  Aligned_cols=77  Identities=19%  Similarity=0.327  Sum_probs=59.3

Q ss_pred             CCccEEEEeecC--C--CCCH-------HHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCce
Q psy13227        163 DDTTAIRISNLS--V--NTSE-------NDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG  231 (247)
Q Consensus       163 ~~~~tl~V~nLp--~--~~te-------~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~  231 (247)
                      ...++|.+.|+=  .  ..+.       ++|.+-..+||+|.+|.|.-    ..+.|.+-|.|.+.++|..+|+.|+|..
T Consensus       263 r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~GR~  338 (382)
T KOG1548|consen  263 RADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDGRW  338 (382)
T ss_pred             cCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcCee
Confidence            445688888872  1  2232       34455568999999987642    3468999999999999999999999999


Q ss_pred             eCCeEEEEeecC
Q psy13227        232 YDHLILSVDWSK  243 (247)
Q Consensus       232 i~g~~L~V~~ak  243 (247)
                      |+|+.|......
T Consensus       339 fdgRql~A~i~D  350 (382)
T KOG1548|consen  339 FDGRQLTASIWD  350 (382)
T ss_pred             ecceEEEEEEeC
Confidence            999999877543

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

Probab=96.76  E-value=0.0076  Score=44.81  Aligned_cols=54  Identities=17%  Similarity=0.310  Sum_probs=42.9

Q ss_pred             EEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcC
Q psy13227        167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG  229 (247)
Q Consensus       167 tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG  229 (247)
                      ..+|+ +|..+...||.++|++||.|. |.++.|.       -|||...+++.+..++..++-
T Consensus        11 VFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   11 VFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             EEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHHHHTT
T ss_pred             EEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHHHhcc
Confidence            45665 999999999999999999986 7777764       799999999999999988764

; 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.

>KOG0120|consensus

Probab=96.50  E-value=0.0077  Score=58.31  Aligned_cols=63  Identities=16%  Similarity=0.353  Sum_probs=51.2

Q ss_pred             HHHHHhhccCCeeEEEEeecCCC---CceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        181 DLEDLVKQFGPTSKMYLSRDKTN---GLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       181 dL~~lF~~fG~I~~i~l~~d~~t---g~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      +++.-+++||.|..|.+++.-..   .-..|--||+|.+.+++++|++.|+|..|.|+++...|-.
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            34445678999999999887222   3345778999999999999999999999999999887743

>KOG1456|consensus

Probab=96.47  E-value=0.019  Score=53.52  Aligned_cols=75  Identities=20%  Similarity=0.283  Sum_probs=61.8

Q ss_pred             cEEEEeecC--CCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC-C-eEEEEee
Q psy13227        166 TAIRISNLS--VNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD-H-LILSVDW  241 (247)
Q Consensus       166 ~tl~V~nLp--~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~-g-~~L~V~~  241 (247)
                      ..|.++=|+  +.++-+.|..+..+.|+|.+|.|.+.  +|.   -|.|+|.+.+.|++|...|||..|. | ..|+|+|
T Consensus       121 ~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIey  195 (494)
T KOG1456|consen  121 KVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEY  195 (494)
T ss_pred             eEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechhHHHHHHHhhcccccccccceeEEEEe
Confidence            345555554  55788999999999999999988765  454   5899999999999999999999854 4 5799999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      |+|.
T Consensus       196 AkP~  199 (494)
T KOG1456|consen  196 AKPT  199 (494)
T ss_pred             cCcc
Confidence            9985

>KOG2193|consensus

Probab=96.36  E-value=0.0026  Score=59.94  Aligned_cols=73  Identities=27%  Similarity=0.351  Sum_probs=58.5

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccC-CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCce-eCCeEEEEeecC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFG-PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG-YDHLILSVDWSK  243 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG-~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~-i~g~~L~V~~ak  243 (247)
                      ..+|++||++.++.+||..+|...- ....-+++       -.||+||++.+...|.+|++.++|.. +.|.++.|+.+-
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~-------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee-------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            4699999999999999999997541 11111222       24799999999999999999999985 889999998877


Q ss_pred             CC
Q psy13227        244 ST  245 (247)
Q Consensus       244 p~  245 (247)
                      |+
T Consensus        75 ~k   76 (584)
T KOG2193|consen   75 PK   76 (584)
T ss_pred             hH
Confidence            65

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.35  E-value=0.025  Score=46.33  Aligned_cols=70  Identities=17%  Similarity=0.286  Sum_probs=50.7

Q ss_pred             cEEEEeecCC------CCCH---HHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeE
Q psy13227        166 TAIRISNLSV------NTSE---NDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLI  236 (247)
Q Consensus       166 ~tl~V~nLp~------~~te---~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~  236 (247)
                      .||.|+-+.+      ..++   .+|.+.|..||.+.-++++-+        --+|+|.+-+.|.+|+. |+|..+.|+.
T Consensus        28 aTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g~~   98 (146)
T PF08952_consen   28 ATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNGRT   98 (146)
T ss_dssp             -EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEETTEE
T ss_pred             ceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEECCEE
Confidence            4777876662      2232   256677889998877776554        47899999999999999 8999999999


Q ss_pred             EEEeecCC
Q psy13227        237 LSVDWSKS  244 (247)
Q Consensus       237 L~V~~akp  244 (247)
                      |.|..-.|
T Consensus        99 l~i~LKtp  106 (146)
T PF08952_consen   99 LKIRLKTP  106 (146)
T ss_dssp             EEEEE---
T ss_pred             EEEEeCCc
Confidence            99987665

; PDB: 1UFW_A 2DNR_A.

>KOG2202|consensus

Probab=96.03  E-value=0.0031  Score=55.75  Aligned_cols=62  Identities=19%  Similarity=0.359  Sum_probs=51.3

Q ss_pred             HHHHHHhh-ccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        180 NDLEDLVK-QFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       180 ~dL~~lF~-~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +||...|. +||.|..+.|-.+. .-.-.|-+||.|...++|++|+..||+..|.|+.|..+++
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            34444445 89999998776664 4456789999999999999999999999999999998875

>KOG0128|consensus

Probab=96.01  E-value=0.0024  Score=64.40  Aligned_cols=78  Identities=21%  Similarity=0.280  Sum_probs=71.7

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      ..++|+|+|+..+.++|+.++..+|.+.+..++..+ .|+++|.|||.|.+..++.+++...++..+.-..+.|..+.|
T Consensus       737 ~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  737 ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            469999999999999999999999999999998886 799999999999999999999999888888888888887665

>KOG2416|consensus

Probab=96.00  E-value=0.0082  Score=58.67  Aligned_cols=77  Identities=21%  Similarity=0.357  Sum_probs=62.2

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhcc-CCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCcee---CCeE
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQF-GPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGY---DHLI  236 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~f-G~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i---~g~~  236 (247)
                      +...++.|||.||-.-+|.-+|+.|+.+- |.|...  ..|+    -+..|||.|.+.++|...+..|||..|   +.+.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHH--HHHH----hhcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            44567899999999999999999999955 445544  3342    466999999999999999999999986   4677


Q ss_pred             EEEeecC
Q psy13227        237 LSVDWSK  243 (247)
Q Consensus       237 L~V~~ak  243 (247)
                      |.+.|..
T Consensus       514 L~adf~~  520 (718)
T KOG2416|consen  514 LIADFVR  520 (718)
T ss_pred             eEeeecc
Confidence            8888864

>KOG0129|consensus

Probab=95.80  E-value=0.03  Score=53.94  Aligned_cols=64  Identities=13%  Similarity=0.271  Sum_probs=48.8

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCC---CCceee---EEEEEecCHHHHHHHHHHh
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKT---NGLCKG---FAYIHFKNKADAAKAIQYL  227 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~---tg~skG---faFV~F~s~e~A~~Ai~~L  227 (247)
                      .-++.|||++||++++|+.|...|..||.+. +.++...+   --.++|   |+|+.|.++.....-+...
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            4457899999999999999999999999865 55542211   123456   9999999988887766653

>KOG0128|consensus

Probab=95.75  E-value=0.00049  Score=69.26  Aligned_cols=71  Identities=25%  Similarity=0.343  Sum_probs=61.0

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD  233 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~  233 (247)
                      .+..++||+||+..+.+.+|...|..+|.+..+++.....+++.+|+||+.|...+++.+||....+..++
T Consensus       665 R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  665 RDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            34578999999999999999999999998887777655568999999999999999999999876665554

>KOG4307|consensus

Probab=95.55  E-value=0.019  Score=57.16  Aligned_cols=79  Identities=18%  Similarity=0.131  Sum_probs=67.4

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeE-EEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSK-MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~-i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      +.....|||..||..+.+.++.++|.....|.. |+|.+.+ +++.++-|||.|...+.+..|...-..+.+++++|+|+
T Consensus       431 ~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~  509 (944)
T KOG4307|consen  431 GGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVD  509 (944)
T ss_pred             CCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEee
Confidence            355679999999999999999999987766665 8887775 88899999999999888888887667777888999997


Q ss_pred             e
Q psy13227        241 W  241 (247)
Q Consensus       241 ~  241 (247)
                      -
T Consensus       510 s  510 (944)
T KOG4307|consen  510 S  510 (944)
T ss_pred             c
Confidence            4

>KOG1365|consensus

Probab=95.49  E-value=0.072  Score=49.90  Aligned_cols=70  Identities=17%  Similarity=0.292  Sum_probs=53.8

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhcc----CCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQF----GPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH  234 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~f----G~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g  234 (247)
                      .+.-.|++.+||+++++.|+.++|.+-    |....|.++... .|+..|-|||.|..+++|+.|+.. |...++-
T Consensus       159 ~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGq  232 (508)
T KOG1365|consen  159 ENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK-HRQNIGQ  232 (508)
T ss_pred             ccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH-HHHHHhH
Confidence            344679999999999999999999732    244456555553 789999999999999999999984 4333333

>KOG1855|consensus

Probab=95.47  E-value=0.011  Score=55.76  Aligned_cols=69  Identities=20%  Similarity=0.295  Sum_probs=56.6

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeec---CCC--Cce--------eeEEEEEecCHHHHHHHHHHhcC
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRD---KTN--GLC--------KGFAYIHFKNKADAAKAIQYLNG  229 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d---~~t--g~s--------kGfaFV~F~s~e~A~~Ai~~LnG  229 (247)
                      -.+++|.+-|||.+-.-+-|.+||+.+|.|..|+|..-   ++.  +..        +-+|||+|...+.|.+|.+.||-
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            36789999999999888999999999999999998765   222  222        45799999999999999998865


Q ss_pred             ce
Q psy13227        230 YG  231 (247)
Q Consensus       230 ~~  231 (247)
                      ..
T Consensus       309 e~  310 (484)
T KOG1855|consen  309 EQ  310 (484)
T ss_pred             hh
Confidence            44

>KOG0129|consensus

Probab=95.41  E-value=0.038  Score=53.26  Aligned_cols=64  Identities=20%  Similarity=0.258  Sum_probs=59.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhh-ccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHH
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVK-QFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY  226 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~-~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~  226 (247)
                      |...||||++||.-++-.+|-.+|. -||.|..+.|-.|++-+.++|-|=|+|.+...--+||..
T Consensus       368 DprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  368 DPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            5567999999999999999999998 799999999999988899999999999999999999984

>KOG0112|consensus

Probab=95.25  E-value=0.021  Score=58.26  Aligned_cols=77  Identities=22%  Similarity=0.326  Sum_probs=66.4

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC--eEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH--LILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g--~~L~V~  240 (247)
                      ...+.++|++|..++....|...|..||.|..|.+-    .|.  -||||.|.+...++.|+..|-|..+++  +.|+|.
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~----hgq--~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvd  526 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR----HGQ--PYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVD  526 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcceeeecc----cCC--cceeeecccCccchhhHHHHhcCcCCCCCcccccc
Confidence            455789999999999999999999999999987662    233  499999999999999999999999885  569999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      |+.+.
T Consensus       527 la~~~  531 (975)
T KOG0112|consen  527 LASPP  531 (975)
T ss_pred             cccCC
Confidence            88753

>KOG2068|consensus

Probab=95.19  E-value=0.0076  Score=55.19  Aligned_cols=80  Identities=20%  Similarity=0.370  Sum_probs=60.6

Q ss_pred             cEEEEeecCCCCC-HHHHH--HHhhccCCeeEEEEeecCC--CCc-eeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEE
Q psy13227        166 TAIRISNLSVNTS-ENDLE--DLVKQFGPTSKMYLSRDKT--NGL-CKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV  239 (247)
Q Consensus       166 ~tl~V~nLp~~~t-e~dL~--~lF~~fG~I~~i~l~~d~~--tg~-skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V  239 (247)
                      .-+||.+|+.... +..|.  +.|.+||.|..|.+.+++.  .+. .-.-++|+|...++|..||...+|..++|+.|+.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            4578888887764 44554  6799999999998887752  111 1123799999999999999999999999988777


Q ss_pred             eecCCC
Q psy13227        240 DWSKST  245 (247)
Q Consensus       240 ~~akp~  245 (247)
                      .+..++
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            666543

>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=94.83  E-value=0.061  Score=45.37  Aligned_cols=80  Identities=18%  Similarity=0.227  Sum_probs=50.1

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhc-cCCe---eEEE--EeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC--
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQ-FGPT---SKMY--LSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH--  234 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~-fG~I---~~i~--l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g--  234 (247)
                      .+...|-|.+||+.++++++.+.+++ ++..   ..+.  ............-|||.|.+.++...-...++|+.+.+  
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            44568999999999999999998887 6665   2332  11111111234579999999999999999999988642  


Q ss_pred             ---eEEEEeec
Q psy13227        235 ---LILSVDWS  242 (247)
Q Consensus       235 ---~~L~V~~a  242 (247)
                         ....|++|
T Consensus        85 g~~~~~~VE~A   95 (176)
T PF03467_consen   85 GNEYPAVVEFA   95 (176)
T ss_dssp             S-EEEEEEEE-
T ss_pred             CCCcceeEEEc
Confidence               23456655

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.

>KOG2135|consensus

Probab=94.71  E-value=0.026  Score=53.87  Aligned_cols=76  Identities=18%  Similarity=0.322  Sum_probs=61.3

Q ss_pred             CCccEEEEeecCCCC-CHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        163 DDTTAIRISNLSVNT-SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~-te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      .+.+.|-+.-.+... +..+|...|.+||.|..|.+-..      --.|.|+|.+..+|-.|.. ..+..|+++.|+|.|
T Consensus       370 ~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~w  442 (526)
T KOG2135|consen  370 VDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFW  442 (526)
T ss_pred             cccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEEEE
Confidence            355566666666655 55889999999999999987554      2378999999999977766 699999999999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      -+|.
T Consensus       443 hnps  446 (526)
T KOG2135|consen  443 HNPS  446 (526)
T ss_pred             ecCC
Confidence            8874

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

Probab=94.71  E-value=0.18  Score=35.47  Aligned_cols=54  Identities=20%  Similarity=0.325  Sum_probs=44.5

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhcc---CCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHh
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQF---GPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL  227 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~f---G~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~L  227 (247)
                      ..|+|.++.. ++.+||+.+|..|   ....+|.++-|.       -|-|.|.+.+.|.+|+..|
T Consensus         6 eavhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            4799999955 7788999999988   235679999885       5779999999999999764

>KOG0115|consensus

Probab=94.70  E-value=0.038  Score=49.08  Aligned_cols=63  Identities=24%  Similarity=0.337  Sum_probs=55.4

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG  229 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG  229 (247)
                      ..|||.||+..++-+.|...|+.||+|.+..+.-| ..++..+-++|.|...-.|..|+..++-
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~~   94 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCRE   94 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhcc
Confidence            67999999999999999999999999998776666 3688888999999999999999987643

>KOG4676|consensus

Probab=93.82  E-value=0.1  Score=48.91  Aligned_cols=76  Identities=14%  Similarity=0.273  Sum_probs=57.1

Q ss_pred             EEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCC---CCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKT---NGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       167 tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~---tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .|.|.||++.++.++++.||.-.|.|..+.|..+..   -....-.|||.|.+...+..|...-|-..++--.|.+-+.
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecC
Confidence            799999999999999999999999999988765321   1234568999999999999887744444444444444443

>KOG1996|consensus

Probab=93.78  E-value=0.2  Score=45.46  Aligned_cols=63  Identities=14%  Similarity=0.229  Sum_probs=49.8

Q ss_pred             HHHHHHhhccCCeeEEEEeecCCCCcee-eEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        180 NDLEDLVKQFGPTSKMYLSRDKTNGLCK-GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       180 ~dL~~lF~~fG~I~~i~l~~d~~tg~sk-GfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +++.+-..+||.|.+|.|...+.--... ---||+|...+.|-+|+--|||..|+|+.++..|.
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            4566778899999998877664222222 24699999999999999999999999999887664

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=93.25  E-value=1  Score=35.20  Aligned_cols=67  Identities=15%  Similarity=0.171  Sum_probs=49.4

Q ss_pred             cEEEEee-cCCCCCHHHHHHHhhccC-CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC
Q psy13227        166 TAIRISN-LSVNTSENDLEDLVKQFG-PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH  234 (247)
Q Consensus       166 ~tl~V~n-Lp~~~te~dL~~lF~~fG-~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g  234 (247)
                      +.+.|-- .|..+.-++|..+.+.+- .|..++|++|.  ..++-.+.+.|.+.++|..-...+||..++.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            3444444 445555566766666553 57788998884  3467789999999999999999999999875

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4660|consensus

Probab=92.92  E-value=0.16  Score=49.47  Aligned_cols=83  Identities=22%  Similarity=0.354  Sum_probs=61.9

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhc----------------------------cCCeeEEEEeecCCCCceeeEEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQ----------------------------FGPTSKMYLSRDKTNGLCKGFAYIHF  214 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~----------------------------fG~I~~i~l~~d~~tg~skGfaFV~F  214 (247)
                      +..+++-|.|++......||..++..                            .|.-..++++.|-.+....|||||.|
T Consensus       359 ~~Rtt~~i~ni~n~~~~~dl~~Ildge~~rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm  438 (549)
T KOG4660|consen  359 DRRTTVMIKNIPNKYGQLDLLRILDGECPRTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINM  438 (549)
T ss_pred             cchhhhhhhccccchhHHHHHHHHhCcCchhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEee
Confidence            44466777777776666666655431                            34445678888877778899999999


Q ss_pred             cCHHHHHHHHHHhcCceeC----CeEEEEeecCCC
Q psy13227        215 KNKADAAKAIQYLNGYGYD----HLILSVDWSKST  245 (247)
Q Consensus       215 ~s~e~A~~Ai~~LnG~~i~----g~~L~V~~akp~  245 (247)
                      .+.+++..+.+++||+.+.    .++..+.||+-+
T Consensus       439 ~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQ  473 (549)
T KOG4660|consen  439 TSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQ  473 (549)
T ss_pred             cCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhh
Confidence            9999999999999999754    455677777643

>KOG2253|consensus

Probab=92.43  E-value=0.2  Score=49.74  Aligned_cols=81  Identities=16%  Similarity=0.172  Sum_probs=66.3

Q ss_pred             ccCCCCCCCCCCCCcCCCcccCCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHH
Q psy13227        140 YVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD  219 (247)
Q Consensus       140 yvpp~~r~~~~~~~~~~~~~~~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~  219 (247)
                      |++|.+.-- .          -....-++||+|+...+..+-+..++..+|.|.++..+.         |+|..|.....
T Consensus        26 ~~~p~qp~~-~----------~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~   85 (668)
T KOG2253|consen   26 YVVPIQPVF-Q----------PLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIG   85 (668)
T ss_pred             cccCCcccc-c----------CCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHH
Confidence            888877655 1          124446899999999999999999999999887765432         99999999999


Q ss_pred             HHHHHHHhcCceeCCeEEEEe
Q psy13227        220 AAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       220 A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ..+|+..|+-..++|..|.+.
T Consensus        86 ~~ra~r~~t~~~~~~~kl~~~  106 (668)
T KOG2253|consen   86 DLRASRLLTELNIDDQKLIEN  106 (668)
T ss_pred             HHHHHHHhcccCCCcchhhcc
Confidence            999999999888988776553

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=92.30  E-value=0.76  Score=32.91  Aligned_cols=60  Identities=13%  Similarity=0.207  Sum_probs=36.6

Q ss_pred             CCCCCHHHHHHHhhccCC-----eeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        174 SVNTSENDLEDLVKQFGP-----TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       174 p~~~te~dL~~lF~~fG~-----I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      -..++..+|..++...+.     |-+|.+..+        |+||+... +.|..++..|++..+.|+.|+|+.|
T Consensus        10 ~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   10 KDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             ccCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            345788889888877654     456766443        89998874 5889999999999999999999865

; PDB: 2G0C_A 3MOJ_B.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=91.97  E-value=0.79  Score=37.63  Aligned_cols=74  Identities=23%  Similarity=0.401  Sum_probs=56.0

Q ss_pred             CCCccEEEEeecCCCCCH-HHHH---HHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEE
Q psy13227        162 NDDTTAIRISNLSVNTSE-NDLE---DLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLIL  237 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te-~dL~---~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L  237 (247)
                      .....||-|.=|..++.. +||+   ..++.||+|.+|.+.     |  +--|.|.|.+...|=.|+.+++. ..-|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            456678999877766643 4444   557889999998763     3  33799999999999999998776 5667788


Q ss_pred             EEeecC
Q psy13227        238 SVDWSK  243 (247)
Q Consensus       238 ~V~~ak  243 (247)
                      .+.|-.
T Consensus       155 qCsWqq  160 (166)
T PF15023_consen  155 QCSWQQ  160 (166)
T ss_pred             Eeeccc
Confidence            888854

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=91.90  E-value=0.075  Score=32.36  Aligned_cols=19  Identities=26%  Similarity=0.779  Sum_probs=15.7

Q ss_pred             eeeeeecc-CCccccCCCCc
Q psy13227         77 FISCRTCK-GAHFTNNCPFK   95 (247)
Q Consensus        77 ~~~Cr~C~-g~h~t~~CP~k   95 (247)
                      ..+|++|+ ..||...||.+
T Consensus         8 ~Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    8 GYVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CCEeecCCCCCccHhHCCCC
Confidence            57999993 46999999973

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=91.88  E-value=0.39  Score=40.88  Aligned_cols=61  Identities=21%  Similarity=0.319  Sum_probs=44.8

Q ss_pred             HHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhc--CceeCCeEEEEeecCCC
Q psy13227        179 ENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN--GYGYDHLILSVDWSKST  245 (247)
Q Consensus       179 e~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~Ln--G~~i~g~~L~V~~akp~  245 (247)
                      ...|+++|..|+.+..+.+.+.      -+-..|.|.+.+.|.+|...|+  +..++|..|+|-|+.+.
T Consensus         9 ~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    9 LAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             HHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            4788999999999887766554      2357899999999999999999  99999999999988643

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG4285|consensus

Probab=91.59  E-value=0.86  Score=41.60  Aligned_cols=63  Identities=17%  Similarity=0.185  Sum_probs=48.7

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeE
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLI  236 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~  236 (247)
                      +=|-|-++++.- -..|..+|.+||.|.+....      ..-.|-+|.|.++-+|++||. .||..|+|..
T Consensus       198 ~WVTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALs-kng~ii~g~v  260 (350)
T KOG4285|consen  198 TWVTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALS-KNGTIIDGDV  260 (350)
T ss_pred             ceEEEeccCccc-hhHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhh-hcCeeeccce
Confidence            345666777753 35677889999999876543      223499999999999999999 5999998865

>KOG0112|consensus

Probab=90.95  E-value=0.053  Score=55.37  Aligned_cols=78  Identities=12%  Similarity=0.124  Sum_probs=63.9

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.+||++||...+++.+|+..|..+|.|.+|.|-.-+ -+.---|+||.|.+...+.+|...+.+..|..-.+++.+.
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            45689999999999999999999999999998875543 2333459999999999999999999998876555555554

>KOG4210|consensus

Probab=89.47  E-value=0.21  Score=45.29  Aligned_cols=80  Identities=18%  Similarity=0.118  Sum_probs=64.4

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...+++|++++.+++.+.++..++..+|......+........++|++++.|...+.+..++.....+...+..+...+.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            45689999999999999988889999998777777666678899999999999999999999954445666655544433

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=89.02  E-value=0.18  Score=26.64  Aligned_cols=16  Identities=31%  Similarity=0.953  Sum_probs=13.6

Q ss_pred             eeeeeccC-CccccCCC
Q psy13227         78 ISCRTCKG-AHFTNNCP   93 (247)
Q Consensus        78 ~~Cr~C~g-~h~t~~CP   93 (247)
                      ++|..|+. +|+...||
T Consensus         1 ~~C~~C~~~GH~~~~Cp   17 (18)
T PF00098_consen    1 RKCFNCGEPGHIARDCP   17 (18)
T ss_dssp             SBCTTTSCSSSCGCTSS
T ss_pred             CcCcCCCCcCcccccCc
Confidence            36999955 99999998

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=88.58  E-value=0.18  Score=32.68  Aligned_cols=18  Identities=33%  Similarity=0.931  Sum_probs=15.2

Q ss_pred             eeeeeeccC-CccccCCCC
Q psy13227         77 FISCRTCKG-AHFTNNCPF   94 (247)
Q Consensus        77 ~~~Cr~C~g-~h~t~~CP~   94 (247)
                      .+.|..|.+ +|||.-||-
T Consensus         4 ~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCcCcccCCCCcchhhCCC
Confidence            467999954 999999995

>KOG0804|consensus

Probab=84.65  E-value=3.1  Score=39.92  Aligned_cols=68  Identities=22%  Similarity=0.331  Sum_probs=58.6

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhcc-CCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQF-GPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH  234 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~f-G~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g  234 (247)
                      .+.|.|-.+|-.++--||..|...| -.|..|++++|.  --.+-..+|.|.+..+|..-...+||..|+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~--~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG--MPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC--CCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            6789999999999999999998876 468999999974  2345577999999999999999999998875

>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=84.53  E-value=5.5  Score=28.24  Aligned_cols=55  Identities=15%  Similarity=0.339  Sum_probs=42.3

Q ss_pred             CCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEE
Q psy13227        176 NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV  239 (247)
Q Consensus       176 ~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V  239 (247)
                      .++-++++..|..|+- .  .|..|+ ||     =||.|.+..+|+++....+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-~--~I~~d~-tG-----fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-D--RIRDDR-TG-----FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-c--eEEecC-CE-----EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            3567899999999964 2  233443 33     379999999999999999999988777665

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	247
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		2e-23
1h6k_Z	98	Nuclear Cap Binding Complex Length = 98		4e-07
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		5e-07
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		5e-07
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		6e-07
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		9e-07
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		1e-06
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		2e-06
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		6e-06
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-05
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-05
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		2e-05
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		3e-05
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		3e-05
1no8_A	106	Solution Structure Of The Nuclear Factor Aly Rbd Do		4e-05
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		5e-05
3ulh_A	107	Crystal Structure Of A Rna Binding Domain Of Tho Co		8e-05
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		8e-05
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		1e-04
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		1e-04
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		2e-04
2f3j_A	177	The Solution Structure Of The Ref2-I Mrna Export Fa		2e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		2e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		2e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-04
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		2e-04
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		2e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		2e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		3e-04
2yka_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		3e-04
2kt5_A	124	Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To H		3e-04
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		3e-04
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		3e-04
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		4e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		5e-04
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		5e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		6e-04
2cpx_A	115	Solution Structure Of Rna Binding Domain In Hypothe		7e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		8e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		8e-04
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		9e-04

>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 3 Subunit 4 Length = 103

Iteration: 1
 Score =  105 bits (263), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 48/88 (54%), Positives = 67/88 (76%), Gaps = 1/88 (1%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           RR DD   IR++NLS +T E DL++L + FG  S++YL++DKT G  KGFA+I F  + D
Sbjct: 10  RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69
Query: 220 AAKAIQYLNGYGYDHLILSVDWSK-STN 246
           AA+AI  ++G+GYDHLIL+V+W+K STN
Sbjct: 70  AARAIAGVSGFGYDHLILNVEWAKPSTN 97

>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex Length = 98

Iteration: 1
 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
           +  + + NLS  T+E  + +L  + G   K+ +  DK    C GF ++ + ++ADA  A+
Sbjct: 18  SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC-GFCFVEYYSRADAENAM 76
Query: 225 QYLNGYGYDHLILSVDW 241
           +Y+NG   D  I+  DW
Sbjct: 77  RYINGTRLDDRIIRTDW 93

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 28/95 (29%), Positives = 50/95 (52%), Gaps = 6/95 (6%)
Query: 148 GPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
           GP G R         D    + +  LS+ T+E DL ++  ++GP + + +  D+ +   +
Sbjct: 1   GPLGSRAN------PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 54
Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS 242
           GFA+++F+N  DA +A +  NG   D   + VD+S
Sbjct: 55  GFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 89

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 46/80 (57%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           D    + +  LS+ T+E DL ++  ++GP + + +  D+ +   +GFA+++F+N  DA +
Sbjct: 44  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103
Query: 223 AIQYLNGYGYDHLILSVDWS 242
           A +  NG   D   + VD+S
Sbjct: 104 AKERANGMELDGRRIRVDFS 123

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 50.8 bits (120), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 46/80 (57%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           D    + +  LS+ T+E DL ++  ++GP + + +  D+ +   +GFA+++F+N  DA +
Sbjct: 13  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 223 AIQYLNGYGYDHLILSVDWS 242
           A +  NG   D   + VD+S
Sbjct: 73  AKERANGMELDGRRIRVDFS 92

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 50.4 bits (119), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 44/78 (56%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T++++ NL+  TS + L  + +++G    +Y+ RD+     +GFA++ F +K DA  A+ 
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 226 YLNGYGYDHLILSVDWSK 243
            ++G   D   L V  ++
Sbjct: 108 AMDGAVLDGRELRVQMAR 125

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 41/77 (53%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
           +  + + NLS  T+E  + +L  + G   K+ +  DK      GF ++ + ++ADA  A+
Sbjct: 39  SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 225 QYLNGYGYDHLILSVDW 241
           +Y+NG   D  I+  DW
Sbjct: 99  RYINGTRLDDRIIRTDW 115

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 44/78 (56%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T++++ NL+  TS + L  + +++G    +Y+ RD+     +GFA++ F +K DA  A+ 
Sbjct: 71  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 226 YLNGYGYDHLILSVDWSK 243
            ++G   D   L V  ++
Sbjct: 131 AMDGAVLDGRELRVQMAR 148

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 47.8 bits (112), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 22/79 (27%), Positives = 42/79 (53%)
Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
           D   + +  LS +T+E  LE +  ++G  S++ + +D+     +GF ++ F+N  DA  A
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 224 IQYLNGYGYDHLILSVDWS 242
           +  +NG   D   + VD +
Sbjct: 71  MMAMNGKSVDGRQIRVDQA 89

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 40.4 bits (93), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 20/82 (24%), Positives = 40/82 (48%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + ++ L  N ++++L  L    G      L RDK  G   G+ ++++    DA +AI 
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 226 YLNGYGYDHLILSVDWSKSTNQ 247
            LNG       + V +++ +++
Sbjct: 63  TLNGLRLQSKTIKVSYARPSSE 84

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 40.4 bits (93), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 20/82 (24%), Positives = 40/82 (48%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + ++ L  N ++++L  L    G      L RDK  G   G+ ++++    DA +AI 
Sbjct: 3   TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 226 YLNGYGYDHLILSVDWSKSTNQ 247
            LNG       + V +++ +++
Sbjct: 63  TLNGLRLQSKTIKVSYARPSSE 84

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 44/82 (53%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           D    + +  LS+ T+E DL ++  ++GP + + +  D+ +   +GFA+++F+N  DA +
Sbjct: 13  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72
Query: 223 AIQYLNGYGYDHLILSVDWSKS 244
           A +  NG   D   + V    S
Sbjct: 73  AKERANGMELDGRRIRVSGPSS 94

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 36/70 (51%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NLS  +SE DLE L   +GP S+++   D      KGFA++ F     A KA   ++G
Sbjct: 13  VRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDG 72
Query: 230 YGYDHLILSV 239
             +   +L V
Sbjct: 73  QVFQGRMLHV 82

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           D    + I  L+  T+E  L+ +  + GP S++ L +D+T+   +GFA+I F+N ADA  
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKN 63
Query: 223 AIQYLNGYGYDHLILSVDWSK 243
           A + +NG       + V+ +K
Sbjct: 64  AAKDMNGKSLHGKAIKVEQAK 84

>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain Length = 106

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + +SNL    S+ D+++L  +FG   K  +  D++ G   G A +HF+ KADA KA++  
Sbjct: 31  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMKQY 89
Query: 228 NGYGYD 233
           NG   D
Sbjct: 90  NGVPLD 95

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/84 (25%), Positives = 41/84 (48%)
Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
           N  +  + + ++  + +E  + DL    GP   + +  D   G  KG+A+I F++   +A
Sbjct: 1   NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 60
Query: 222 KAIQYLNGYGYDHLILSVDWSKST 245
            A++ LNGY      L   +S ++
Sbjct: 61  SAVRNLNGYQLGSRFLKCGYSSNS 84

>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A Resolution Length = 107

Iteration: 1
 Score = 43.9 bits (102), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + +SNL    S+ D+++L  +FG   K  +  D++ G   G A +HF+ KADA KA +  
Sbjct: 32  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAXKQY 90
Query: 228 NGYGYD 233
           NG   D
Sbjct: 91  NGVPLD 96

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 43.9 bits (102), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/82 (24%), Positives = 41/82 (50%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
           +  + + ++  + +E  + DL    GP   + +  D   G  KG+A+I F++   +A A+
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 225 QYLNGYGYDHLILSVDWSKSTN 246
           + LNGY      L   +S +++
Sbjct: 62  RNLNGYQLGSRFLKCGYSSNSD 83

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/82 (24%), Positives = 41/82 (50%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
           +  + + ++  + +E  + DL    GP   + +  D   G  KG+A+I F++   +A A+
Sbjct: 3   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 225 QYLNGYGYDHLILSVDWSKSTN 246
           + LNGY      L   +S +++
Sbjct: 63  RNLNGYQLGSRFLKCGYSSNSD 84

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/78 (25%), Positives = 39/78 (50%)
Query: 167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
           ++ + N+    +E  L+D+  + GP     L  D+  G  KG+ +  ++++  A  A++ 
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 227 LNGYGYDHLILSVDWSKS 244
           LNG  +    L VD + S
Sbjct: 70  LNGREFSGRALRVDNAAS 87

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/81 (24%), Positives = 41/81 (50%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           D    +++ NL+  TS + L  + +++G    +Y+ R+      +GFA++ F ++ DA  
Sbjct: 11  DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQD 70
Query: 223 AIQYLNGYGYDHLILSVDWSK 243
           A   ++G   D   L V  ++
Sbjct: 71  AEAAMDGAELDGRELRVQVAR 91

>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor (Residues 1-155) Length = 177

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +SNL    S+ D+++L  +FG   K  +  D++ G   G A +HF+ +ADA KA++   G
Sbjct: 93  VSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMKQYKG 151
Query: 230 YGYDHLILSV 239
              D   + +
Sbjct: 152 VPLDGRPMDI 161

>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 = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/94 (25%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 149 PGGKR-VEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
           PG +R VEG+          + ++ +    +E D+ D   ++G    ++L+ D+  G  K
Sbjct: 1   PGPQRSVEGW---------ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 51
Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW 241
           G+  + ++   +A  A++ LNG       +SVDW
Sbjct: 52  GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 85

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/94 (25%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 149 PGGKR-VEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
           PG +R VEG+          + ++ +    +E D+ D   ++G    ++L+ D+  G  K
Sbjct: 15  PGPQRSVEGW---------ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65
Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW 241
           G+  + ++   +A  A++ LNG       +SVDW
Sbjct: 66  GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99

>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 = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/82 (23%), Positives = 42/82 (51%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           +R+ +   + ++ +    +E D+ D   ++G    ++L+ D+  G  KG+  + ++   +
Sbjct: 2   QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 220 AAKAIQYLNGYGYDHLILSVDW 241
           A  A++ LNG       +SVDW
Sbjct: 62  AQAAMEGLNGQDLMGQPISVDW 83

>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: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 36/66 (54%)
Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
           ++ + + +L  N +E+ L  + + FG    + L +D   G  KG+ +I F +   A +A+
Sbjct: 5   SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 225 QYLNGY 230
           + LNG+
Sbjct: 65  EQLNGF 70

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/82 (23%), Positives = 42/82 (51%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           +R+ +   + ++ +    +E D+ D   ++G    ++L+ D+  G  KG+  + ++   +
Sbjct: 2   QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 220 AAKAIQYLNGYGYDHLILSVDW 241
           A  A++ LNG       +SVDW
Sbjct: 62  AQAAMEGLNGQDLMGQPISVDW 83

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 5/78 (6%)
Query: 171 SNLSVNTSENDLED-----LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           +NL VN    D+ D     L +  GP +   + RD   G   G+A++ F ++ D+ +AI+
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 226 YLNGYGYDHLILSVDWSK 243
            LNG    +  L V +++
Sbjct: 64  VLNGITVRNKRLKVSYAR 81

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/94 (25%), Positives = 46/94 (48%), Gaps = 10/94 (10%)
Query: 149 PGGKR-VEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
           PG +R VEG+          + ++ +    +E D+ D   ++G    ++L+ D+  G  K
Sbjct: 14  PGPQRSVEGW---------ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 64
Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW 241
           G+  + ++   +A  A++ LNG       +SVDW
Sbjct: 65  GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98

>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs Orf57 Peptide Length = 124

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + +SNL    S+ D+++L  +FG   K  +  D++ G   G A +HF+ +ADA KA++  
Sbjct: 38  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMKQY 96
Query: 228 NGYGYD 233
            G   D
Sbjct: 97  KGVPLD 102

>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1 Icp27 Peptide Length = 124

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + +SNL    S+ D+++L  +FG   K  +  D++ G   G A +HF+ +ADA KA++  
Sbjct: 38  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMKQY 96
Query: 228 NGYGYD 233
            G   D
Sbjct: 97  KGVPLD 102

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/82 (23%), Positives = 42/82 (51%)
Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           +R+ +   + ++ +    +E D+ D   ++G    ++L+ D+  G  KG+  + ++   +
Sbjct: 2   QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 220 AAKAIQYLNGYGYDHLILSVDW 241
           A  A++ LNG       +SVDW
Sbjct: 62  AQAAMEGLNGQDLMGQPISVDW 83

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 5/78 (6%)
Query: 171 SNLSVNTSENDLED-----LVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           +NL VN    D+ D     L +  GP +   + RD   G   G+A++ F ++ D+ +AI+
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 226 YLNGYGYDHLILSVDWSK 243
            LNG    +  L V +++
Sbjct: 64  VLNGITVRNKRLKVSYAR 81

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 156 GYNARRND-DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHF 214
           G NA +N+ D     +  LS +TS+ DL+D   +FG      +  D   G  +GF +I F
Sbjct: 1   GINASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF 60
Query: 215 KNKADAAKAIQ 225
           K+ A   K + 
Sbjct: 61  KDAASVEKVLD 71

>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 = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 35/75 (46%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + +LS   +  D++     FG  S   + +D   G  KG+ ++ F NK DA  AIQ +
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 228 NGYGYDHLILSVDWS 242
            G       +  +W+
Sbjct: 78  GGQWLGGRQIRTNWA 92

>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 = 5e-04,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 33/63 (52%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + +L  N +E+ L  + + FG    + L  D   G  KG+ +I F +   A KA++ L
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 228 NGY 230
           NG+
Sbjct: 89  NGF 91

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/78 (25%), Positives = 42/78 (53%)
Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + ++ L  + ++ +L  L +  GP +   + RD   G   G+A++ F ++ D+ +AI+
Sbjct: 15  TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 226 YLNGYGYDHLILSVDWSK 243
            LNG    +  L V +++
Sbjct: 75  VLNGITVRNKRLKVSYAR 92

>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical Protein Flj11016 Length = 115

Iteration: 1
 Score = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/85 (28%), Positives = 39/85 (45%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           +    + + NLS   +E DL  L  +F       +      G  +G A+I F NK  A +
Sbjct: 23  EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82
Query: 223 AIQYLNGYGYDHLILSVDWSKSTNQ 247
           A+  +NGY     IL +++ K+  Q
Sbjct: 83  ALHLVNGYKLYGKILVIEFGKNKKQ 107

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 170 ISNLSVNTSENDLEDLVKQFGP--TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           +S L    S+ ++E L  Q+G   TS++ L  D+  G+ +G  +I F  + +A +AI+ L
Sbjct: 6   VSGLPKTMSQKEMEQLFSQYGRIITSRILL--DQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 228 NG 229
           NG
Sbjct: 64  NG 65

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/75 (25%), Positives = 35/75 (46%)
Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + +LS   +  D++     FG  S   + +D   G  KG+ ++ F NK DA  AI ++
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 228 NGYGYDHLILSVDWS 242
            G       +  +W+
Sbjct: 78  GGQWLGGRQIRTNWA 92

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 40.4 bits (93), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 21/84 (25%), Positives = 41/84 (48%)
Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           D  T + ++ L  N ++++ + L    G      L RDK  G   G+ ++++ +  DA K
Sbjct: 2   DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 223 AIQYLNGYGYDHLILSVDWSKSTN 246
           AI  LNG       + V +++ ++
Sbjct: 62  AINTLNGLKLQTKTIKVSYARPSS 85

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	247
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	5e-32
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-21
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-21
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-17
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-17
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-17
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-16
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-16
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-16
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-16
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	7e-16
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-15
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-11
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-09
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-15
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-15
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	6e-15
1x4e_A	85	RNA binding motif, single-stranded interacting pro	7e-15
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	8e-15
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-14
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-14
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-14
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-14
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-14
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-14
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-14
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-14
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	5e-14
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	6e-14
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	6e-14
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	9e-14
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-12
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-13
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-13
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-13
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-13
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-13
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-13
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-11
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-13
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-13
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-13
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	5e-13
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	5e-13
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	7e-13
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-13
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-11
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-12
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	1e-12
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-12
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-12
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-12
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-11
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-10
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-12
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-12
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-12
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-12
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-12
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-12
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-12
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-12
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	6e-12
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	6e-12
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-12
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-12
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	7e-12
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-12
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-09
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	8e-12
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	9e-12
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	9e-12
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-11
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-11
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-07
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-11
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-09
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-11
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-11
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-11
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-11
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-08
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-11
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-11
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	3e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-11
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-11
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-11
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	5e-11
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-11
2div_A	99	TRNA selenocysteine associated protein; structural	5e-11
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	7e-11
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	6e-08
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-10
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-10
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-10
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-10
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-10
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-10
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-10
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	7e-10
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	7e-10
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	8e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-07
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	9e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-09
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-09
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-09
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-09
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-09
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	3e-09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-09
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-09
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	5e-09
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-09
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-09
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	8e-09
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-08
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-08
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-08
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-08
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	2e-08
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-08
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-08
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-08
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-08
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-08
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	5e-08
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	5e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-07
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	5e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-07
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-06
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-06
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-06
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-06
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-06
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	7e-06
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	9e-06
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-05
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	3e-05
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-05
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	4e-05
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	4e-05
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	5e-05
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	9e-05
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-04
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-04
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	5e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-04
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	6e-04
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	7e-04

>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 =  112 bits (282), Expect = 5e-32
 Identities = 45/84 (53%), Positives = 64/84 (76%)

Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           RR DD   IR++NLS +T E DL++L + FG  S++YL++DKT G  KGFA+I F  + D
Sbjct: 10  RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69

Query: 220 AAKAIQYLNGYGYDHLILSVDWSK 243
           AA+AI  ++G+GYDHLIL+V+W+K
Sbjct: 70  AARAIAGVSGFGYDHLILNVEWAK 93

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 85.9 bits (213), Expect = 1e-21
 Identities = 27/126 (21%), Positives = 53/126 (42%), Gaps = 1/126 (0%)

Query: 118 MAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNT 177
           M +S             G     +    + G G            +  T++++ NL+  T
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDV-EGMTSLKVDNLTYRT 59

Query: 178 SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLIL 237
           S + L  + +++G    +Y+ RD+     +GFA++ F +K DA  A+  ++G   D   L
Sbjct: 60  SPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 119

Query: 238 SVDWSK 243
            V  ++
Sbjct: 120 RVQMAR 125

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 85.6 bits (212), Expect = 4e-21
 Identities = 26/104 (25%), Positives = 46/104 (44%)

Query: 140 YVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSR 199
           YV  S       +       +    +  + + NLS  T+E  + +L  + G   K+ +  
Sbjct: 14  YVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGL 73

Query: 200 DKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
           DK      GF ++ + ++ADA  A++Y+NG   D  I+  DW  
Sbjct: 74  DKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA 117

>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 = 74.6 bits (184), Expect = 1e-17
 Identities = 21/88 (23%), Positives = 43/88 (48%)

Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
           G +    D    +++ NL+  TS + L  + +++G    +Y+ R+      +GFA++ F 
Sbjct: 4   GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63

Query: 216 NKADAAKAIQYLNGYGYDHLILSVDWSK 243
           ++ DA  A   ++G   D   L V  ++
Sbjct: 64  DRRDAQDAEAAMDGAELDGRELRVQVAR 91

>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 = 75.3 bits (185), Expect = 3e-17
 Identities = 31/145 (21%), Positives = 57/145 (39%), Gaps = 1/145 (0%)

Query: 99  LFLADANKKPFNTVPGTNIMAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYN 158
           L L     K   T    +   A    K+     G  G               G      +
Sbjct: 5   LILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHH-H 63

Query: 159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
               +  T++++ NL+  TS + L  + +++G    +Y+ RD+     +GFA++ F +K 
Sbjct: 64  HMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKR 123

Query: 219 DAAKAIQYLNGYGYDHLILSVDWSK 243
           DA  A+  ++G   D   L V  ++
Sbjct: 124 DAEDAMDAMDGAVLDGRELRVQMAR 148

>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 = 73.3 bits (180), Expect = 6e-17
 Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 6/86 (6%)

Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
           G +       T I   NL   T   ++++   +FG   ++ L            A + F 
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFL 54

Query: 216 NKADAAKAIQYLNGYGYDHLILSVDW 241
              +A KA ++L    + H+ L ++W
Sbjct: 55  EPLEARKAFRHLAYSKFHHVPLYLEW 80

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 74.1 bits (182), Expect = 1e-16
 Identities = 28/122 (22%), Positives = 49/122 (40%), Gaps = 3/122 (2%)

Query: 125 KKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTA--IRISNLSVNTSENDL 182
           + +   GG         P  L +       +          T   + +SNL    S+ D+
Sbjct: 46  RPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADI 105

Query: 183 EDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS 242
           ++L  +FG   K  +  D++ G   G A +HF+ +ADA KA++   G   D   + +   
Sbjct: 106 QELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV 164

Query: 243 KS 244
            S
Sbjct: 165 AS 166

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 71.6 bits (176), Expect = 1e-16
 Identities = 18/90 (20%), Positives = 40/90 (44%), Gaps = 6/90 (6%)

Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFG--PTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           +     I + N++ +T  + +   +  +     + + L +DK     +GFA++   +  D
Sbjct: 6   HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMD 65

Query: 220 AAKAIQYLNGYGYDHLI----LSVDWSKST 245
           A++ +Q L        I    + VD++KS 
Sbjct: 66  ASQLLQILQSLHPPLKIDGKTIGVDFAKSA 95

>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 = 72.5 bits (178), Expect = 2e-16
 Identities = 27/112 (24%), Positives = 52/112 (46%)

Query: 132 GAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGP 191
           G     +     +  +  G       N    D    + +  LS+ T+E DL ++  ++GP
Sbjct: 13  GLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGP 72

Query: 192 TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
            + + +  D+ +   +GFA+++F+N  DA +A +  NG   D   + VD+S 
Sbjct: 73  IADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSI 124

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 71.7 bits (176), Expect = 2e-16
 Identities = 12/77 (15%), Positives = 30/77 (38%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           +  + L+ N  E  L+D+ +++G   ++ +          G A + F +   A + ++ L
Sbjct: 9   VTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNL 68

Query: 228 NGYGYDHLILSVDWSKS 244
           +       I+       
Sbjct: 69  HLTSVMGNIIHAQLDIK 85

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 70.4 bits (173), Expect = 7e-16
 Identities = 23/97 (23%), Positives = 41/97 (42%), Gaps = 3/97 (3%)

Query: 148 GPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
             G            ++   I + NL  +    D+ED+  ++G    + L   K      
Sbjct: 5   SSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGP 61

Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
            FA++ F++  DA  A+   +GY YD   L V++ +S
Sbjct: 62  PFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS 98

>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 = 69.2 bits (170), Expect = 1e-15
 Identities = 25/94 (26%), Positives = 46/94 (48%)

Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
           G      N    D    + +  LS+ T+E DL ++  ++GP + + +  D+ +   +GFA
Sbjct: 1   GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60

Query: 211 YIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
           +++F+N  DA +A +  NG   D   + V    S
Sbjct: 61  FVYFENVDDAKEAKERANGMELDGRRIRVSGPSS 94

>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 = 72.4 bits (177), Expect = 1e-15
 Identities = 23/141 (16%), Positives = 45/141 (31%), Gaps = 2/141 (1%)

Query: 109 FNTVPGTNIMAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAI 168
           +      ++         + G           +PP++ +  G                A+
Sbjct: 12  YGGHDQIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIAL 71

Query: 169 RISNLSVNTSENDLEDLVKQFGPTS--KMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
            I NL+  T++ DL + V   G     ++    ++ NG  KGFA +   ++A + K +  
Sbjct: 72  YIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDL 131

Query: 227 LNGYGYDHLILSVDWSKSTNQ 247
           L           V        
Sbjct: 132 LPKRELHGQNPVVTPVNKQFL 152

>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 = 73.1 bits (180), Expect = 2e-15
 Identities = 20/82 (24%), Positives = 37/82 (45%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
             + ++NL  + ++   E+LV+ FG   + +L   +  G  KG+ +  +  K  AA+A  
Sbjct: 96  ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 155

Query: 226 YLNGYGYDHLILSVDWSKSTNQ 247
            L G       L V W+ +   
Sbjct: 156 DLLGKPLGPRTLYVHWTDAGQL 177

>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 = 60.8 bits (148), Expect = 4e-11
 Identities = 18/110 (16%), Positives = 35/110 (31%), Gaps = 11/110 (10%)

Query: 135 GGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSEND-LEDLVKQFGPTS 193
           G   +YV  +         +             + +  L    ++ D L   +      +
Sbjct: 163 GPRTLYVHWTDAGQLTPALLHSRC---------LCVDRLPPGFNDVDALCRALSAVHSPT 213

Query: 194 KMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
              L+  +  G  KGFA + ++    A +A Q  +G       L V +  
Sbjct: 214 FCQLACGQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCA 262

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 55.0 bits (133), Expect = 3e-09
 Identities = 16/88 (18%), Positives = 32/88 (36%), Gaps = 7/88 (7%)

Query: 157 YNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
           +  R+  +   I I  L  + +  ++ DL+  +      ++ + K      G A++   N
Sbjct: 14  HTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKY-CFVDKYK------GTAFVTLLN 66

Query: 217 KADAAKAIQYLNGYGYDHLILSVDWSKS 244
              A  AI   +        LSV    +
Sbjct: 67  GEQAEAAINAFHQSRLRERELSVQLQPT 94

>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 = 69.5 bits (170), Expect = 5e-15
 Identities = 20/125 (16%), Positives = 47/125 (37%)

Query: 120 ASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSE 179
                 + G   G+       +    R             +R+ +   + ++++     E
Sbjct: 27  KEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQE 86

Query: 180 NDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV 239
           +++++    +G    ++L+ D+  G  KG+A + ++    A  A + LNG       + V
Sbjct: 87  DEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 146

Query: 240 DWSKS 244
           DW   
Sbjct: 147 DWCFV 151

>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 = 69.5 bits (171), Expect = 6e-15
 Identities = 19/78 (24%), Positives = 41/78 (52%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           ++ L  + ++ +L  L +  GP +   + RD   G   G+A++ F ++ D+ +AI+ LNG
Sbjct: 8   VNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNG 67

Query: 230 YGYDHLILSVDWSKSTNQ 247
               +  L V +++   +
Sbjct: 68  ITVRNKRLKVSYARPGGE 85

>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 = 59.1 bits (144), Expect = 4e-11
 Identities = 16/71 (22%), Positives = 36/71 (50%)

Query: 159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
              +   T + ++NL    +++ L+ +  ++G   +  + RDK  G  +G A++ +  + 
Sbjct: 83  GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE 142

Query: 219 DAAKAIQYLNG 229
           +A +AI  LN 
Sbjct: 143 EAQEAISALNN 153

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 67.5 bits (165), Expect = 6e-15
 Identities = 14/84 (16%), Positives = 33/84 (39%), Gaps = 3/84 (3%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
           +  +      ++I N+  +     L+ L+ Q+G           +         + + +K
Sbjct: 8   SVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSK 64

Query: 218 ADAAKAIQYLNGYGYDHLILSVDW 241
             A +A+  LNG+  ++  L V +
Sbjct: 65  DQARQALDKLNGFQLENFTLKVAY 88

>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 = 66.8 bits (164), Expect = 7e-15
 Identities = 19/72 (26%), Positives = 33/72 (45%)

Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
           +  ++ + I  L   T++ DL  L + +G         DKT   CKG+ ++ F + + A 
Sbjct: 2   SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61

Query: 222 KAIQYLNGYGYD 233
           KA+  L   G  
Sbjct: 62  KAVTALKASGVQ 73

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 67.8 bits (166), Expect = 8e-15
 Identities = 19/93 (20%), Positives = 44/93 (47%)

Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
            +  +    +R+ +   + ++ +    +E D+ D   ++G    ++L+ D+  G  KG+ 
Sbjct: 8   EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 67

Query: 211 YIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
            + ++   +A  A++ LNG       +SVDW  
Sbjct: 68  LVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 100

>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 = 66.5 bits (163), Expect = 2e-14
 Identities = 17/93 (18%), Positives = 41/93 (44%)

Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
                    +R+ +   + ++++     E+++++    +G    ++L+ D+  G  KG+A
Sbjct: 12  DDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYA 71

Query: 211 YIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
            + ++    A  A + LNG       + VDW  
Sbjct: 72  LVEYETHKQALAAKEALNGAEIMGQTIQVDWCF 104

>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 = 66.1 bits (162), Expect = 2e-14
 Identities = 25/84 (29%), Positives = 40/84 (47%)

Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
             +  +  + + NLS  +SE DLE L   +GP S+++   D      KGFA++ F     
Sbjct: 3   SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62

Query: 220 AAKAIQYLNGYGYDHLILSVDWSK 243
           A KA   ++G  +   +L V  S 
Sbjct: 63  AVKAYAEVDGQVFQGRMLHVLPST 86

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 66.1 bits (162), Expect = 2e-14
 Identities = 19/98 (19%), Positives = 44/98 (44%)

Query: 146 REGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL 205
                 +  +    +R+ +   + ++ +    +E D+ D   ++G    ++L+ D+  G 
Sbjct: 4   DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 63

Query: 206 CKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
            KG+  + ++   +A  A++ LNG       +SVDW  
Sbjct: 64  LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 101

>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 = 66.2 bits (162), Expect = 2e-14
 Identities = 23/87 (26%), Positives = 39/87 (44%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
           +    +    + + NLS   +E DL  L  +F       +      G  +G A+I F NK
Sbjct: 18  SYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNK 77

Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKS 244
             A +A+  +NGY     IL +++ K+
Sbjct: 78  EIAWQALHLVNGYKLYGKILVIEFGKN 104

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 65.7 bits (161), Expect = 3e-14
 Identities = 26/100 (26%), Positives = 41/100 (41%), Gaps = 11/100 (11%)

Query: 148 GPGGKRVE-GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLC 206
           G  G   + GY   + + TT + +  L  NTS   L     +FG    +   +       
Sbjct: 1   GSSGSSGKIGYG--KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD----- 53

Query: 207 KGFAYIHFKNKADAAKAIQYLNGY--GYDHLILSVDWSKS 244
             FAYI +++   A  A   + G+  G     L VD++KS
Sbjct: 54  -SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKS 92

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 65.8 bits (161), Expect = 3e-14
 Identities = 21/88 (23%), Positives = 45/88 (51%), Gaps = 1/88 (1%)

Query: 157 YNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
           +    + +   + IS L  + ++ +LE++ K  G    + L  ++  G  KG AY+ ++N
Sbjct: 9   FRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYEN 67

Query: 217 KADAAKAIQYLNGYGYDHLILSVDWSKS 244
           ++ A++A+  ++G      I+ V  S S
Sbjct: 68  ESQASQAVMKMDGMTIKENIIKVAISNS 95

>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 = 66.8 bits (163), Expect = 4e-14
 Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 5/86 (5%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
           +         + + NL  N ++ +LE     +GP   ++++R+       GFA++ F++ 
Sbjct: 66  HRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDP 120

Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSK 243
            DAA A++ L+G       + V+ S 
Sbjct: 121 RDAADAVRELDGRTLCGCRVRVELSN 146

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 65.4 bits (160), Expect = 4e-14
 Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 5/77 (6%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + NL     + +LE     +GP   ++++R+       GFA++ F++  DA  A++ L
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGL 57

Query: 228 NGYGYDHLILSVDWSKS 244
           +G       + V+ S  
Sbjct: 58  DGKVICGSRVRVELSTG 74

>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 = 65.5 bits (160), Expect = 5e-14
 Identities = 28/117 (23%), Positives = 47/117 (40%), Gaps = 8/117 (6%)

Query: 128 GGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVK 187
            G       P  +       G GG           +    + +SNL    S+ D+++L  
Sbjct: 5   TGGQQMGRDPDKWQHDLFDSGCGG-------GEGVETGAKLLVSNLDFGVSDADIQELFA 57

Query: 188 QFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
           +FG   K  +  D++ G   G A +HF+ +ADA KA++   G   D   + +    S
Sbjct: 58  EFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVAS 113

>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 = 65.0 bits (159), Expect = 6e-14
 Identities = 23/94 (24%), Positives = 43/94 (45%), Gaps = 1/94 (1%)

Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
           G     G  + RN D T + +  L    SE  L +L  Q GP    ++ +D+  G  +G+
Sbjct: 1   GSSGSSGPISERNQDAT-VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGY 59

Query: 210 AYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
            ++ F ++ DA  AI+ ++        + V+ + 
Sbjct: 60  GFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS 93

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 64.6 bits (158), Expect = 6e-14
 Identities = 20/93 (21%), Positives = 39/93 (41%)

Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
           G     G +       + + +SNL  + + NDL  +  ++G   K+ + +DK     KG 
Sbjct: 1   GSSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGV 60

Query: 210 AYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS 242
           A+I F +K  A    + +N       ++    +
Sbjct: 61  AFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 66.1 bits (162), Expect = 9e-14
 Identities = 19/78 (24%), Positives = 36/78 (46%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           ++ L  N ++ +   L    G      L RDK  G   G+ ++++ +  DA KAI  LNG
Sbjct: 7   VNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG 66

Query: 230 YGYDHLILSVDWSKSTNQ 247
                  + V +++ ++ 
Sbjct: 67  LRLQTKTIKVSYARPSSA 84

>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 = 61.0 bits (149), Expect = 6e-12
 Identities = 18/74 (24%), Positives = 35/74 (47%)

Query: 157 YNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
             +  +     + +S L    ++ +LE L  Q+G      +  D+  G+ +G  +I F  
Sbjct: 80  RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDK 139

Query: 217 KADAAKAIQYLNGY 230
           + +A +AI+ LNG 
Sbjct: 140 RIEAEEAIKGLNGQ 153

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 63.9 bits (156), Expect = 1e-13
 Identities = 24/110 (21%), Positives = 35/110 (31%), Gaps = 10/110 (9%)

Query: 135 GGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSK 194
           G   I +PP +        V+          T   I N+    +E DL  L + FG    
Sbjct: 1   GSQTIGLPPQVNPQA----VDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILD 56

Query: 195 MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
                +K      G  +I +     AA  I  L  + +    L   W K 
Sbjct: 57  FKHYPEK------GCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKE 100

>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 = 63.3 bits (155), Expect = 2e-13
 Identities = 16/67 (23%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTN-GLCKGFAYIHFKNKADAAKAIQY 226
           + I  L+ N +++ + ++   +G    + +  ++ +  L KG+AY+ F+N  +A KA+++
Sbjct: 7   VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66

Query: 227 LNGYGYD 233
           ++G   D
Sbjct: 67  MDGGQID 73

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 63.8 bits (156), Expect = 2e-13
 Identities = 21/93 (22%), Positives = 43/93 (46%), Gaps = 3/93 (3%)

Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
           G         R+  +  + +  LS +T+E  L++    F  + +  +  D+  G  KGF 
Sbjct: 1   GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKES---FDGSVRARIVTDRETGSSKGFG 57

Query: 211 YIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
           ++ F ++ DA  A + +     D   +++DW+K
Sbjct: 58  FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90

>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 = 63.5 bits (155), Expect = 2e-13
 Identities = 14/82 (17%), Positives = 31/82 (37%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
              T I++ N+    S +++ D    +         +    G+  G A + F+++ +A  
Sbjct: 13  PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72

Query: 223 AIQYLNGYGYDHLILSVDWSKS 244
           A+  LN        + +    S
Sbjct: 73  AVIDLNDRPIGSRKVKLSGPSS 94

>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 = 64.0 bits (156), Expect = 2e-13
 Identities = 24/103 (23%), Positives = 44/103 (42%), Gaps = 12/103 (11%)

Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFG----------PTSKMYLSRD 200
           G      +   + D +AI +  L+ + + +DL D  KQ G          P   +Y   D
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIY--LD 58

Query: 201 KTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
           K  G  KG A + +++   A  A+++ +G  +    L V  ++
Sbjct: 59  KETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 101

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 65.4 bits (160), Expect = 3e-13
 Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 3/92 (3%)

Query: 159 ARRNDDTTAIR---ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
           A+R      +    + ++     E+ +      FGP   + +S D      KGFA++ ++
Sbjct: 19  AQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYE 78

Query: 216 NKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
               A  A++ +N        + V    +  Q
Sbjct: 79  VPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQ 110

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 60.8 bits (148), Expect = 2e-11
 Identities = 20/95 (21%), Positives = 41/95 (43%), Gaps = 1/95 (1%)

Query: 135 GGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSK 194
           GG  I V      G     ++            I ++++  + S++D++ + + FG    
Sbjct: 96  GGRNIKVGRPSNIGQAQPIIDQLAEEARAFNR-IYVASVHQDLSDDDIKSVFEAFGKIKS 154

Query: 195 MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
             L+RD T G  KG+ +I ++    +  A+  +N 
Sbjct: 155 ATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNL 189

>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 = 63.1 bits (154), Expect = 4e-13
 Identities = 20/84 (23%), Positives = 37/84 (44%)

Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           + +     + + +L  N +E+ L  + + FG    + L  D   G  KG+ +I F +   
Sbjct: 21  KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC 80

Query: 220 AAKAIQYLNGYGYDHLILSVDWSK 243
           A KA++ LNG+      + V    
Sbjct: 81  AKKALEQLNGFELAGRPMKVGHVT 104

>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 = 62.7 bits (153), Expect = 4e-13
 Identities = 19/75 (25%), Positives = 38/75 (50%)

Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
           G +  ++ D   + I  +  N  E DL+ L ++FG   ++ + +D+  G+ KG A++ + 
Sbjct: 4   GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYC 63

Query: 216 NKADAAKAIQYLNGY 230
            +  A KA   L+  
Sbjct: 64  ERESALKAQSALHEQ 78

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 62.7 bits (153), Expect = 4e-13
 Identities = 15/87 (17%), Positives = 37/87 (42%), Gaps = 6/87 (6%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
             +     + + + NL  + +E ++  L +++G   ++++ +DK      GF +I  + +
Sbjct: 8   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETR 61

Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKS 244
             A  A   L+        L V ++  
Sbjct: 62  TLAEIAKVELDNMPLRGKQLRVRFACH 88

>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 = 62.3 bits (152), Expect = 5e-13
 Identities = 14/94 (14%), Positives = 32/94 (34%)

Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
           G       +      T I++ N+    S +++ D    +         +    G+  G A
Sbjct: 1   GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 211 YIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
            + F+++ +A  A+  LN        + +     
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 63.6 bits (155), Expect = 5e-13
 Identities = 19/84 (22%), Positives = 32/84 (38%)

Query: 146 REGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL 205
           R   GG    G +         + +  L+    +  L      FG  + + +  D     
Sbjct: 44  RHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEK 103

Query: 206 CKGFAYIHFKNKADAAKAIQYLNG 229
            +GFA++ F+   DAA AI  +N 
Sbjct: 104 HRGFAFVEFELAEDAAAAIDNMNE 127

>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 = 62.3 bits (152), Expect = 7e-13
 Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 2/80 (2%)

Query: 155 EGYNARRNDDTTA-IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIH 213
            G+      +T   + +SNL    S+ D+++L  +FG   K  +  D++ G   G A +H
Sbjct: 18  SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVH 76

Query: 214 FKNKADAAKAIQYLNGYGYD 233
           F+ KADA KA++  NG   D
Sbjct: 77  FERKADALKAMKQYNGVPLD 96

>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 = 63.8 bits (156), Expect = 7e-13
 Identities = 21/98 (21%), Positives = 42/98 (42%), Gaps = 5/98 (5%)

Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
           G   VEG  +        + I NL+ N S  +L+  + +    + + +   +T G  + F
Sbjct: 1   GSHMVEG--SESTTPFN-LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT-GTNRKF 56

Query: 210 AYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
            Y+ F++  D  KA++ L G       + ++  K  + 
Sbjct: 57  GYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDS 93

>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 = 58.8 bits (143), Expect = 5e-11
 Identities = 21/86 (24%), Positives = 43/86 (50%), Gaps = 5/86 (5%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
           ++++      +   NLS N +E++L+++ +         +     +G  KG AYI FK++
Sbjct: 92  DSKKVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYIEFKSE 146

Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSK 243
           ADA K ++   G   D   +S+ ++ 
Sbjct: 147 ADAEKNLEEKQGAEIDGRSVSLYYTG 172

>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 = 61.6 bits (150), Expect = 1e-12
 Identities = 21/96 (21%), Positives = 35/96 (36%), Gaps = 12/96 (12%)

Query: 155 EGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFG----------PTSKMYLSRDKTNG 204
             ++   + D   I +  L  N +   + D  KQ G          P   +Y   D+  G
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLY--TDRETG 60

Query: 205 LCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD 240
             KG A + F +   A  AI + +G  +    + V 
Sbjct: 61  KLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVS 96

>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 = 61.1 bits (149), Expect = 1e-12
 Identities = 20/74 (27%), Positives = 36/74 (48%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + ++  + +E  + DL    GP   + +  D   G  KG+A+I F++   +A A++ LNG
Sbjct: 7   LGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNG 66

Query: 230 YGYDHLILSVDWSK 243
           Y      L   +S 
Sbjct: 67  YQLGSRFLKCGYSS 80

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 62.6 bits (152), Expect = 1e-12
 Identities = 21/131 (16%), Positives = 46/131 (35%), Gaps = 3/131 (2%)

Query: 119 AASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTS 178
                 +        P  P    P           +  Y+  RN    A+ + + S  T+
Sbjct: 10  GVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNR-RAAVYVGSFSWWTT 68

Query: 179 ENDLEDLVKQFGPT--SKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLI 236
           +  L  +++  G     ++  + ++ NG  KG+A +   ++    K ++ L G   +   
Sbjct: 69  DQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEK 128

Query: 237 LSVDWSKSTNQ 247
           + V  +   N 
Sbjct: 129 VDVRPATRQNL 139

>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 = 61.1 bits (149), Expect = 2e-12
 Identities = 20/82 (24%), Positives = 39/82 (47%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
               ++ + N+    +E  L+D+  + GP     L  D+  G  KG+ +  ++++  A  
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65

Query: 223 AIQYLNGYGYDHLILSVDWSKS 244
           A++ LNG  +    L VD + S
Sbjct: 66  AMRNLNGREFSGRALRVDNAAS 87

>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 = 60.8 bits (148), Expect = 2e-12
 Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 6/85 (7%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
                + + NL ++TSE  +E       P +       +     + +A++HF N+ DA +
Sbjct: 13  SSVKILYVRNLMLSTSEEMIEKEFNNIKPGA------VERVKKIRDYAFVHFSNREDAVE 66

Query: 223 AIQYLNGYGYDHLILSVDWSKSTNQ 247
           A++ LNG   D   + V  +K  ++
Sbjct: 67  AMKALNGKVLDGSPIEVTLAKPVDK 91

>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 = 61.2 bits (149), Expect = 2e-12
 Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 2/96 (2%)

Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTN-GLCKGF 209
           G         +   T+ I + N+    ++ ++ +L   FG    + L +  T  G  +GF
Sbjct: 1   GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60

Query: 210 AYIHFKNKADAAKAIQYL-NGYGYDHLILSVDWSKS 244
            ++ F  K DA KA   L +        L ++W+ S
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 96

>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 = 64.6 bits (158), Expect = 2e-12
 Identities = 18/99 (18%), Positives = 38/99 (38%), Gaps = 6/99 (6%)

Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGP-TSKMYLSRDKTNGLCKG 208
           G   +         + T + ++N   + ++ ++ DL++        + L   +     + 
Sbjct: 106 GQNEII---VSHLTECT-LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRR 160

Query: 209 FAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
           FAYI   +K DA   ++ LNG   +   L    S    +
Sbjct: 161 FAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEK 199

>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 = 61.2 bits (149), Expect = 3e-11
 Identities = 20/101 (19%), Positives = 33/101 (32%), Gaps = 4/101 (3%)

Query: 146 REGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL 205
             G   K+      R  + TT + + NL  + ++N +    K  GP   + ++       
Sbjct: 23  AAGLTSKKANEALTRNRELTT-VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL--KK 79

Query: 206 CKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTN 246
              FA I F     A  AI   +     + I  V       
Sbjct: 80  NFRFARIEFARYDGALAAITKTHKVVGQNEI-IVSHLTECT 119

>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 = 57.3 bits (139), Expect = 5e-10
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 168 IRISNLSVN-TSENDLEDLVKQFGPTSKMYLSRD-KTNGLCKGFAYIHFKNKADAAKAIQ 225
           I I NLS     EN L +  + FG   K+ +    K +      A++ F+NK  A +A+Q
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ 272

Query: 226 YLNGYGYDHLILSVDWSKS 244
            +N     +  +SV  +  
Sbjct: 273 -MNRSLLGNREISVSLADK 290

>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 = 2e-12
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG 231
           NLS + +E  +  L  Q GP     +  + T+     + ++ F    DAA A+  +NG  
Sbjct: 22  NLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRK 79

Query: 232 YDHLILSVDWSKS 244
                + V+W+ +
Sbjct: 80  ILGKEVKVNWATT 92

>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 = 61.2 bits (149), Expect = 2e-12
 Identities = 26/81 (32%), Positives = 44/81 (54%), Gaps = 1/81 (1%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           D    + I  L+  T+E  L+ +  + GP S++ L +D+T    +GFA+I F+N ADA  
Sbjct: 5   DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT-SKSRGFAFITFENPADAKN 63

Query: 223 AIQYLNGYGYDHLILSVDWSK 243
           A + +NG       + V+ +K
Sbjct: 64  AAKDMNGKSLHGKAIKVEQAK 84

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 60.9 bits (148), Expect = 2e-12
 Identities = 21/92 (22%), Positives = 35/92 (38%), Gaps = 8/92 (8%)

Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFG--------PTSKMYLSRDKTNGLCKGFAY 211
           + N D   I +  L  N +   + D  KQ G            + L  D+  G  KG A 
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61

Query: 212 IHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
           + F +   A  AI + +G  +    + V ++ 
Sbjct: 62  VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 93

>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 = 59.9 bits (146), Expect = 3e-12
 Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 1/85 (1%)

Query: 159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
           +        + +  L+    +  L      FG  + + +  D      +GFA++ F+   
Sbjct: 2   SMATTKRV-LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60

Query: 219 DAAKAIQYLNGYGYDHLILSVDWSK 243
           DAA AI  +N        + V+ +K
Sbjct: 61  DAAAAIDNMNESELFGRTIRVNLAK 85

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 60.8 bits (148), Expect = 3e-12
 Identities = 21/98 (21%), Positives = 40/98 (40%), Gaps = 2/98 (2%)

Query: 146 REGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL 205
                  R    N         + +SN+     + DL  +  QFG    + +  ++    
Sbjct: 10  HSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS- 68

Query: 206 CKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
            KGF ++ F+N ADA +A + L+G   +   + V+ + 
Sbjct: 69  -KGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 105

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 60.3 bits (147), Expect = 3e-12
 Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 1/88 (1%)

Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
           G +         + +  L+    +  L      FG  + + +  D      +GFA++ F+
Sbjct: 4   GSSGMATTKRV-LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 62

Query: 216 NKADAAKAIQYLNGYGYDHLILSVDWSK 243
              DAA AI  +N        + V+ +K
Sbjct: 63  LAEDAAAAIDNMNESELFGRTIRVNLAK 90

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 60.1 bits (146), Expect = 3e-12
 Identities = 17/64 (26%), Positives = 26/64 (40%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I +  V   +  L  L  + G    M    D+  G  KGF ++   +  DA K I+  +G
Sbjct: 17  IPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76

Query: 230 YGYD 233
              D
Sbjct: 77  KRLD 80

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 60.3 bits (146), Expect = 4e-12
 Identities = 15/81 (18%), Positives = 32/81 (39%), Gaps = 6/81 (7%)

Query: 168 IRISNLSVNTSENDL---EDLVKQFGPTSKMYLSRDKTNGLCK---GFAYIHFKNKADAA 221
           + +  LS   ++ ++    +   +FG   K+ ++   +    +     AY+ +    DA 
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 222 KAIQYLNGYGYDHLILSVDWS 242
           +AIQ +N    D   L     
Sbjct: 78  RAIQCVNNVVVDGRTLKASLG 98

>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 = 60.0 bits (146), Expect = 4e-12
 Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 2/87 (2%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
            A+   D T + + NL     E  L +L  Q GP +K+ + +D+  G  K F ++ FK+ 
Sbjct: 10  PAQEEADRT-VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHP 67

Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKS 244
              + AI  LNG       ++V    S
Sbjct: 68  ESVSYAIALLNGIRLYGRPINVSGPSS 94

>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 = 59.9 bits (146), Expect = 4e-12
 Identities = 19/82 (23%), Positives = 39/82 (47%)

Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
           +  ++ + + +L  N +E+ L  + + FG    + L +D   G  KG+ +I F +   A 
Sbjct: 2   SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61

Query: 222 KAIQYLNGYGYDHLILSVDWSK 243
           +A++ LNG+      + V    
Sbjct: 62  RALEQLNGFELAGRPMRVGHVT 83

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 60.1 bits (146), Expect = 6e-12
 Identities = 24/117 (20%), Positives = 37/117 (31%)

Query: 127 SGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLV 186
           +G P           P +                   +   + I +L    ++ DL    
Sbjct: 2   AGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTF 61

Query: 187 KQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
             FG      +  DK   L K F ++ F N   A  AI+ +NG+      L V   K
Sbjct: 62  LPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118

>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 = 59.6 bits (145), Expect = 6e-12
 Identities = 20/93 (21%), Positives = 43/93 (46%), Gaps = 4/93 (4%)

Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
           G      N+  + ++  + +SNLS + +E  L+++ ++     K+       NG  KG+A
Sbjct: 1   GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI-KVP---QNQNGKSKGYA 56

Query: 211 YIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
           +I F +  DA +A+   N    +   + ++   
Sbjct: 57  FIEFASFEDAKEALNSCNKREIEGRAIRLELQG 89

>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 = 60.5 bits (147), Expect = 6e-12
 Identities = 20/112 (17%), Positives = 45/112 (40%), Gaps = 1/112 (0%)

Query: 133 APGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPT 192
            P G    +    ++          N   +     + ++ +     E  L  L +++GP 
Sbjct: 11  DPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLM-VNYIPTTVDEVQLRQLFERYGPI 69

Query: 193 SKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
             + +  D+     +G+ ++ F++ + A +AI  LNG+   +  L V  + S
Sbjct: 70  ESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS 121

>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 = 59.2 bits (144), Expect = 7e-12
 Identities = 21/87 (24%), Positives = 42/87 (48%), Gaps = 5/87 (5%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
            +++      +   NLS N +E++L+++ +         +     +G  KG AYI FK++
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYIEFKSE 63

Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKS 244
           ADA K ++   G   D   +S+ ++  
Sbjct: 64  ADAEKNLEEKQGAEIDGRSVSLYYTGE 90

>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 = 7e-12
 Identities = 22/88 (25%), Positives = 38/88 (43%)

Query: 142 PPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDK 201
            P + E P        +    D    + I  L    +++ +++L+  FGP     L +D 
Sbjct: 91  LPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS 150

Query: 202 TNGLCKGFAYIHFKNKADAAKAIQYLNG 229
             GL KG+A+  + +     +AI  LNG
Sbjct: 151 ATGLSKGYAFCEYVDINVTDQAIAGLNG 178

>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 = 53.5 bits (129), Expect = 5e-09
 Identities = 10/79 (12%), Positives = 26/79 (32%), Gaps = 6/79 (7%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSR-----DKTNGLCKGFAYIHFKNKADAAKAI 224
           + N+    +E  + D          +  +             K FA++ F++  +  +A+
Sbjct: 9   VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 68

Query: 225 QYLNGYGYDHLILSVDWSK 243
              +G  +    L +    
Sbjct: 69  A-FDGIIFQGQSLKIRRPH 86

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 58.7 bits (143), Expect = 8e-12
 Identities = 19/80 (23%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPT--SKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I NL+  T++ DL + V   G     ++    ++ NG  KGFA +   ++A + K +  L
Sbjct: 6   IGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLL 65

Query: 228 NGYGYDHLILSVDWSKSTNQ 247
                      V  S     
Sbjct: 66  PKRELHGQNPVVTPSNKLEH 85

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 59.2 bits (144), Expect = 9e-12
 Identities = 22/82 (26%), Positives = 42/82 (51%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
            D   + +  LS +T+E  LE +  ++G  S++ + +D+     +GF ++ F+N  DA  
Sbjct: 10  SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69

Query: 223 AIQYLNGYGYDHLILSVDWSKS 244
           A+  +NG   D   + VD +  
Sbjct: 70  AMMAMNGKSVDGRQIRVDQAGK 91

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 58.8 bits (143), Expect = 9e-12
 Identities = 17/89 (19%), Positives = 39/89 (43%), Gaps = 8/89 (8%)

Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
           G +      +T + + N+S   +  +L    +++GP  +  + +         +A++H +
Sbjct: 1   GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHME 52

Query: 216 NKADAAKAIQYLNGYGYDHLILSVDWSKS 244
              DA +AI+ L+   +    + V  S S
Sbjct: 53  RAEDAVEAIRGLDNTEFQGKRMHVQLSTS 81

>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 = 59.3 bits (144), Expect = 1e-11
 Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 7/101 (6%)

Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
           G     G  +   +  T + I NLS ++ E  L ++++QFG    + +         KG 
Sbjct: 1   GSSGSSGLPSDVTEGKT-VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGC 59

Query: 210 AYIHFKNKADAAKAIQYLN------GYGYDHLILSVDWSKS 244
           A+  F  +  A K +   +      G   D   L VD + +
Sbjct: 60  AFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 100

>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 = 61.1 bits (149), Expect = 1e-11
 Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 3/83 (3%)

Query: 148 GPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
           GP G       A      + + + +L  + +E  L +     GP   + + RD       
Sbjct: 1   GPLGSMNPS--APSYPMAS-LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSL 57

Query: 208 GFAYIHFKNKADAAKAIQYLNGY 230
           G+AY++F+  ADA +A+  +N  
Sbjct: 58  GYAYVNFQQPADAERALDTMNFD 80

>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 = 48.4 bits (116), Expect = 3e-07
 Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 2/90 (2%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
            + R      I I NL  +     L D    FG      +  D      KG+ ++HF+ +
Sbjct: 96  PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQ 153

Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
             A +AI+ +NG   +   + V   KS  +
Sbjct: 154 EAAERAIEKMNGMLLNDRKVFVGRFKSRKE 183

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 58.8 bits (143), Expect = 1e-11
 Identities = 22/101 (21%), Positives = 45/101 (44%), Gaps = 10/101 (9%)

Query: 146 REGPGGKRVEGYNARRNDD--TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTN 203
                  R    + R+  +   T + +    ++  E++L ++   FGP  ++ +      
Sbjct: 10  HSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL----- 64

Query: 204 GLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
               GFA++ F+    AAKAI+ ++G  + +  L V +SK 
Sbjct: 65  ---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKL 102

>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 = 58.5 bits (142), Expect = 1e-11
 Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 6/81 (7%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
             +    ++   ++  +      FG   ++ +  +K      G++++ F     AA AI 
Sbjct: 26  CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIV 79

Query: 226 YLNGYGYDHLILSVDWSKSTN 246
            +NG   +  ++   W K + 
Sbjct: 80  SVNGTTIEGHVVKCYWGKESP 100

>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 = 61.6 bits (150), Expect = 2e-11
 Identities = 22/81 (27%), Positives = 31/81 (38%), Gaps = 3/81 (3%)

Query: 151 GKRVEGYNARRN--DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKG 208
           G  ++    R        A+ + NLS   S   LE    QFGP  K  +  D   G   G
Sbjct: 80  GTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDR-GRATG 138

Query: 209 FAYIHFKNKADAAKAIQYLNG 229
             ++ F  K  A KA++    
Sbjct: 139 KGFVEFAAKPPARKALERCGD 159

>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 = 60.9 bits (148), Expect = 3e-11
 Identities = 21/111 (18%), Positives = 44/111 (39%), Gaps = 16/111 (14%)

Query: 136 GPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKM 195
           G  I +   L+ G                     + NL  + +E D + L +++G  S++
Sbjct: 3   GFTIDIKSFLKPG---------EKTYTQRCRLF-VGNLPTDITEEDFKRLFERYGEPSEV 52

Query: 196 YLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTN 246
           +++RD+      GF +I  +++  A  A   L+G       L + ++    
Sbjct: 53  FINRDR------GFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGA 97

>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 = 22/79 (27%), Positives = 35/79 (44%), Gaps = 7/79 (8%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I NLS   + +DL  L           L       L  G+A++ + ++  A +AI+ L+G
Sbjct: 13  IGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSG 66

Query: 230 YGYDH-LILSVDWSKSTNQ 247
               H  I+ VD+S S   
Sbjct: 67  KVELHGKIMEVDYSVSKKL 85

>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 = 59.5 bits (145), Expect = 2e-11
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG 231
           NL    +E+ L+   +  GP + + +  DK       +A++ +    DA  A+Q LNG  
Sbjct: 7   NLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQ 65

Query: 232 YDHLILSVDWSKSTNQ 247
            ++ I+ ++W+  + Q
Sbjct: 66  IENNIVKINWAFQSQQ 81

>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 = 54.1 bits (131), Expect = 2e-09
 Identities = 17/72 (23%), Positives = 34/72 (47%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
               +DDT  + + +L+VN  +  L +  K F      ++  D   G  +G+ ++ F ++
Sbjct: 80  QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ 139

Query: 218 ADAAKAIQYLNG 229
            DA  A+  + G
Sbjct: 140 DDAQNAMDSMQG 151

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 57.5 bits (140), Expect = 2e-11
 Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
           D  +I + N+    +  +LE      G  +++ +  DK +G  KGFAYI F +K     +
Sbjct: 5   DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64

Query: 224 IQYLNGY 230
           +  L+  
Sbjct: 65  LA-LDES 70

>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 = 58.2 bits (141), Expect = 2e-11
 Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 3/75 (4%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I NL    +  ++ D+  ++GP  ++   R       +G AY+ +++  DA  A+ +L+G
Sbjct: 13  IRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKNAVDHLSG 69

Query: 230 YGYDHLILSVDWSKS 244
           +   +  L V +  +
Sbjct: 70  FNVSNRYLVVLYYNA 84

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 59.5 bits (145), Expect = 3e-11
 Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I  +S   +END+  +   FG   +  + R    GL +G A++ F  +A A  AI+ ++ 
Sbjct: 100 IGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQ 158

>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 = 59.2 bits (144), Expect = 3e-11
 Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL--CKGFAYIHFKNKADAA 221
           D   + +  +    SE DL +L +Q+G   ++ + RD++      KG  ++ F  +  A 
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 222 KAIQYLNG 229
           +A   L+ 
Sbjct: 62  EAQNALHN 69

>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 = 59.6 bits (145), Expect = 3e-11
 Identities = 18/73 (24%), Positives = 35/73 (47%)

Query: 157 YNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
           ++ +       + I  L    +++ +++L+  FGP     L +D   GL KG+A+  + +
Sbjct: 86  HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 145

Query: 217 KADAAKAIQYLNG 229
                +AI  LNG
Sbjct: 146 INVTDQAIAGLNG 158

>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 = 51.8 bits (125), Expect = 2e-08
 Identities = 10/83 (12%), Positives = 26/83 (31%), Gaps = 6/83 (7%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSR-----DKTNGLCKGFAYIHFKNKADAAKAI 224
           + N+    +E  + D          +  +             K FA++ F++  +  +A+
Sbjct: 9   VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 68

Query: 225 QYLNGYGYDHLILSVDWSKSTNQ 247
              +G  +    L +        
Sbjct: 69  A-FDGIIFQGQSLKIRRPHDYQP 90

>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 = 57.7 bits (140), Expect = 3e-11
 Identities = 20/87 (22%), Positives = 41/87 (47%), Gaps = 2/87 (2%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
           N+        + +SN+     + DL  +  QFG    + +  ++     KGF ++ F+N 
Sbjct: 8   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENS 65

Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKS 244
           ADA +A + L+G   +   + V+ + +
Sbjct: 66  ADADRAREKLHGTVVEGRKIEVNNATA 92

>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 = 58.2 bits (141), Expect = 3e-11
 Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 1/85 (1%)

Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           ++  D  ++ + N+   ++  DLE      G  +++ +  DK +G  KG+AYI F  +  
Sbjct: 31  KKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNS 90

Query: 220 AAKAIQYLNGYGYDHLILSVDWSKS 244
              A+  ++   +    + V   ++
Sbjct: 91  VDAAVA-MDETVFRGRTIKVLPKRT 114

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 57.5 bits (139), Expect = 3e-11
 Identities = 17/97 (17%), Positives = 34/97 (35%), Gaps = 5/97 (5%)

Query: 148 GPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
             G                 + + NL  +   +DL+  +++ G        R    G  +
Sbjct: 2   SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP----LRLTWQGP-R 56

Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
             A++H+ + A A +A+  L G       L V  ++ 
Sbjct: 57  RRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ 93

>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 = 57.2 bits (139), Expect = 4e-11
 Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 8/85 (9%)

Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
             +     + I NL    +E ++  L +Q+G   +  +         K + ++H ++K  
Sbjct: 3   SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTA 54

Query: 220 AAKAIQYLNGYGYDHLILSVDWSKS 244
           A  AI+ L+ Y    + ++V+ SK+
Sbjct: 55  AEDAIRNLHHYKLHGVNINVEASKN 79

>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 = 57.4 bits (139), Expect = 4e-11
 Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 2/88 (2%)

Query: 158 NARRNDDTTAIRI--SNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
           + ++ D +    +   +LS   +  D++     FG  S   + +D   G  KG+ ++ F 
Sbjct: 6   SGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFF 65

Query: 216 NKADAAKAIQYLNGYGYDHLILSVDWSK 243
           NK DA  AIQ + G       +  +W+ 
Sbjct: 66  NKWDAENAIQQMGGQWLGGRQIRTNWAT 93

>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 = 56.8 bits (138), Expect = 4e-11
 Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 8/85 (9%)

Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
             + +T  I + N+S   +  +L  L ++ G   +  +         K +A++H + +AD
Sbjct: 4   GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEAD 55

Query: 220 AAKAIQYLNGYGYDHLILSVDWSKS 244
           A  AI  LNG       ++V+ S  
Sbjct: 56  AKAAIAQLNGKEVKGKRINVELSTK 80

>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 = 57.3 bits (139), Expect = 5e-11
 Identities = 24/99 (24%), Positives = 37/99 (37%), Gaps = 9/99 (9%)

Query: 132 GAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGP 191
           G+ G   +        G   +  EG N         + I +L     + DL  +   FG 
Sbjct: 1   GSSGSSGLTQQSIGAAGSQKEGPEGAN---------LFIYHLPQEFGDQDLLQMFMPFGN 51

Query: 192 TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGY 230
                +  DK   L K F ++ + N   A  AIQ +NG+
Sbjct: 52  VVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGF 90

>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 = 57.6 bits (139), Expect = 5e-11
 Identities = 14/108 (12%), Positives = 31/108 (28%), Gaps = 6/108 (5%)

Query: 118 MAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNT 177
           M +S             G     +    + G G    +      + +   +R+  L    
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSNSAD------SANDGFVRLRGLPFGC 54

Query: 178 SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           ++ ++                     G   G A++ F ++  A KA+ 
Sbjct: 55  TKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG 102

>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 = 56.9 bits (138), Expect = 5e-11
 Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPT-SKMYLSRDKTNGLCKGFAYIHFKN 216
           ++  +    ++ + +L     EN +       G T   + + R++  G+  G+ ++ F +
Sbjct: 2   SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61

Query: 217 KADAAKAIQYLNG 229
            A A K +  +NG
Sbjct: 62  LATAEKCLHKING 74

>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 = 56.9 bits (138), Expect = 7e-11
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
           +  R      + +  L+   SE D+  L + FG   +  + R   +G  KG A++ F + 
Sbjct: 8   SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSH 66

Query: 218 ADAAKAIQYLNG 229
            +A  AI  L+G
Sbjct: 67  TEAQAAIHALHG 78

>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 = 55.9 bits (135), Expect = 1e-10
 Identities = 16/83 (19%), Positives = 33/83 (39%), Gaps = 7/83 (8%)

Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
           +  ++ I + NL  +++  ++ DL+K +         +       K  A++   N   A 
Sbjct: 2   SSGSSGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQAQ 54

Query: 222 KAIQYLNGYGYDHLILSVDWSKS 244
            AIQ  + Y +    L V    +
Sbjct: 55  NAIQMFHQYSFRGKDLIVQLQPT 77

>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 = 57.8 bits (139), Expect = 2e-10
 Identities = 14/126 (11%), Positives = 34/126 (26%)

Query: 105 NKKPFNTVPGTNIMAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDD 164
           N            ++           G   G  +       R        +    R    
Sbjct: 63  NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHP 122

Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
           +  +   N  +  +E +  ++  + G      +              + + +K+DA + +
Sbjct: 123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETL 182

Query: 225 QYLNGY 230
            +LN Y
Sbjct: 183 GFLNHY 188

>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 = 50.5 bits (120), Expect = 6e-08
 Identities = 14/84 (16%), Positives = 31/84 (36%), Gaps = 6/84 (7%)

Query: 164 DTTAIRISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           D+  + +  L     + + + ++   +G   K+   + K      G A +   +     +
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDR 57

Query: 223 AIQYLNGYGYDHLILSVDWSKSTN 246
           AI +LN        ++V  SK   
Sbjct: 58  AITHLNNNFMFGQKMNVCVSKQPA 81

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 55.3 bits (134), Expect = 2e-10
 Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 2/61 (3%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL  + +   L+D   + G      +  +  NG  KG   + F++   A +A + +NG
Sbjct: 13  VRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNG 70

Query: 230 Y 230
            
Sbjct: 71  M 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 = 55.4 bits (134), Expect = 2e-10
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 8/76 (10%)

Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG 231
           NL+   +E  LE    QFG   ++   +D        +A+IHF  +  A KA++ +NG  
Sbjct: 18  NLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEMNGKD 69

Query: 232 YDHLILSVDWSKSTNQ 247
            +   + + ++K  +Q
Sbjct: 70  LEGENIEIVFAKPPDQ 85

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 54.9 bits (133), Expect = 2e-10
 Identities = 19/72 (26%), Positives = 31/72 (43%)

Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG 231
           +LS   +   +      FG  S   + +D   G  KG+ ++ F NK DA  AIQ + G  
Sbjct: 13  DLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQW 72

Query: 232 YDHLILSVDWSK 243
                +  +W+ 
Sbjct: 73  LGGRQIRTNWAT 84

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 54.8 bits (133), Expect = 2e-10
 Identities = 17/83 (20%), Positives = 37/83 (44%)

Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
           T  + + +L+VN  +  L +  K F      ++  D   G  +G+ ++ F ++ DA  A+
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60

Query: 225 QYLNGYGYDHLILSVDWSKSTNQ 247
             + G   +   L ++W+     
Sbjct: 61  DSMQGQDLNGRPLRINWAAKLEH 83

>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 = 55.0 bits (133), Expect = 2e-10
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 3/83 (3%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLC---KGFAYIHFKNKADA 220
            ++ + I NL+ +T+E  L+ +  + G      +S+ K         GF ++ +K    A
Sbjct: 4   GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 221 AKAIQYLNGYGYDHLILSVDWSK 243
            KA++ L G+  D   L V  S+
Sbjct: 64  QKALKQLQGHTVDGHKLEVRISE 86

>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 = 55.0 bits (133), Expect = 3e-10
 Identities = 17/88 (19%), Positives = 32/88 (36%), Gaps = 9/88 (10%)

Query: 160 RRNDDTTAIRISNLSVNT-SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
           R +   + + I NL +   S+ DL  +   +G   ++ +           F +I F N  
Sbjct: 17  RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQ 68

Query: 219 DAAKAIQYLNGYGYDHLILSVDWSKSTN 246
               AI+  +        L ++ S S  
Sbjct: 69  SVRDAIEXESQEMNFGKKLILEVSSSNA 96

>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 = 56.0 bits (135), Expect = 3e-10
 Identities = 17/106 (16%), Positives = 34/106 (32%), Gaps = 3/106 (2%)

Query: 120 ASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSE 179
            SS        G  P G  +      ++   G     +  +       + +  L    +E
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHC-VHMRGLPYKATE 60

Query: 180 NDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           ND+ +      P   +++     +G   G A + F    +A  A+ 
Sbjct: 61  NDIYNFFSPLNPVR-VHIEIGP-DGRVTGEADVEFATHEEAVAAMS 104

>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 = 55.0 bits (133), Expect = 4e-10
 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 157 YNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
              ++  D T + ISNL ++  E +LE+++K FG      + RD + G  +G  +   ++
Sbjct: 17  MAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS-GTSRGVGFARMES 75

Query: 217 KADAAKAIQYLNGY 230
                  I + NG 
Sbjct: 76  TEKCEAVIGHFNGK 89

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 54.4 bits (131), Expect = 7e-10
 Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 4/82 (4%)

Query: 148 GPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
           G  G   EG     N       I+N+  + ++ D+   ++               NG   
Sbjct: 1   GSSGSSGEG---DVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGL 57

Query: 208 GFAYIHFKNKADAAKAIQYLNG 229
           G A + FKN+ DA K+ + L+ 
Sbjct: 58  GQALVQFKNEDDARKSER-LHR 78

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 54.2 bits (131), Expect = 7e-10
 Identities = 19/86 (22%), Positives = 31/86 (36%), Gaps = 1/86 (1%)

Query: 159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
           +    D   +    L+      DLED     G    + +  D+ +   KG AY+ F    
Sbjct: 19  SPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ 78

Query: 219 DAAKAIQYLNGYGYDHLILSVDWSKS 244
               AI  L G     + + V  S++
Sbjct: 79  SVPLAIG-LTGQRLLGVPIIVQASQA 103

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 53.9 bits (130), Expect = 7e-10
 Identities = 22/119 (18%), Positives = 42/119 (35%), Gaps = 23/119 (19%)

Query: 127 SGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVN-TSENDLEDL 185
           SG  G +    A  V           RV  +            I NL+     ++D+E +
Sbjct: 3   SGSSGMSLKLQASNVTNKNDPKSINSRV--F------------IGNLNTALVKKSDVETI 48

Query: 186 VKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
             ++G  +   +         KG+A++ + N+  A  A+   NG       L ++ +  
Sbjct: 49  FSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE 99

>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 = 54.2 bits (131), Expect = 8e-10
 Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I NL  +     L D    FG      +  D+     KG+ ++HF+ +  A +AI+ +NG
Sbjct: 10  IKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNG 67

Query: 230 YGYDHLILSVDWSKS 244
              +   + V   KS
Sbjct: 68  MLLNDRKVFVGRFKS 82

>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 = 56.2 bits (135), Expect = 8e-10
 Identities = 27/137 (19%), Positives = 47/137 (34%), Gaps = 6/137 (4%)

Query: 111 TVPGTNIMAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARR-NDDTTAIR 169
            + G  I    S  +    P        +            K+    N +     +  + 
Sbjct: 96  KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLH 155

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           +SN+  + SE DL+ L    G   K +    K     +  A I   +  +A +A+  L+ 
Sbjct: 156 LSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHN 211

Query: 230 YGYDH-LILSVDWSKST 245
           +       L V +SKST
Sbjct: 212 HDLGENHHLRVSFSKST 228

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 49.2 bits (117), Expect = 2e-07
 Identities = 21/121 (17%), Positives = 38/121 (31%), Gaps = 21/121 (17%)

Query: 127 SGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSV-NTSENDLEDL 185
           S G             P L                    + + +SNL+    +   L  L
Sbjct: 11  SSGLVPRGSHMGRIAIPGLAGAGN---------------SVLLVSNLNPERVTPQSLFIL 55

Query: 186 VKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST 245
              +G   ++ +  +K     K  A +   +   A  A+ +LNG+      + +  SK  
Sbjct: 56  FGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ 110

Query: 246 N 246
           N
Sbjct: 111 N 111

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 53.9 bits (130), Expect = 9e-10
 Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           ++NL        L+++    G   +  +  DK +G  +G   + F+   +A +AI   NG
Sbjct: 20  VANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNG 78

Query: 230 Y 230
            
Sbjct: 79  Q 79

>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 = 55.7 bits (134), Expect = 1e-09
 Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 5/88 (5%)

Query: 159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
                 +  + +SN+  + SE DL+ L    G   K +    K     +  A I   +  
Sbjct: 114 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVE 169

Query: 219 DAAKAIQYLNGYGYDH-LILSVDWSKST 245
           +A +A+  L+ +       L V +SKST
Sbjct: 170 EAVQALIDLHNHDLGENHHLRVSFSKST 197

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 49.5 bits (118), Expect = 1e-07
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 170 ISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
           +SNL+    +   L  L   +G   ++ +  +K     K  A +   +   A  A+ +LN
Sbjct: 8   VSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLN 62

Query: 229 GYGYDHLILSVDWSKSTNQ 247
           G+      + +  SK  N 
Sbjct: 63  GHKLHGKPIRITLSKHQNV 81

>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 = 57.2 bits (137), Expect = 1e-09
 Identities = 16/75 (21%), Positives = 42/75 (56%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           ++ ++ +T+E+ L    + +GP  ++++   K +G  +G+A+I ++++ D   A ++ +G
Sbjct: 107 VARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADG 166

Query: 230 YGYDHLILSVDWSKS 244
              D   + VD  + 
Sbjct: 167 KKIDGRRVLVDVERG 181

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 53.4 bits (129), Expect = 1e-09
 Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGP-TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
           I NL     E  L D    FG       + RD   G  KG+A+I+F +   +  AI+ +N
Sbjct: 10  IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN 69

Query: 229 G 229
           G
Sbjct: 70  G 70

>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 = 52.7 bits (127), Expect = 1e-09
 Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 7/80 (8%)

Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
            T + +  L    +E DL +   QFG    + + + +        A+I F  +  A  A 
Sbjct: 12  ITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQFATRQAAEVAA 65

Query: 225 QY-LNGYGYDHLILSVDWSK 243
           +   N    +   L+V W +
Sbjct: 66  EKSFNKLIVNGRRLNVKWGR 85

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 52.8 bits (127), Expect = 2e-09
 Identities = 12/75 (16%), Positives = 25/75 (33%)

Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
           G      N+    +   +R+  L    S+ ++                     G   G A
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 211 YIHFKNKADAAKAIQ 225
           ++ F ++  A KA++
Sbjct: 61  FVQFASQEIAEKALK 75

>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 = 53.3 bits (128), Expect = 2e-09
 Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 7/81 (8%)

Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
           GG     Y          + +S L  + S  DL+D +++ G      + RD       G 
Sbjct: 1   GGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GT 53

Query: 210 AYIHFKNKADAAKAIQYLNGY 230
             + F  K D   A++ L+  
Sbjct: 54  GVVEFVRKEDMTYAVRKLDNT 74

>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 = 52.5 bits (126), Expect = 2e-09
 Identities = 13/79 (16%), Positives = 29/79 (36%), Gaps = 8/79 (10%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + +  L  +  E DL + +++FG    + +         K  A + F+N   A + + + 
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFA 71

Query: 228 NGYGY--DHLILSVDWSKS 244
                         ++S S
Sbjct: 72  ADVPVYIAGQQAFFNYSTS 90

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 52.5 bits (126), Expect = 2e-09
 Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 8/77 (10%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I  L     E DL + +++FGP S + +         K  A + F++   A  A+ Y   
Sbjct: 26  IRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAAD 79

Query: 230 YGY--DHLILSVDWSKS 244
                      V++S S
Sbjct: 80  NQIYIAGHPAFVNYSTS 96

>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 = 52.2 bits (126), Expect = 3e-09
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 1/63 (1%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
             + NL  + +E  +++  +    ++             KGF Y  F++      A+  L
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-L 80

Query: 228 NGY 230
           N  
Sbjct: 81  NEE 83

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 51.8 bits (125), Expect = 3e-09
 Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I + NL  + +   +++L  QFG    + L  D+     KGF ++  +     ++AI  L
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62

Query: 228 NGYGYDHLILSVDWSK 243
           +   +    + V  + 
Sbjct: 63  DNTDFMGRTIRVTEAN 78

>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 = 52.5 bits (126), Expect = 3e-09
 Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
           G     G    R  +   + +S L  + S  DL+D +++ G      + RD       G 
Sbjct: 1   GSSGSSGGPPSRRSENR-VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GT 52

Query: 210 AYIHFKNKADAAKAIQYLNGY 230
             + F  K D   A++ L+  
Sbjct: 53  GVVEFVRKEDMTYAVRKLDNT 73

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 52.5 bits (126), Expect = 3e-09
 Identities = 15/97 (15%), Positives = 31/97 (31%), Gaps = 4/97 (4%)

Query: 143 PSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKT 202
                     R    +         I + NL    S  DL+DL ++    +         
Sbjct: 7   HHHHSSGLVPRGSHMSKLPAKRYR-ITMKNLPEGCSWQDLKDLARENSLETTF---SSVN 62

Query: 203 NGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV 239
                G   + F ++    +A++ LN   +   +++V
Sbjct: 63  TRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 51.8 bits (125), Expect = 3e-09
 Identities = 17/76 (22%), Positives = 29/76 (38%), Gaps = 9/76 (11%)

Query: 170 ISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
           I NL + N S+ DL  +   +G   ++ +           F +I F N      AI+  +
Sbjct: 15  IGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAIECES 66

Query: 229 GYGYDHLILSVDWSKS 244
                   L ++ S S
Sbjct: 67  QEMNFGKKLILEVSSS 82

>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 = 51.7 bits (124), Expect = 4e-09
 Identities = 11/82 (13%), Positives = 31/82 (37%), Gaps = 4/82 (4%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPT-SKMYLSRDKTN-GLCKGFAYIHFKNKADAAKAIQYL 227
           I  +       ++ + + +       + +     +    +GFA++ +++   AA A + L
Sbjct: 13  IGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKL 72

Query: 228 NGYGY--DHLILSVDWSKSTNQ 247
                      ++VDW++    
Sbjct: 73  MPGRIQLWGHQIAVDWAEPEID 94

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 52.2 bits (125), Expect = 5e-09
 Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 7/79 (8%)

Query: 170 ISNLSVNTSENDL----EDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           I+N++    +  L      L    G    + +     +    G AYI F  +  A   ++
Sbjct: 34  ITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVE 90

Query: 226 YLNGYGYDHLILSVDWSKS 244
              GY +    L + +S++
Sbjct: 91  AFQGYPFQGNPLVITFSET 109

>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 = 51.5 bits (124), Expect = 5e-09
 Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I NL+ N S  +L+  + +    + + +   +T G  + F Y+ F++  D  KA++ L G
Sbjct: 22  IGNLNPNKSVAELKVAISELFAKNDLAVVDVRT-GTNRKFGYVDFESAEDLEKALE-LTG 79

Query: 230 YGYDHLILSVDWSKS 244
                  + ++  K 
Sbjct: 80  LKVFGNEIKLEKPKG 94

>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 = 51.8 bits (124), Expect = 7e-09
 Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 1/80 (1%)

Query: 147 EGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLC 206
           + P G++     +        + +  L        + D  K+              NG  
Sbjct: 8   KSPSGQKRSRSRSPHEAGFC-VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKA 66

Query: 207 KGFAYIHFKNKADAAKAIQY 226
            G  ++ F+N+AD   A+  
Sbjct: 67  TGEGFVEFRNEADYKAALCR 86

>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 = 51.1 bits (123), Expect = 8e-09
 Identities = 13/80 (16%), Positives = 28/80 (35%), Gaps = 1/80 (1%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
             + NL  + +E  +++  +    ++             KGF Y  F++      A+  L
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-L 76

Query: 228 NGYGYDHLILSVDWSKSTNQ 247
           N     +  + VD +     
Sbjct: 77  NEESLGNKRIRVDVADQAQD 96

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 9/69 (13%), Positives = 30/69 (43%), Gaps = 1/69 (1%)

Query: 157 YNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN 216
           +  + +    ++ I     + + +D+++ ++  G    + + R   +   KG  ++ F +
Sbjct: 3   WILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDS 61

Query: 217 KADAAKAIQ 225
              A K ++
Sbjct: 62  IESAKKFVE 70

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 12/55 (21%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 179 ENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD 233
           +N +  +  +FG  +  +   +  +G  KG+ ++ + + A A  A++  +GY  D
Sbjct: 35  KNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLD 87

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
             + NL  NT + D++ + K     S + L RDK     KGF Y+ F       +A+   
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLSIRS-VRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-Y 75

Query: 228 NGYGYDHLILSVDWSK 243
           +G       L VD ++
Sbjct: 76  DGALLGDRSLRVDIAE 91

>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 = 51.0 bits (122), Expect = 2e-08
 Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 5/80 (6%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTS-----KMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
           + NL+ +  E DL+ +  ++   S      M+  R    G  KG A+I   N+  AAKA+
Sbjct: 50  VKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKAL 109

Query: 225 QYLNGYGYDHLILSVDWSKS 244
           +  NGY      + V +++S
Sbjct: 110 KEANGYVLFGKPMVVQFARS 129

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 49.3 bits (118), Expect = 2e-08
 Identities = 12/55 (21%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 179 ENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD 233
           +N +  +  +FG  +  +    + +G  KG+ ++ + + A A  A++  +GY  D
Sbjct: 21  KNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 73

>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 = 49.2 bits (118), Expect = 3e-08
 Identities = 12/56 (21%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           +  + V   E ++     ++G   ++ +  D+T G+ KG+ ++ F N  D  K ++
Sbjct: 14  VGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSFYNDVDVQKIVE 68

>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 = 49.5 bits (119), Expect = 3e-08
 Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 2/74 (2%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL     +  L      FG  +   +  +   G  KGF ++ F +  +A KA+  +NG
Sbjct: 20  VKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNG 77

Query: 230 YGYDHLILSVDWSK 243
                  L V  ++
Sbjct: 78  RIVATKPLYVALAQ 91

>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 = 49.3 bits (118), Expect = 3e-08
 Identities = 14/76 (18%), Positives = 27/76 (35%), Gaps = 3/76 (3%)

Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
           G     G + +       + +  L    +END+ +      P   +++     +G   G 
Sbjct: 1   GSSGSSGSSFQSTTGHC-VHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGP-DGRVTGE 57

Query: 210 AYIHFKNKADAAKAIQ 225
           A + F    DA  A+ 
Sbjct: 58  ADVEFATHEDAVAAMA 73

>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 = 49.5 bits (118), Expect = 3e-08
 Identities = 10/66 (15%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
           +  +    L    S N L  ++++ G    + +  +K       +++  ++   ++ +A 
Sbjct: 27  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAY 80

Query: 225 QYLNGY 230
             LNG 
Sbjct: 81  VTLNGK 86

>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 = 48.8 bits (117), Expect = 4e-08
 Identities = 16/79 (20%), Positives = 40/79 (50%), Gaps = 7/79 (8%)

Query: 170 ISNLSVNTSENDLE----DLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           I+NL+    +++L+     +  +FG    + +SR       +G A++ FK  + A  A++
Sbjct: 13  INNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATNALR 69

Query: 226 YLNGYGYDHLILSVDWSKS 244
            + G+ +    + + ++K+
Sbjct: 70  SMQGFPFYDKPMRIQYAKT 88

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 48.8 bits (117), Expect = 4e-08
 Identities = 11/82 (13%), Positives = 29/82 (35%), Gaps = 8/82 (9%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
             + +    +  +   L      FG    + +   +        A++ ++    A +A+ 
Sbjct: 16  NTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVA 67

Query: 226 YLNGYGYDHLILSVDWSKSTNQ 247
            LNG   + + L V+ ++    
Sbjct: 68  ELNGTQVESVQLKVNIARKQPM 89

>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 = 49.4 bits (118), Expect = 4e-08
 Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 2/76 (2%)

Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
           G     G     N D   + +  +  +  END+ D        + ++L +D   G   G 
Sbjct: 1   GSSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRVDA-VHLLKDH-VGRNNGN 58

Query: 210 AYIHFKNKADAAKAIQ 225
             + F +  D  +A++
Sbjct: 59  GLVKFLSPQDTFEALK 74

>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 = 48.5 bits (116), Expect = 5e-08
 Identities = 10/70 (14%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
           G +         +++     N +E ++ + +    P + + + R+  +G   G+ ++ F 
Sbjct: 1   GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVA-IRIVRNA-HGNKTGYIFVDFS 58

Query: 216 NKADAAKAIQ 225
           N+ +  +A++
Sbjct: 59  NEEEVKQALK 68

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 49.1 bits (117), Expect = 5e-08
 Identities = 13/84 (15%), Positives = 27/84 (32%), Gaps = 3/84 (3%)

Query: 146 REGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLS---RDKT 202
               GG   E       ++   +R+  L    +  ++     Q  P +            
Sbjct: 4   GSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP 63

Query: 203 NGLCKGFAYIHFKNKADAAKAIQY 226
           +G   G A++ F  +  A  A++ 
Sbjct: 64  DGRPTGDAFVLFACEEYAQNALRK 87

>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 = 51.4 bits (122), Expect = 6e-08
 Identities = 17/79 (21%), Positives = 40/79 (50%), Gaps = 7/79 (8%)

Query: 170 ISNLSVNTSENDLE----DLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           I+NL+    +++L+     +  QFG    + +SR       +G A++ FK  + A  A++
Sbjct: 14  INNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM---RGQAFVIFKEVSSATNALR 70

Query: 226 YLNGYGYDHLILSVDWSKS 244
            + G+ +    + + ++K+
Sbjct: 71  SMQGFPFYDKPMRIQYAKT 89

>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 = 48.3 bits (114), Expect = 6e-07
 Identities = 28/199 (14%), Positives = 50/199 (25%), Gaps = 18/199 (9%)

Query: 45  NTTIIGEEVHIQFISNKEEVEKPEEENLEKLKFISCRTCKGAHFTNNCPFKDSALFLADA 104
                 + + IQ+     ++    +    +      +    +  T               
Sbjct: 74  GFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPV 133

Query: 105 NKKPFNTVPGTNIMAASSDDKKSGG---PGGAPGGPAIYVPPSLREGPGGKRVEGYNARR 161
                  VPG   M  +           P   P G       +  + P G          
Sbjct: 134 VGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPG 193

Query: 162 NDDTTAIR----------ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAY 211
                             ++NL   T+E  L  L  QF    ++ L   +        A+
Sbjct: 194 QMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAF 248

Query: 212 IHFKNKADAAKAIQYLNGY 230
           + F N+  A  A   L G+
Sbjct: 249 VEFDNEVQAGAARDALQGF 267

>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 = 48.5 bits (115), Expect = 1e-07
 Identities = 14/115 (12%), Positives = 31/115 (26%), Gaps = 6/115 (5%)

Query: 118 MAASSDDKKSGGPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNT 177
           M +S             G        S+  G    R          +   +++  L  + 
Sbjct: 1   MGSSHHHHHHSSGLVPRGSH----MASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSC 56

Query: 178 SENDLEDLVKQFGPTSKMYLSR--DKTNGLCKGFAYIHFKNKADAAKAIQYLNGY 230
           S  D+++ +                   G   G A++   ++ D   A++     
Sbjct: 57  SVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRES 111

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 47.2 bits (112), Expect = 2e-07
 Identities = 12/77 (15%), Positives = 27/77 (35%), Gaps = 8/77 (10%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I  L ++ +E ++  L   FG  + + + +       K  A+I    +  A   + Y   
Sbjct: 21  IRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTS 74

Query: 230 YGYDHL--ILSVDWSKS 244
                    + + +S  
Sbjct: 75  VTPVLRGQPIYIQFSNH 91

>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 = 47.9 bits (113), Expect = 5e-07
 Identities = 20/160 (12%), Positives = 51/160 (31%), Gaps = 14/160 (8%)

Query: 69  EENLEKLKFISCRTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDDKKSG 128
           + NL + KF+  +      +    P +    F      +        N++  +    K+ 
Sbjct: 26  DFNLPRDKFLKEQIKLDEGW---VPLEIMIKF-----NRLNRLTTDFNVIVEALSKSKAE 77

Query: 129 GPGGAPGGPAIYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQ 188
               +     I   PS               + +    ++ I     + + +D+++ ++ 
Sbjct: 78  LMEISEDKTKIRRSPSKP-----LPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLED 132

Query: 189 FGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
            G    + + R       KG  ++ F +   A K ++   
Sbjct: 133 KGQVLNIQMRRTLHKAF-KGSIFVVFDSIESAKKFVETPG 171

>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 = 46.8 bits (112), Expect = 7e-07
 Identities = 15/86 (17%), Positives = 29/86 (33%), Gaps = 7/86 (8%)

Query: 151 GKRVEGYNA---RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
           GK ++   A      D T  I +  +  +    + E+   Q+G      L  DK  G  +
Sbjct: 70  GKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSR 129

Query: 208 GFAYIHFKNKADAAKAI----QYLNG 229
           GF ++ + +     +           
Sbjct: 130 GFGFVTYDSADAVDRVCQNKFIDFKD 155

>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 = 46.4 bits (111), Expect = 1e-06
 Identities = 11/56 (19%), Positives = 31/56 (55%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           I  L+ +T+E++L +   ++G  + + + +D   G  +GF ++ F+  +   + ++
Sbjct: 8   IGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63

>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 = 45.7 bits (108), Expect = 8e-07
 Identities = 12/77 (15%), Positives = 27/77 (35%), Gaps = 8/77 (10%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I  L ++ +E ++  L   FG  + + + +       K  A+I    +  A   + Y   
Sbjct: 36  IRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTS 89

Query: 230 YGYDHL--ILSVDWSKS 244
                    + + +S  
Sbjct: 90  VTPVLRGQPIYIQFSNH 106

>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 = 45.2 bits (107), Expect = 1e-06
 Identities = 11/77 (14%), Positives = 26/77 (33%), Gaps = 8/77 (10%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I  L    +E ++  L   FG  + + + +       K  A++    +  A   + Y + 
Sbjct: 20  IRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSA 73

Query: 230 YGYDHL--ILSVDWSKS 244
                    + + +S  
Sbjct: 74  VTPHLRNQPIYIQYSNH 90

>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 = 46.9 bits (112), Expect = 1e-06
 Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 4/81 (4%)

Query: 153 RVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYI 212
           R +      +     I +  +  +T E+ L D  +Q+G    + +  D+ +G  +GFA++
Sbjct: 92  REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 151

Query: 213 HFKNKADAAKAI----QYLNG 229
            F +     K +      +NG
Sbjct: 152 TFDDHDSVDKIVIQKYHTVNG 172

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 44.2 bits (105), Expect = 1e-05
 Identities = 12/56 (21%), Positives = 24/56 (42%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           I  LS  T++  L    +Q+G  +   + RD      +GF ++ +    +   A+ 
Sbjct: 18  IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73

>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 = 45.3 bits (107), Expect = 1e-06
 Identities = 8/76 (10%), Positives = 28/76 (36%), Gaps = 4/76 (5%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQF---GPTSKMYLSRDKTNGLCKGFAYIHF 214
                 +   +++  L  + S  D+++ +         + ++    +  G   G A++  
Sbjct: 10  LGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVEL 68

Query: 215 KNKADAAKAIQYLNGY 230
           +++ D   A++     
Sbjct: 69  ESEDDVKLALKKDRES 84

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
           G +      +  I +  +  N  E +L +  K+FG  +++ +  D      +GF +I F+
Sbjct: 1   GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60

Query: 216 NKADAAKAI----QYLNG 229
           ++    +A+      + G
Sbjct: 61  DEQSVDQAVNMHFHDIMG 78

>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 = 43.7 bits (103), Expect = 3e-06
 Identities = 13/65 (20%), Positives = 25/65 (38%), Gaps = 2/65 (3%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSR--DKTNGLCKGFAYIHFKNKADA 220
           DD   IR   L  + +  D+ +        +           +G  +G A I  +++ D 
Sbjct: 9   DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDV 68

Query: 221 AKAIQ 225
            KA++
Sbjct: 69  QKALE 73

>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 = 43.1 bits (102), Expect = 7e-06
 Identities = 14/73 (19%), Positives = 35/73 (47%)

Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
            + ++++   T I +  L  +T++  L    + FG   +  +  D+  G  +G+ ++   
Sbjct: 8   MHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA 67

Query: 216 NKADAAKAIQYLN 228
           ++A A +A +  N
Sbjct: 68  DRAAAERACKDPN 80

>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 = 41.7 bits (99), Expect = 9e-06
 Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 4/64 (6%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI----Q 225
           +  LS +T E  + +    FG    + L  D      +GF +I FK +    K +     
Sbjct: 4   VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYH 63

Query: 226 YLNG 229
            +  
Sbjct: 64  NVGL 67

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 41.9 bits (99), Expect = 1e-05
 Identities = 9/56 (16%), Positives = 18/56 (32%), Gaps = 5/56 (8%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           +S          L +    FGP + + + +DK       FA +   +       + 
Sbjct: 13  VSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGDVGAREAVLS 63

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 40.9 bits (96), Expect = 2e-05
 Identities = 12/78 (15%), Positives = 28/78 (35%), Gaps = 12/78 (15%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSR-----DKTNGLCKGFAYI 212
           +ARR      + + N+    +E  + D          +  +             K FA++
Sbjct: 5   SARR------LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFL 58

Query: 213 HFKNKADAAKAIQYLNGY 230
            F++  +  +A+   +G 
Sbjct: 59  EFRSVDETTQAMA-FDGI 75

>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 = 41.4 bits (97), Expect = 3e-05
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 179 ENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS 238
           E    ++ +++G   +M +  D       G  Y+ F+ + DA KA+  LN   ++   + 
Sbjct: 41  EEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99

Query: 239 VDWS 242
            + S
Sbjct: 100 AELS 103

>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 = 42.4 bits (99), Expect = 3e-05
 Identities = 20/110 (18%), Positives = 39/110 (35%), Gaps = 11/110 (10%)

Query: 139 IYVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLS 198
           + +  S      G  + G +         I + NL    + + L  +  +FG   K+   
Sbjct: 25  LALAASAAAVDAGMAMAGQSP-----VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF 79

Query: 199 RDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH--LILSVDWSKSTN 246
                   +  A + + +   A  A   L+G    +    L +D+SK T+
Sbjct: 80  TKNN----QFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 125

>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 = 41.1 bits (97), Expect = 3e-05
 Identities = 15/75 (20%), Positives = 29/75 (38%)

Query: 151 GKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFA 210
              +    +        + I  LS  T++  L +   QFG   +  + RD      +GF 
Sbjct: 11  SSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFG 70

Query: 211 YIHFKNKADAAKAIQ 225
           ++ F ++A   K + 
Sbjct: 71  FVTFMDQAGVDKVLA 85

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 41.2 bits (96), Expect = 4e-05
 Identities = 20/109 (18%), Positives = 38/109 (34%), Gaps = 11/109 (10%)

Query: 140 YVPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSR 199
            +  S      G  + G +         I + NL    + + L  +  +FG   K+    
Sbjct: 8   ALAASAAAVDAGMAMAGQS-----PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT 62

Query: 200 DKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH--LILSVDWSKSTN 246
                  +  A + + +   A  A   L+G    +    L +D+SK T+
Sbjct: 63  KNN----QFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS 107

>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 = 40.3 bits (95), Expect = 4e-05
 Identities = 8/64 (12%), Positives = 28/64 (43%), Gaps = 5/64 (7%)

Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
           +  ++ + +   + + +E++L +   Q+G    +++ +       + FA++ F +   A 
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQ 56

Query: 222 KAIQ 225
               
Sbjct: 57  SLCG 60

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 39.4 bits (93), Expect = 5e-05
 Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 4/61 (6%)

Query: 173 LSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI----QYLN 228
           LSVNT+  D++   +QFG      L  DKT    +GF ++ F+++    K        +N
Sbjct: 7   LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEIN 66

Query: 229 G 229
            
Sbjct: 67  N 67

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 39.5 bits (93), Expect = 9e-05
 Identities = 7/68 (10%), Positives = 26/68 (38%), Gaps = 5/68 (7%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
           +   +   + + +   + + +  +L+    Q+G    +++ +       + FA++ F + 
Sbjct: 4   SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADD 58

Query: 218 ADAAKAIQ 225
             A     
Sbjct: 59  KVAQSLCG 66

>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 = 39.1 bits (92), Expect = 1e-04
 Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 156 GYNARRND-DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHF 214
           G NA +N+ D   + +  LS +TS+ DL+D   +FG      +  D   G  +GF +I F
Sbjct: 1   GINASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILF 60

Query: 215 KNKADAAKAIQ 225
           K+ A   K + 
Sbjct: 61  KDAASVEKVLD 71

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 16/66 (24%), Positives = 28/66 (42%)

Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           R    T+ + +  L   T+E DL++    FG    + + +D   G  KGF ++ F     
Sbjct: 10  RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69

Query: 220 AAKAIQ 225
             K + 
Sbjct: 70  QVKVMS 75

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 11/64 (17%), Positives = 31/64 (48%), Gaps = 8/64 (12%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSK----MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           + +L+ +  +  L +   +  P+ +    +    D+T G+ KG+ ++ F ++ +  +A+ 
Sbjct: 14  VGDLTPDVDDGMLYEFFVKVYPSCRGGKVV---LDQT-GVSKGYGFVKFTDELEQKRALT 69

Query: 226 YLNG 229
              G
Sbjct: 70  ECQG 73

>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 = 38.4 bits (89), Expect = 3e-04
 Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 7/62 (11%)

Query: 168 IRISNL-SVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
           I +SNL     S++ +  L + +G      L R       K  A+I  + + DA   + +
Sbjct: 28  IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDH 81

Query: 227 LN 228
             
Sbjct: 82  CL 83

>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 = 37.6 bits (88), Expect = 5e-04
 Identities = 15/71 (21%), Positives = 29/71 (40%)

Query: 155 EGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHF 214
            G N    D+   + +  L  +T++  L     Q+G      + +DKT    +GF ++ F
Sbjct: 6   SGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65

Query: 215 KNKADAAKAIQ 225
           K+       + 
Sbjct: 66  KDPNCVGTVLA 76

>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 = 39.8 bits (92), Expect = 6e-04
 Identities = 38/301 (12%), Positives = 68/301 (22%), Gaps = 144/301 (47%)

Query: 3   VESTKVVRTLKVE-KKLV---SKGIA------LRKH------------------LAKY-G 33
           V++ K      +  K L+    K +          H                  L KY  
Sbjct: 253 VQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLD 312

Query: 34  KSANDKPGPQSNTT------IIGEEV-----HIQFI--SNKEEVEKPEEENLEKLKFISC 80
               D P  +  TT      II E +             N +++    E +L  L+    
Sbjct: 313 CRPQDLP-REVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEY 371

Query: 81  RTCKGAHFTNNCPFKDSALFLADANKKPFNTVPGTNIMAASSDDKKSGGPGGAPGGPAIY 140
           R            F   ++F   A+                                   
Sbjct: 372 RKM----------FDRLSVFPPSAH----------------------------------- 386

Query: 141 VPPSLREGPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRD 200
           +P  L                        +S +  +  ++D+  +V +        + + 
Sbjct: 387 IPTIL------------------------LSLIWFDVIKSDVMVVVNKL--HKYSLVEKQ 420

Query: 201 KTNGLCKGFAYIH-----FKNKADAAKAI------QY---------------LNGYGYDH 234
                      I       K K +   A+       Y               L+ Y Y H
Sbjct: 421 PKESTI----SIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH 476

Query: 235 L 235
           +
Sbjct: 477 I 477

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 36.7 bits (86), Expect = 6e-04
 Identities = 15/56 (26%), Positives = 26/56 (46%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           I  LS  T++  L +   QFG   +  + RD      +GF ++ F ++A   K + 
Sbjct: 5   IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

>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 = 37.3 bits (87), Expect = 7e-04
 Identities = 16/68 (23%), Positives = 31/68 (45%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
             R  +    + I  LS  T+E  L +  +Q+G  +   + RD  +   +GF ++ F + 
Sbjct: 20  KKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM 79

Query: 218 ADAAKAIQ 225
           A+   A+ 
Sbjct: 80  AEVDAAMA 87

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	247
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.88
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.85
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.84
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.84
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.84
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.83
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.83
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.83
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.83
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.83
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.82
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.82
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.82
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.82
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.82
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.82
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.82
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.82
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.82
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.81
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.81
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.81
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.81
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.81
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.81
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.81
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.81
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.81
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.81
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.81
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.8
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.8
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.8
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.8
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.8
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.8
2div_A	99	TRNA selenocysteine associated protein; structural	99.8
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.8
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.8
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.8
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.8
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.8
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.8
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.8
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.8
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.8
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.79
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.79
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.79
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.79
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.79
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.79
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.79
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.79
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.79
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.78
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.78
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.78
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.78
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.78
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.78
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.78
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.78
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.78
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.78
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.78
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.78
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.78
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.77
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.77
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.77
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.77
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.77
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.77
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.77
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.77
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.77
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.77
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.77
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.76
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.76
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.76
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.76
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.76
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.76
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.76
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.75
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.75
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.75
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.75
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.74
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.74
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.74
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.74
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.73
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.73
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.73
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.73
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.73
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.73
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.73
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.73
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.73
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.73
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.73
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.73
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.73
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.73
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.72
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.72
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.56
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.72
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.72
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.72
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.72
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.72
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.71
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.71
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.71
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.71
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.71
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.71
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.71
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.71
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.71
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.71
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.71
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.7
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.7
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.7
1x5p_A	97	Negative elongation factor E; structure genomics,	99.7
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.7
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.7
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.7
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.7
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.7
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.7
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.7
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.7
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.69
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.69
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.69
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.69
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.69
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.68
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.68
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.68
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.67
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.67
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.67
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.67
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.67
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.66
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.66
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.66
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.66
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.66
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.65
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.65
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.65
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.65
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.64
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.64
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.64
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.63
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.63
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.63
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.62
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.62
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.62
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.62
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.62
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.61
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.61
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.61
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.61
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.6
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.6
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.6
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.59
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.59
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.58
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.58
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.57
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.57
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.56
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.55
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.55
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.52
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.49
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.49
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.48
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.48
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.47
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.47
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.46
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.46
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.44
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.43
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.43
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.4
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.29
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.23
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.07
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.96
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.94
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.83
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.43
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.51
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.38
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.09
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.02
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.91
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.88
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	95.61
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.56
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	95.44
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	94.87
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	94.54
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	91.19
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	87.26
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	87.17

>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=99.88  E-value=2.9e-22  Score=151.86  Aligned_cols=83  Identities=24%  Similarity=0.457  Sum_probs=80.1

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||+|||+++++++|+++|++||.|.++.+++|+.+|.++|||||+|.+.++|++|++.|||..++|+.|+|+||
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            56689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      +|.
T Consensus        97 kPS   99 (99)
T 4fxv_A           97 RPS   99 (99)
T ss_dssp             CBC
T ss_pred             eCC
Confidence            984

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=1.3e-20  Score=142.48  Aligned_cols=87  Identities=52%  Similarity=0.975  Sum_probs=82.8

Q ss_pred             cCCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEE
Q psy13227        160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV  239 (247)
Q Consensus       160 ~~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V  239 (247)
                      ++.++.++|||+|||.++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|+.|+..|||..++|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (103)
T 2cq0_A           10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNV   89 (103)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            34577789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy13227        240 DWSKSTN  246 (247)
Q Consensus       240 ~~akp~~  246 (247)
                      +|++++.
T Consensus        90 ~~a~~~~   96 (103)
T 2cq0_A           90 EWAKPST   96 (103)
T ss_dssp             EESSCCC
T ss_pred             EECCCCC
Confidence            9999875

>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=99.84  E-value=2.2e-20  Score=135.29  Aligned_cols=82  Identities=20%  Similarity=0.428  Sum_probs=79.7

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST  245 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp~  245 (247)
                      ++|||+|||.++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|+.|+..|||..++|+.|+|+|++++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            68999999999999999999999999999999999889999999999999999999999999999999999999999998


Q ss_pred             CC
Q psy13227        246 NQ  247 (247)
Q Consensus       246 ~~  247 (247)
                      .+
T Consensus        82 ~~   83 (83)
T 3md1_A           82 EH   83 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>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=99.84  E-value=1.9e-20  Score=136.78  Aligned_cols=84  Identities=23%  Similarity=0.389  Sum_probs=77.5

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||+|||.++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|+.|+..|||..++|+.|+|+|+
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            45579999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      ++++
T Consensus        84 ~~kp   87 (87)
T 3bs9_A           84 TRKP   87 (87)
T ss_dssp             C---
T ss_pred             CCCC
Confidence            9875

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.84  E-value=6.5e-21  Score=143.90  Aligned_cols=84  Identities=21%  Similarity=0.411  Sum_probs=78.3

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCC--eeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCc----eeCC
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGP--TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGY----GYDH  234 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~--I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~----~i~g  234 (247)
                      ......||||+|||+++++++|+++|++||.  +..|++++|+.||.++|||||+|.+.++|++|++.|||.    .++|
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            4466789999999999999999999999995  678999999999999999999999999999999999996    5999


Q ss_pred             eEEEEeecCC
Q psy13227        235 LILSVDWSKS  244 (247)
Q Consensus       235 ~~L~V~~akp  244 (247)
                      +.|.|+||+.
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999999986

>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=99.83  E-value=6.6e-20  Score=141.33  Aligned_cols=85  Identities=26%  Similarity=0.390  Sum_probs=81.0

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||.++++++|+++|+.||.|..+.|+.++.++.++|||||+|.+.++|++|++.|||..|+|+.|+|+|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            35568999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus       102 a~~~~  106 (115)
T 2cpz_A          102 KRSKN  106 (115)
T ss_dssp             CCCSC
T ss_pred             cCCCC
Confidence            99864

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.83  E-value=6.6e-20  Score=141.16  Aligned_cols=86  Identities=23%  Similarity=0.417  Sum_probs=82.0

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ...+.++|||+|||+++++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|+.|++.|||..++|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45677899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      |+++++
T Consensus        91 ~a~~~~   96 (115)
T 2dgo_A           91 WATRKP   96 (115)
T ss_dssp             ESSCCC
T ss_pred             EccCCC
Confidence            999764

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.83  E-value=3.5e-21  Score=143.53  Aligned_cols=83  Identities=19%  Similarity=0.389  Sum_probs=77.4

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccC-CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHh-cCceeCCeEEEEeec
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFG-PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL-NGYGYDHLILSVDWS  242 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG-~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~L-nG~~i~g~~L~V~~a  242 (247)
                      +++|||+|||+++++++|+++|++|| .|.+|+|++|+.||.++|||||+|.+.++|++|++.| |+..++|+.|+|+||
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            36899999999999999999999999 7999999999999999999999999999999999977 466799999999999


Q ss_pred             CCCCC
Q psy13227        243 KSTNQ  247 (247)
Q Consensus       243 kp~~~  247 (247)
                      +|++.
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            98763

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.83  E-value=5e-20  Score=142.27  Aligned_cols=82  Identities=15%  Similarity=0.202  Sum_probs=78.7

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ..++|||+|||+++++++|+++|++||.|.++.|++|+.||+++|||||+|.+.++|++|++.|||..++|+.|+|+++.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CC
Q psy13227        244 ST  245 (247)
Q Consensus       244 p~  245 (247)
                      ..
T Consensus        85 ~~   86 (110)
T 3s8s_A           85 KG   86 (110)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=1.3e-19  Score=136.21  Aligned_cols=85  Identities=25%  Similarity=0.451  Sum_probs=80.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||.++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|+.|+..|||..++|+.|+|.|
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4566899999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy13227        242 SKSTNQ  247 (247)
Q Consensus       242 akp~~~  247 (247)
                      ++|+++
T Consensus        93 a~~~~~   98 (100)
T 2do4_A           93 SNSGPS   98 (100)
T ss_dssp             CCCCSC
T ss_pred             CCCCCC
Confidence            998763

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=6.5e-20  Score=135.99  Aligned_cols=82  Identities=22%  Similarity=0.355  Sum_probs=78.6

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||.++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.|||..++|+.|+|+|
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            45668999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cC
Q psy13227        242 SK  243 (247)
Q Consensus       242 ak  243 (247)
                      |+
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            86

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=6.3e-20  Score=140.86  Aligned_cols=86  Identities=24%  Similarity=0.405  Sum_probs=81.6

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCee--------EEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCcee
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTS--------KMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGY  232 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~--------~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i  232 (247)
                      ...+.++|||+|||.++++++|+++|+.||.|.        .|.|+.++.+|.++|||||+|.+.++|+.||..|||..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            456778999999999999999999999999999        699999988999999999999999999999999999999


Q ss_pred             CCeEEEEeecCCCC
Q psy13227        233 DHLILSVDWSKSTN  246 (247)
Q Consensus       233 ~g~~L~V~~akp~~  246 (247)
                      +|+.|+|.|++++.
T Consensus        91 ~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           91 QGSKLKVSLARKKP  104 (113)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCCEEEEEECCCCC
Confidence            99999999999875

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=6.2e-20  Score=139.20  Aligned_cols=86  Identities=21%  Similarity=0.404  Sum_probs=81.8

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||.++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|+.|+..|||..++|+.|.|+|
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            35668999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy13227        242 SKSTNQ  247 (247)
Q Consensus       242 akp~~~  247 (247)
                      ++++++
T Consensus       100 a~~~~~  105 (106)
T 1p27_B          100 CFVRGP  105 (106)
T ss_dssp             SEESSC
T ss_pred             ecCCCC
Confidence            998764

>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=99.82  E-value=6.9e-20  Score=138.70  Aligned_cols=86  Identities=21%  Similarity=0.352  Sum_probs=81.8

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      .....++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|+..|||..++|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34667899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      |++++.
T Consensus        91 ~a~~~~   96 (105)
T 1x5u_A           91 KASAHN   96 (105)
T ss_dssp             ETTTTS
T ss_pred             ECCCCC
Confidence            999874

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=1.5e-19  Score=134.07  Aligned_cols=83  Identities=28%  Similarity=0.462  Sum_probs=79.6

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      .+..++|||+|||.++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|+..|||..++|+.|+|+|
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            45668999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cCC
Q psy13227        242 SKS  244 (247)
Q Consensus       242 akp  244 (247)
                      +++
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            985

>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=99.82  E-value=1.6e-20  Score=139.00  Aligned_cols=81  Identities=25%  Similarity=0.313  Sum_probs=73.1

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccC--CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFG--PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG--~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      .+|||+|||+++++++|+++|++||  .|.++.++.++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999999999999999999999999999999999999999999999999


Q ss_pred             CCC
Q psy13227        244 STN  246 (247)
Q Consensus       244 p~~  246 (247)
                      |++
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            875

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.82  E-value=1.1e-19  Score=132.22  Aligned_cols=81  Identities=21%  Similarity=0.327  Sum_probs=78.1

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||+|||+++++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|+.|++.|||..++|+.|+|+||
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            55689999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             C
Q psy13227        243 K  243 (247)
Q Consensus       243 k  243 (247)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.82  E-value=1.1e-19  Score=136.28  Aligned_cols=85  Identities=29%  Similarity=0.393  Sum_probs=81.0

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|+.|+..|||..++|+.|+|.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            35668999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus        85 a~~~~   89 (99)
T 1whw_A           85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             cCCCc
Confidence            99874

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=1.1e-19  Score=135.10  Aligned_cols=84  Identities=23%  Similarity=0.450  Sum_probs=80.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||.++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|+.|+..|||..++|+.|+|+|+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            34579999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +++.
T Consensus        83 ~~~~   86 (95)
T 2dnz_A           83 TERL   86 (95)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            9875

>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=99.81  E-value=1.4e-19  Score=138.10  Aligned_cols=85  Identities=24%  Similarity=0.357  Sum_probs=81.1

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhc------CceeCCe
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN------GYGYDHL  235 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~Ln------G~~i~g~  235 (247)
                      ....++|||+|||+++++++|+++|+.||.|..|.|++++.++.++|||||+|.+.++|++|+..||      |..++|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            4566899999999999999999999999999999999999999999999999999999999999999      9999999


Q ss_pred             EEEEeecCCCC
Q psy13227        236 ILSVDWSKSTN  246 (247)
Q Consensus       236 ~L~V~~akp~~  246 (247)
                      .|.|.|++++.
T Consensus        92 ~l~v~~a~~~~  102 (111)
T 1x4h_A           92 QLKVDLAVTRD  102 (111)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCc
Confidence            99999999875

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=1.2e-19  Score=137.55  Aligned_cols=86  Identities=23%  Similarity=0.474  Sum_probs=81.4

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeec-CCCCceeeEEEEEecCHHHHHHHHHHh-cCceeCCeEEE
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRD-KTNGLCKGFAYIHFKNKADAAKAIQYL-NGYGYDHLILS  238 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d-~~tg~skGfaFV~F~s~e~A~~Ai~~L-nG~~i~g~~L~  238 (247)
                      .....++|||+|||.++++++|+++|+.||.|..|.|+.+ +.++.++|||||+|.+.++|++|+..| ||..++|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3456789999999999999999999999999999999999 789999999999999999999999999 99999999999


Q ss_pred             EeecCCCC
Q psy13227        239 VDWSKSTN  246 (247)
Q Consensus       239 V~~akp~~  246 (247)
                      |+|++++.
T Consensus        91 v~~a~~~~   98 (107)
T 2cph_A           91 LEWADSEV   98 (107)
T ss_dssp             EEECCCCC
T ss_pred             EEeCCCCC
Confidence            99999875

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=9e-20  Score=137.36  Aligned_cols=85  Identities=26%  Similarity=0.479  Sum_probs=81.0

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|+.|++.|||..++|+.|+|+|
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            35668999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus        89 a~~~~   93 (102)
T 1x5s_A           89 AGKSS   93 (102)
T ss_dssp             EECCC
T ss_pred             CCCCC
Confidence            99864

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=8e-20  Score=138.04  Aligned_cols=86  Identities=23%  Similarity=0.460  Sum_probs=81.5

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ...+.++|||+|||.++++++|+++|+.||.|..+.|+.++.++.++|||||+|.+.++|++|+..|||..++|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34667899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      |+++..
T Consensus        89 ~a~~~~   94 (103)
T 2dnm_A           89 VARYGR   94 (103)
T ss_dssp             ECSSCC
T ss_pred             ECCcCC
Confidence            999763

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1e-19  Score=137.04  Aligned_cols=85  Identities=20%  Similarity=0.310  Sum_probs=81.0

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||.++++++|+++|+.||.|..+.|+.++.++.++|||||+|.+.++|+.|++.|||..++|+.|.|+|
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            35668999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus        89 a~~~~   93 (102)
T 2cqb_A           89 AKPMR   93 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            99874

>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=99.81  E-value=1.2e-19  Score=138.56  Aligned_cols=86  Identities=20%  Similarity=0.409  Sum_probs=81.6

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ...+.++|||+|||.++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|+.|+..|||..++|+.|.|.
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  101 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  101 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      |+++++
T Consensus       102 ~a~~~~  107 (110)
T 1oo0_B          102 WCFVKG  107 (110)
T ss_dssp             ESEESS
T ss_pred             EcccCC
Confidence            998775

>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=99.81  E-value=1.6e-19  Score=134.78  Aligned_cols=82  Identities=24%  Similarity=0.530  Sum_probs=79.1

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      +++|||+|||.++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|+.|++.|||..++|+.|.|+|+++
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            46899999999999999999999999999999999998999999999999999999999999999999999999999998


Q ss_pred             CC
Q psy13227        245 TN  246 (247)
Q Consensus       245 ~~  246 (247)
                      ++
T Consensus        82 ~~   83 (96)
T 2x1f_A           82 SD   83 (96)
T ss_dssp             SS
T ss_pred             CC
Confidence            74

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=8.9e-20  Score=135.75  Aligned_cols=84  Identities=26%  Similarity=0.377  Sum_probs=80.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEE-EEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKM-YLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i-~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ...++|||+|||.++++++|+++|+.||.|..+ .+++++.++.++|||||+|.+.++|+.|+..|||..++|+.|.|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345799999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus        83 a~~~~   87 (96)
T 1x5t_A           83 AFKKD   87 (96)
T ss_dssp             SCCCC
T ss_pred             ecccC
Confidence            99875

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=2e-19  Score=134.86  Aligned_cols=84  Identities=17%  Similarity=0.341  Sum_probs=80.0

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||.++++++|+++|+.||.|..+.|+.++.++.++|||||+|.+.++|++|++ ||+..++|+.|.|.|
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            3566899999999999999999999999999999999999899999999999999999999999 999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus        86 a~~~~   90 (99)
T 2dgs_A           86 AEPRD   90 (99)
T ss_dssp             CCCCC
T ss_pred             CCCCc
Confidence            99874

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.81  E-value=3.8e-19  Score=137.48  Aligned_cols=83  Identities=25%  Similarity=0.362  Sum_probs=78.6

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ...+.++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34667899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             ecC
Q psy13227        241 WSK  243 (247)
Q Consensus       241 ~ak  243 (247)
                      |++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            985

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=2.4e-19  Score=135.42  Aligned_cols=84  Identities=20%  Similarity=0.338  Sum_probs=79.6

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ...+.++|||+|||+++++++|+++|++||.|..+.|+.+  ++.++|||||+|.+.++|+.|+..|||..++|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            3467789999999999999999999999999999999998  89999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      |++++.
T Consensus        89 ~a~~~~   94 (103)
T 2d9p_A           89 LAQRKE   94 (103)
T ss_dssp             ECSSCC
T ss_pred             Eecccc
Confidence            999864

>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=99.80  E-value=2e-19  Score=137.99  Aligned_cols=86  Identities=23%  Similarity=0.419  Sum_probs=81.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|+.|++.|||..++|+.|+|+|
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            35568999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy13227        242 SKSTNQ  247 (247)
Q Consensus       242 akp~~~  247 (247)
                      ++++..
T Consensus       103 a~~k~d  108 (108)
T 2jrs_A          103 VTERTD  108 (108)
T ss_dssp             SCSSCC
T ss_pred             cccCCC
Confidence            999863

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=2e-19  Score=134.51  Aligned_cols=84  Identities=26%  Similarity=0.418  Sum_probs=78.9

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCC---CCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEE
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKT---NGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV  239 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~---tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V  239 (247)
                      .+.++|||+|||+++++++|+++|+.||.|..+.++.++.   |+.++|||||+|.+.++|+.|+..|||..++|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4557999999999999999999999999999999999876   6699999999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy13227        240 DWSKSTN  246 (247)
Q Consensus       240 ~~akp~~  246 (247)
                      +|++++.
T Consensus        83 ~~a~~~~   89 (98)
T 2cpf_A           83 RISERAT   89 (98)
T ss_dssp             ECSSCSS
T ss_pred             EEccCCC
Confidence            9999764

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.80  E-value=4.6e-19  Score=134.00  Aligned_cols=83  Identities=24%  Similarity=0.403  Sum_probs=78.6

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||+++++++|+++|+.|| |..|.|++++.++.++|||||+|.+.++|+.|+ .|||..++|+.|+|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            35568999999999999999999999997 999999999999999999999999999999999 7999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus        90 a~~~~   94 (103)
T 2dng_A           90 AEGRK   94 (103)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            99875

>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=99.80  E-value=3.3e-19  Score=138.05  Aligned_cols=80  Identities=26%  Similarity=0.367  Sum_probs=75.4

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      .++|||+|||+++++++|+++|++||.|.++.|++++  +.++|||||+|.+.++|++||+.|||..++|+.|.|.|+++
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999985  55899999999999999999999999999999999999987


Q ss_pred             CC
Q psy13227        245 TN  246 (247)
Q Consensus       245 ~~  246 (247)
                      +.
T Consensus        83 ~~   84 (115)
T 4f25_A           83 RK   84 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            64

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=1.8e-19  Score=136.51  Aligned_cols=85  Identities=16%  Similarity=0.293  Sum_probs=80.8

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ...+.++|||+|||+++++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|++||.. |+..|+|+.|.|+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            456778999999999999999999999999999999999998999999999999999999999998 9999999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      |++++.
T Consensus        91 ~a~~~~   96 (105)
T 2dh8_A           91 PCTPRG   96 (105)
T ss_dssp             CSCCSS
T ss_pred             EccCCC
Confidence            999864

>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=99.80  E-value=2.5e-19  Score=130.88  Aligned_cols=84  Identities=19%  Similarity=0.380  Sum_probs=78.9

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCc-eeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL-CKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~-skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ..++|||+|||.++++++|+++|++||.|..+.++.++.++. ++|||||+|.+.++|++|+..|||..++|+.|+|+|+
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            357999999999999999999999999999999999987766 9999999999999999999999999999999999999


Q ss_pred             CCCCC
Q psy13227        243 KSTNQ  247 (247)
Q Consensus       243 kp~~~  247 (247)
                      .|+.+
T Consensus        83 ~~~~~   87 (88)
T 4a8x_A           83 LAPWP   87 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98753

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=1.8e-19  Score=134.99  Aligned_cols=85  Identities=16%  Similarity=0.358  Sum_probs=80.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCee-EEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeE----
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTS-KMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLI----  236 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~-~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~----  236 (247)
                      ....++|||+|||+++++++|+++|++||.|. .+.+++++.++.++|||||+|.+.++|+.|+..|||..++|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            35568999999999999999999999999999 9999999999999999999999999999999999999999999    


Q ss_pred             EEEeecCCCC
Q psy13227        237 LSVDWSKSTN  246 (247)
Q Consensus       237 L~V~~akp~~  246 (247)
                      |+|+|+++..
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999999864

>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=99.80  E-value=5.9e-19  Score=133.52  Aligned_cols=84  Identities=24%  Similarity=0.372  Sum_probs=79.4

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC---eEEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH---LILS  238 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g---~~L~  238 (247)
                      ....++|||+|||.++++++|+++|+.||.|..+.|+.++ +|.++|||||+|.+.++|++|+..|||..+.+   +.|+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            3567899999999999999999999999999999999997 89999999999999999999999999999998   9999


Q ss_pred             EeecCCCC
Q psy13227        239 VDWSKSTN  246 (247)
Q Consensus       239 V~~akp~~  246 (247)
                      |.|++++.
T Consensus        91 V~~a~~~~   98 (105)
T 2dnh_A           91 VKFADTDK   98 (105)
T ss_dssp             EEESCSSC
T ss_pred             EEECccCc
Confidence            99999764

>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=99.80  E-value=2.1e-19  Score=136.28  Aligned_cols=85  Identities=24%  Similarity=0.366  Sum_probs=80.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCcee---CCeEEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGY---DHLILS  238 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i---~g~~L~  238 (247)
                      ..+.++|||+|||.++++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|+.|+..|||..+   +|+.|.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            45678999999999999999999999999999999999998999999999999999999999999999998   899999


Q ss_pred             EeecCCCC
Q psy13227        239 VDWSKSTN  246 (247)
Q Consensus       239 V~~akp~~  246 (247)
                      |.|++++.
T Consensus        90 v~~a~~~~   97 (106)
T 2dgp_A           90 VKPADSES   97 (106)
T ss_dssp             EEECCCCS
T ss_pred             EEECCccc
Confidence            99998764

>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=99.80  E-value=3.4e-19  Score=134.96  Aligned_cols=82  Identities=21%  Similarity=0.353  Sum_probs=78.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCC-CceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTN-GLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~t-g~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ...++|||+|||+++++++|+++|+.|| |..|.|+.++.+ |.++|||||+|.+.++|++|| .|||..++|+.|.|+|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            4568999999999999999999999999 999999999887 999999999999999999999 8999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus        91 a~~~~   95 (104)
T 1wi8_A           91 ADQAQ   95 (104)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            99875

>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=99.80  E-value=2.1e-19  Score=131.76  Aligned_cols=82  Identities=23%  Similarity=0.371  Sum_probs=78.4

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      +.++|||+|||+++++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|++|+ .|||..++|+.|+|.|++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            3579999999999999999999999999999999999889999999999999999999999 899999999999999999


Q ss_pred             CCC
Q psy13227        244 STN  246 (247)
Q Consensus       244 p~~  246 (247)
                      ++.
T Consensus        84 ~~~   86 (89)
T 3ucg_A           84 TNR   86 (89)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            864

>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=99.80  E-value=4.2e-19  Score=131.83  Aligned_cols=82  Identities=27%  Similarity=0.406  Sum_probs=77.8

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||+++++++|+++|++||.|..+.++.++ +|.++|||||+|.+.++|++|+..|||..++|+.|+|+|
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            4566899999999999999999999999999999999997 499999999999999999999999999999999999999


Q ss_pred             cCC
Q psy13227        242 SKS  244 (247)
Q Consensus       242 akp  244 (247)
                      ++.
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            874

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.80  E-value=4e-20  Score=139.81  Aligned_cols=82  Identities=23%  Similarity=0.289  Sum_probs=78.5

Q ss_pred             CccEEEEeecCC------CCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC-eE
Q psy13227        164 DTTAIRISNLSV------NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH-LI  236 (247)
Q Consensus       164 ~~~tl~V~nLp~------~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g-~~  236 (247)
                      ..++|||+|||.      ++++++|+++|++||.|.++.|++++.||+++|||||+|.+.++|++|++.|||..++| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            357999999999      99999999999999999999999999999999999999999999999999999999999 99


Q ss_pred             EEEeecCCC
Q psy13227        237 LSVDWSKST  245 (247)
Q Consensus       237 L~V~~akp~  245 (247)
                      |+|.|+.|+
T Consensus        85 l~V~~a~~~   93 (100)
T 3ns6_A           85 LFLYTMKDV   93 (100)
T ss_dssp             CEEEESHHH
T ss_pred             EEEEECchh
Confidence            999999764

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.80  E-value=5e-19  Score=132.85  Aligned_cols=82  Identities=24%  Similarity=0.408  Sum_probs=78.3

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeE--------EEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSK--------MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD  233 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~--------i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~  233 (247)
                      ....++|||+|||.++++++|+++|++||.|..        +.++.++.+|.++|||||+|.+.++|++|++.|||..++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~   89 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   89 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            355689999999999999999999999999999        999999989999999999999999999999999999999


Q ss_pred             CeEEEEeecC
Q psy13227        234 HLILSVDWSK  243 (247)
Q Consensus       234 g~~L~V~~ak  243 (247)
                      |+.|+|+||+
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999985

>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=99.80  E-value=4.6e-19  Score=136.29  Aligned_cols=86  Identities=19%  Similarity=0.252  Sum_probs=79.1

Q ss_pred             CCCCccEEEEeecCCCCCHHHHH---HHhhccCCeeEEEEeecCCCC---ceeeEEEEEecCHHHHHHHHHHhcCceeCC
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLE---DLVKQFGPTSKMYLSRDKTNG---LCKGFAYIHFKNKADAAKAIQYLNGYGYDH  234 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~---~lF~~fG~I~~i~l~~d~~tg---~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g  234 (247)
                      +..+.++|||+|||+++++++|+   ++|++||.|..+.|+.++.++   .++|||||+|.+.++|++||+.|||..++|
T Consensus        11 r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g   90 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   90 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC
Confidence            34566799999999999999999   999999999999999987654   566999999999999999999999999999


Q ss_pred             eEEEEeecCCCC
Q psy13227        235 LILSVDWSKSTN  246 (247)
Q Consensus       235 ~~L~V~~akp~~  246 (247)
                      +.|+|+|+++++
T Consensus        91 r~l~V~~a~~k~  102 (111)
T 2cpi_A           91 RTLKASLGTTKY  102 (111)
T ss_dssp             EEEEEESCCCCS
T ss_pred             EEEEEEeccccc
Confidence            999999999875

>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=99.80  E-value=1e-18  Score=131.97  Aligned_cols=83  Identities=23%  Similarity=0.377  Sum_probs=77.6

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|..|.|+.++.  .++|||||+|.+.++|++|+..|||..++|+.|.|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45668999999999999999999999999999999999863  3899999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus        90 a~~~~   94 (103)
T 2cq3_A           90 ATARV   94 (103)
T ss_dssp             CCSSC
T ss_pred             cccCC
Confidence            99875

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=5.5e-19  Score=136.32  Aligned_cols=84  Identities=19%  Similarity=0.321  Sum_probs=79.3

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      .....++|||+|||+++++++|+++|+.||.|..|.|++++.++.++|||||+|.+.++|++||..||+ .++|+.|.|+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            346678999999999999999999999999999999999999999999999999999999999999998 8999999999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      |+++.
T Consensus        92 ~a~~~   96 (116)
T 2cqd_A           92 LAYLG   96 (116)
T ss_dssp             ESTTT
T ss_pred             EcccC
Confidence            99764

>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=99.79  E-value=1.1e-18  Score=131.74  Aligned_cols=84  Identities=21%  Similarity=0.378  Sum_probs=77.8

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.++.  .++|||||+|.+.++|++|+..|||..++|+.|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            346678999999999999999999999999999999999863  368999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      |++++.
T Consensus        89 ~a~~~~   94 (103)
T 2cqi_A           89 WATTPS   94 (103)
T ss_dssp             ECCCTT
T ss_pred             ECCCCc
Confidence            999864

>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=99.79  E-value=8.1e-19  Score=133.19  Aligned_cols=82  Identities=30%  Similarity=0.462  Sum_probs=78.3

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||+.+++++|+++|++||.|..+.|+.++ +|.++|||||+|.+.++|++|+..|||..++|+.|.|+|
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            4567899999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             cCC
Q psy13227        242 SKS  244 (247)
Q Consensus       242 akp  244 (247)
                      +..
T Consensus       105 a~s  107 (107)
T 3ulh_A          105 VTS  107 (107)
T ss_dssp             ECC
T ss_pred             eCC
Confidence            863

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=1.4e-18  Score=133.28  Aligned_cols=83  Identities=18%  Similarity=0.283  Sum_probs=78.3

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||+++++++|+++|..||.|..+.|+.++ ++.++|||||+|.+.++|+.|+..|||..++|+.|.|+|
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            3556899999999999999999999999999999999997 799999999999999999999999999999999999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      +++.
T Consensus        91 a~~~   94 (114)
T 2do0_A           91 DERA   94 (114)
T ss_dssp             CSCC
T ss_pred             cccC
Confidence            9754

>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=99.79  E-value=4.8e-19  Score=132.42  Aligned_cols=84  Identities=15%  Similarity=0.223  Sum_probs=79.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +..++|||+|||+++++++|+++|..||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|+|+
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            45579999999999999999999999999998888888889999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      ++++
T Consensus        93 ~~~~   96 (98)
T 2cqp_A           93 SGPS   96 (98)
T ss_dssp             SCSS
T ss_pred             CCCC
Confidence            8764

>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=99.79  E-value=6.5e-19  Score=131.95  Aligned_cols=82  Identities=18%  Similarity=0.268  Sum_probs=76.9

Q ss_pred             CCccEEEEeecCCCCCHHHHH----HHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEE
Q psy13227        163 DDTTAIRISNLSVNTSENDLE----DLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS  238 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~----~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~  238 (247)
                      .+.++|||+|||+++++++|+    ++|++||.|.++.|+.++.+   +|||||+|.+.++|++|++.|||..++|+.|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            456899999999999999999    99999999999999999755   89999999999999999999999999999999


Q ss_pred             EeecCCCCC
Q psy13227        239 VDWSKSTNQ  247 (247)
Q Consensus       239 V~~akp~~~  247 (247)
                      |+|++++++
T Consensus        84 V~~a~~~~~   92 (96)
T 2dgx_A           84 VSLATGASG   92 (96)
T ss_dssp             EEECCCSSC
T ss_pred             EEEcCCCCC
Confidence            999998753

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.79  E-value=4e-19  Score=145.41  Aligned_cols=83  Identities=17%  Similarity=0.313  Sum_probs=77.9

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccC--CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFG--PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG--~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      .+.++|||+|||+++++++|+++|+.||  .|..|.|+.|+.+|.++|||||+|.+.++|++||..|||..|+|+.|.|.
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEE
Confidence            4558999999999999999999999999  99999999999999999999999999999999999999999999999999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      +++++
T Consensus       133 ~a~~~  137 (156)
T 3n9u_C          133 PATRQ  137 (156)
T ss_dssp             ECCHH
T ss_pred             EcCCC
Confidence            99864

>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=99.79  E-value=5.2e-19  Score=137.38  Aligned_cols=84  Identities=30%  Similarity=0.484  Sum_probs=79.9

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      .++.++|||+|||.++++++|+++|+.||.|..|.++.++ +|.++|||||+|.+.++|+.|+..|||..++|+.|.|+|
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4566899999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus        83 a~~~~   87 (116)
T 2fy1_A           83 AKKPS   87 (116)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            98764

>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=99.79  E-value=3.7e-19  Score=140.99  Aligned_cols=86  Identities=28%  Similarity=0.488  Sum_probs=81.6

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      .+..++|||+|||.++++++|+++|++||.|..|.++.++.+|.++|||||+|.+.++|++||..|||..|+|+.|.|+|
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35668999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy13227        242 SKSTNQ  247 (247)
Q Consensus       242 akp~~~  247 (247)
                      ++++.+
T Consensus       123 a~~~~p  128 (129)
T 2kxn_B          123 SITKRP  128 (129)
T ss_dssp             CSSSSC
T ss_pred             ecCCCC
Confidence            998753

>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=99.78  E-value=2e-19  Score=144.30  Aligned_cols=82  Identities=13%  Similarity=0.219  Sum_probs=77.3

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCC---eeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEE
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGP---TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLIL  237 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~---I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L  237 (247)
                      ...+.++|||+|||+++++++|+++|+.||.   |..|.|++++. |+++|||||+|.+.++|++||+ |||..++|+.|
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i  117 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYI  117 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEE
Confidence            4566789999999999999999999999999   89999999986 9999999999999999999999 99999999999


Q ss_pred             EEeecCC
Q psy13227        238 SVDWSKS  244 (247)
Q Consensus       238 ~V~~akp  244 (247)
                      .|.++.+
T Consensus       118 ~V~~a~~  124 (136)
T 2hgl_A          118 EVFKSHR  124 (136)
T ss_dssp             EEEECCH
T ss_pred             EEEECCh
Confidence            9999875

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=4.7e-19  Score=133.85  Aligned_cols=84  Identities=11%  Similarity=0.256  Sum_probs=79.6

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhc-cCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCce-eCCeEEEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQ-FGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG-YDHLILSV  239 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~-fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~-i~g~~L~V  239 (247)
                      ....++|||+|||+++++++|+++|+. ||.|..+.|+.++ +|.++|||||+|.+.++|..|+..|||.. ++|+.|.|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            355689999999999999999999999 9999999999998 99999999999999999999999999999 99999999


Q ss_pred             eecCCCC
Q psy13227        240 DWSKSTN  246 (247)
Q Consensus       240 ~~akp~~  246 (247)
                      .|++++.
T Consensus        85 ~~a~~~~   91 (104)
T 2dhg_A           85 SVAIPKA   91 (104)
T ss_dssp             CBCCCCC
T ss_pred             EEccCCC
Confidence            9998764

>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=99.78  E-value=2.6e-18  Score=129.67  Aligned_cols=84  Identities=20%  Similarity=0.332  Sum_probs=78.6

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ...+.++|||+|||+++++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|+.|+.  +++.++|+.|.|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            34566899999999999999999999999999999999999899999999999999999999999  6889999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      |++++.
T Consensus        89 ~a~~~~   94 (103)
T 2cqg_A           89 LPNSKQ   94 (103)
T ss_dssp             CCCTTC
T ss_pred             ecCCCC
Confidence            999864

>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=99.78  E-value=4.6e-19  Score=138.52  Aligned_cols=85  Identities=21%  Similarity=0.410  Sum_probs=80.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|+.|+..|||..|+|+.|.|+|
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            35568999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      +++++
T Consensus        99 a~~~~  103 (126)
T 3ex7_B           99 CFVRG  103 (126)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            98764

>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=99.78  E-value=3.8e-19  Score=134.20  Aligned_cols=84  Identities=24%  Similarity=0.465  Sum_probs=80.1

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||+|||.++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|+.|++.|||..++|+.|+|.|+
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            34578999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +++.
T Consensus        86 ~~~~   89 (104)
T 1p1t_A           86 ASEK   89 (104)
T ss_dssp             TCTT
T ss_pred             CCcc
Confidence            9864

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.78  E-value=1.1e-18  Score=138.51  Aligned_cols=85  Identities=21%  Similarity=0.416  Sum_probs=81.2

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||.++++++|+++|+.||.|..|.|++++.+|.++|||||+|.+.++|.+|+..|||..++|+.|+|+|
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45668999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus       119 a~~~~  123 (139)
T 1u6f_A          119 AASGH  123 (139)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            99764

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.78  E-value=1.1e-18  Score=128.87  Aligned_cols=82  Identities=20%  Similarity=0.282  Sum_probs=77.6

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||.++++++|+++|++||.|..+.+.++  +|.++|||||+|.+.++|+.|+..|||..++|+.|+|+|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            55689999999999999999999999999999999884  7999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +++.
T Consensus        84 ~~~~   87 (92)
T 2dgv_A           84 RNAS   87 (92)
T ss_dssp             SCCS
T ss_pred             CCCC
Confidence            9864

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=2e-18  Score=132.57  Aligned_cols=85  Identities=25%  Similarity=0.419  Sum_probs=79.5

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCcee--------
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGY--------  232 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i--------  232 (247)
                      ...+.++|||+|||.++++++|+++|+.||.|..+.|+.++ ++.++|||||+|.+.++|+.|+..|||..+        
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~   99 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   99 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccC
Confidence            34567899999999999999999999999999999999998 999999999999999999999999999999        


Q ss_pred             CCeEEEEeecCCCC
Q psy13227        233 DHLILSVDWSKSTN  246 (247)
Q Consensus       233 ~g~~L~V~~akp~~  246 (247)
                      .++.|.|.|+.|+.
T Consensus       100 ~~~~l~v~~a~p~~  113 (114)
T 1x5o_A          100 PTEPLLCKFSGPSS  113 (114)
T ss_dssp             CSSCBEEEECCCSC
T ss_pred             CCCceeEEccCCCC
Confidence            57789999999864

>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=99.78  E-value=3.5e-18  Score=130.34  Aligned_cols=82  Identities=26%  Similarity=0.475  Sum_probs=75.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||+++++++|+++|++||.|..+.|..+   +.++|||||+|.+.++|+.|++.||+..++|+.|.|+|
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            356689999999999999999999999999999999654   56899999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus        96 a~~~~  100 (109)
T 1x4a_A           96 PRSGR  100 (109)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            99864

>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=99.78  E-value=1.7e-18  Score=126.66  Aligned_cols=80  Identities=25%  Similarity=0.439  Sum_probs=75.8

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++ +++..++|+.|.|++
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            4566899999999999999999999999999999999999899999999999999999999997 689999999999998


Q ss_pred             c
Q psy13227        242 S  242 (247)
Q Consensus       242 a  242 (247)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.78  E-value=5e-18  Score=132.53  Aligned_cols=84  Identities=27%  Similarity=0.432  Sum_probs=79.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||.++++++|+++|+.||.|..+.+..++ +|.++|||||+|.+.++|+.|+..|||..++|+.|+|+|
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3566899999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      |.+..
T Consensus       111 a~~~~  115 (124)
T 2kt5_A          111 VASQI  115 (124)
T ss_dssp             ECCTT
T ss_pred             eCCCC
Confidence            98753

>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=99.78  E-value=2.3e-18  Score=139.54  Aligned_cols=84  Identities=27%  Similarity=0.546  Sum_probs=80.6

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||+|||.++++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|+.||..|||..|+|+.|.|+|+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            56689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      ++..
T Consensus       117 ~~~~  120 (156)
T 1h2v_Z          117 AGFK  120 (156)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8754

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=2.8e-18  Score=126.69  Aligned_cols=83  Identities=14%  Similarity=0.301  Sum_probs=78.3

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||+++++++|+++|+.| .|..+.|+++ .+|.++|||||+|.+.++|+.|+. |||..++|+.|.|.+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            3556899999999999999999999999 9999999999 699999999999999999999999 999999999999999


Q ss_pred             cCCCCC
Q psy13227        242 SKSTNQ  247 (247)
Q Consensus       242 akp~~~  247 (247)
                      ++++++
T Consensus        84 a~~~~~   89 (91)
T 2dgw_A           84 EKSGPS   89 (91)
T ss_dssp             ESSCCC
T ss_pred             CCcCCC
Confidence            998763

>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=99.77  E-value=7.7e-19  Score=133.75  Aligned_cols=85  Identities=13%  Similarity=0.217  Sum_probs=79.2

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCC-eeEEEEe-ecCCCCceeeEEEEEecCHHHHHHHHHHhc--CceeCCeEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGP-TSKMYLS-RDKTNGLCKGFAYIHFKNKADAAKAIQYLN--GYGYDHLIL  237 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~-I~~i~l~-~d~~tg~skGfaFV~F~s~e~A~~Ai~~Ln--G~~i~g~~L  237 (247)
                      ..+.++|||+|||+++++++|+++|..||. |..+.++ .++.+|.++|||||+|.+.++|+.|+..||  +..++|+.|
T Consensus         5 s~~~~~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            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            355689999999999999999999999998 9999998 888899999999999999999999999996  589999999


Q ss_pred             EEeecCCCC
Q psy13227        238 SVDWSKSTN  246 (247)
Q Consensus       238 ~V~~akp~~  246 (247)
                      .|+|++|+.
T Consensus        85 ~V~~a~~~~   93 (109)
T 2dis_A           85 AVDWAEPEI   93 (109)
T ss_dssp             EEEESCSSC
T ss_pred             EEEEcCCCC
Confidence            999999874

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.77  E-value=3.7e-19  Score=140.70  Aligned_cols=83  Identities=22%  Similarity=0.413  Sum_probs=78.5

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeE--EEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCc----eeCCeE
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSK--MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGY----GYDHLI  236 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~--i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~----~i~g~~  236 (247)
                      ...++|||+|||+++++++|+++|++||.|..  |+|++|+.+|+++|||||+|.+. +|.+|+..|||.    .++|+.
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~   99 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKT   99 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEE
Confidence            45579999999999999999999999999977  99999999999999999999999 999999999999    999999


Q ss_pred             EEEeecCCCC
Q psy13227        237 LSVDWSKSTN  246 (247)
Q Consensus       237 L~V~~akp~~  246 (247)
                      |.|+|++++.
T Consensus       100 l~V~~a~~~~  109 (131)
T 2m2b_A          100 INVEFAKGSK  109 (131)
T ss_dssp             CCCEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999999863

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.77  E-value=2.2e-18  Score=134.28  Aligned_cols=83  Identities=20%  Similarity=0.342  Sum_probs=78.9

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||+|||.++++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|+.|+ .|||..++|+.|+|+|+
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  112 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK  112 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            45679999999999999999999999999999999999889999999999999999999999 79999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      ++..
T Consensus       113 ~~~~  116 (124)
T 2jwn_A          113 RTNM  116 (124)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8764

>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=99.77  E-value=4.5e-19  Score=133.79  Aligned_cols=83  Identities=19%  Similarity=0.329  Sum_probs=76.9

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecC-CCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDK-TNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~-~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ...++|||+|||.++++++|+++|+.|| |..+.++.++ .+|.++|||||+|.+.++|.+|+ .|||..++|+.|+|+|
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~~   94 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDV   94 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEEe
Confidence            5568999999999999999999999999 9999999998 69999999999999999999999 8999999999999999


Q ss_pred             cCCCCC
Q psy13227        242 SKSTNQ  247 (247)
Q Consensus       242 akp~~~  247 (247)
                      +++++.
T Consensus        95 a~~~~~  100 (100)
T 2j76_E           95 ADQAQD  100 (100)
T ss_dssp             CCCSCC
T ss_pred             ccCCCC
Confidence            999863

>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=99.77  E-value=8.6e-19  Score=130.14  Aligned_cols=82  Identities=17%  Similarity=0.236  Sum_probs=76.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+++++++|+++|.+||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            44589999999999999999999999999999999998889999999999999999999999999999999999999998


Q ss_pred             CC
Q psy13227        243 KS  244 (247)
Q Consensus       243 kp  244 (247)
                      .+
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            74

>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=99.77  E-value=6.4e-19  Score=135.53  Aligned_cols=82  Identities=23%  Similarity=0.314  Sum_probs=78.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||+|||.++++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|++|| .|||..|+|+.|.|.|+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            45679999999999999999999999999999999999989999999999999999999999 89999999999999998


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      +++
T Consensus       102 ~~~  104 (114)
T 2cq4_A          102 QAE  104 (114)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            764

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.77  E-value=2.7e-18  Score=140.76  Aligned_cols=85  Identities=19%  Similarity=0.395  Sum_probs=80.3

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|+.||..|||..|+|+.|.|.|
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      +++++
T Consensus       149 a~~~~  153 (165)
T 1rk8_A          149 CFVKG  153 (165)
T ss_dssp             SEECC
T ss_pred             ecCCC
Confidence            98764

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=3.5e-19  Score=129.81  Aligned_cols=82  Identities=24%  Similarity=0.417  Sum_probs=77.8

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|+.|+..|||..++|+.|++.|+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            34579999999999999999999999999999999999989999999999999999999999999999999999999987


Q ss_pred             CC
Q psy13227        243 KS  244 (247)
Q Consensus       243 kp  244 (247)
                      ++
T Consensus        83 ~s   84 (85)
T 1x4e_A           83 SS   84 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.6e-18  Score=133.63  Aligned_cols=83  Identities=19%  Similarity=0.345  Sum_probs=79.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||+|||+++++++|+++|..||.|..|.|+.++.++.++|||||+|.+.++|+.||.. |+..|+|+.|.|.|+
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            4568999999999999999999999999999999999998999999999999999999999997 999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +++.
T Consensus       104 ~~~~  107 (116)
T 1x4b_A          104 VARE  107 (116)
T ss_dssp             SSCC
T ss_pred             CCCc
Confidence            9874

>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=99.77  E-value=2.6e-19  Score=131.83  Aligned_cols=80  Identities=20%  Similarity=0.365  Sum_probs=74.5

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST  245 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp~  245 (247)
                      ++|||+|||.++++++|+++|++||.|.++.+++++.+|.++|||||+|.+.+ |..|+..|||..++|+.|+|+||.++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            68999999999999999999999999999999999989999999999999999 99999999999999999999999876


Q ss_pred             C
Q psy13227        246 N  246 (247)
Q Consensus       246 ~  246 (247)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.9e-18  Score=132.54  Aligned_cols=84  Identities=23%  Similarity=0.374  Sum_probs=78.2

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ...+.++|||+|||.++++++|+++|++||.|..+.++.++  +.++|||||+|.+.++|++|+..|||..++|+.|+|+
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34667899999999999999999999999999999999985  4589999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      |++++.
T Consensus       103 ~a~~~~  108 (109)
T 2err_A          103 NATARV  108 (109)
T ss_dssp             ECCCSC
T ss_pred             ECCCCc
Confidence            999874

>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=99.76  E-value=4.2e-18  Score=127.33  Aligned_cols=80  Identities=26%  Similarity=0.385  Sum_probs=74.1

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC--CeEEEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD--HLILSV  239 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~--g~~L~V  239 (247)
                      .+..++|||+|||+++++++|+++|++||.|..+.+..+      +|||||+|.+.++|+.|++.|||..++  |+.|+|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEE
Confidence            355689999999999999999999999999999998754      689999999999999999999999999  999999


Q ss_pred             eecCCCCC
Q psy13227        240 DWSKSTNQ  247 (247)
Q Consensus       240 ~~akp~~~  247 (247)
                      +|++++++
T Consensus        88 ~~a~~~~~   95 (97)
T 1why_A           88 DFAKSGPS   95 (97)
T ss_dssp             EECCCCCC
T ss_pred             EECCCCCC
Confidence            99999864

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.76  E-value=3.9e-18  Score=134.88  Aligned_cols=81  Identities=20%  Similarity=0.312  Sum_probs=76.9

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||.++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|+|
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            35568999999999999999999999999999999999998999999999999999999999999999999999999998


Q ss_pred             c
Q psy13227        242 S  242 (247)
Q Consensus       242 a  242 (247)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            6

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=5.5e-18  Score=127.48  Aligned_cols=83  Identities=23%  Similarity=0.432  Sum_probs=76.6

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      .....++|||+|||+++++++|+++|+.|+   .+.++.++.++.++|||||+|.+.++|+.||..|||..|+|+.|.|+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            345668999999999999999999999774   68888898899999999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      |++++.
T Consensus        88 ~a~~~~   93 (102)
T 2fc8_A           88 WAKPKG   93 (102)
T ss_dssp             ECCCCC
T ss_pred             EecCCC
Confidence            999875

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.76  E-value=2e-18  Score=132.51  Aligned_cols=83  Identities=19%  Similarity=0.305  Sum_probs=76.6

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||+|||.++++++|+++|+.||.|..|.+++++.+|.++|||||+|.+.++|++|+..+ +..++|+.|.|.|+
T Consensus        23 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKVA  101 (109)
T ss_dssp             ---CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEEc
Confidence            55679999999999999999999999999999999999989999999999999999999999975 59999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      .++.
T Consensus       102 ~~~~  105 (109)
T 2rs2_A          102 FPRR  105 (109)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9875

>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=99.76  E-value=1.8e-18  Score=139.99  Aligned_cols=84  Identities=26%  Similarity=0.531  Sum_probs=80.1

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+++++++|+++|+.||.|..+.|+.++.+|.++|||||+|.+.++|+.|+..|||..++|+.|+|.|+
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            44579999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +++.
T Consensus       148 ~~~~  151 (158)
T 2kn4_A          148 RYGR  151 (158)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            9763

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.7e-18  Score=132.25  Aligned_cols=80  Identities=15%  Similarity=0.291  Sum_probs=75.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.|++++. |.++|||||+|.+.++|+.|+. +||..++|+.|.|.|
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~   85 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILF   85 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            45568999999999999999999999999999999999986 9999999999999999999999 999999999999998


Q ss_pred             cC
Q psy13227        242 SK  243 (247)
Q Consensus       242 ak  243 (247)
                      +.
T Consensus        86 ~~   87 (103)
T 1s79_A           86 KD   87 (103)
T ss_dssp             HH
T ss_pred             ch
Confidence            75

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=4.8e-18  Score=127.77  Aligned_cols=81  Identities=21%  Similarity=0.375  Sum_probs=74.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||+++++++|+++|++||.|   .++.+ .++.++|||||+|.+.++|++|+..|||..++|+.|+|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            4567899999999999999999999999976   56677 5899999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus        88 a~~~~   92 (101)
T 2fc9_A           88 QGPRG   92 (101)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            98864

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.75  E-value=9.8e-19  Score=124.51  Aligned_cols=75  Identities=24%  Similarity=0.388  Sum_probs=72.6

Q ss_pred             EEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       167 tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++ |||..++|+.|.|+||
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            48999999999999999999999999999999998899999999999999999999998 9999999999999986

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.75  E-value=9.7e-19  Score=139.48  Aligned_cols=85  Identities=26%  Similarity=0.516  Sum_probs=80.6

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|++|+..|||..++|+.|+|+|
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  123 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  123 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus       124 a~~~~  128 (135)
T 2lea_A          124 ARYGR  128 (135)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            99764

>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=99.75  E-value=1e-17  Score=127.95  Aligned_cols=77  Identities=21%  Similarity=0.296  Sum_probs=72.6

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC-----eEE
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH-----LIL  237 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g-----~~L  237 (247)
                      ...++|||+|||+++++++|+++|++||.|..+.|+.+       |||||+|.+.++|+.||+.|||..++|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            44579999999999999999999999999999999876       799999999999999999999999999     999


Q ss_pred             EEeecCCCC
Q psy13227        238 SVDWSKSTN  246 (247)
Q Consensus       238 ~V~~akp~~  246 (247)
                      .|++++++.
T Consensus        86 ~V~~a~~~~   94 (108)
T 1x4c_A           86 RVKVDGPRS   94 (108)
T ss_dssp             EEEESSCCS
T ss_pred             EEEeCCCCC
Confidence            999999875

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=3.8e-18  Score=131.26  Aligned_cols=78  Identities=17%  Similarity=0.323  Sum_probs=72.0

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcC--ceeCCeEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG--YGYDHLILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG--~~i~g~~L~V~  240 (247)
                      ...++|||+|||+++++++|+++|++||.|.++.|+++      +|||||+|.+.++|+.|++.|++  ..++|+.|+|.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            45689999999999999999999999999999999875      68999999999999999998874  68999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      ||+++.
T Consensus        88 ~A~~~~   93 (105)
T 1sjq_A           88 FSNHKE   93 (105)
T ss_dssp             CCSSSS
T ss_pred             EcCCCC
Confidence            999864

>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=99.74  E-value=2.8e-18  Score=132.44  Aligned_cols=81  Identities=19%  Similarity=0.208  Sum_probs=76.4

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCe-eEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPT-SKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I-~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      .+.++|||+|||+++++++|+++|+.||.| ..|.|+.++ +|.++|||||+|.+.++|++||.. ||..|+|+.|.|.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            456799999999999999999999999999 899999998 999999999999999999999996 99999999999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      +.++
T Consensus        91 a~~~   94 (114)
T 2cpy_A           91 VTLE   94 (114)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            9754

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=1.3e-18  Score=124.12  Aligned_cols=77  Identities=21%  Similarity=0.332  Sum_probs=73.9

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|+..+| ..++|+.|.|+||.
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a~   77 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVAF   77 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEECC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEecC
Confidence            479999999999999999999999999999999999899999999999999999999999999 99999999999973

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.74  E-value=7.8e-18  Score=131.06  Aligned_cols=81  Identities=14%  Similarity=0.222  Sum_probs=76.2

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCC---eeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGP---TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS  238 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~---I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~  238 (247)
                      ..+.++|||+|||+++++++|+++|+.||.   |..|.|++++. |+++|||||+|.+.++|++||. |||..|+|+.|.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            356689999999999999999999999999   89999999975 9999999999999999999999 999999999999


Q ss_pred             EeecCC
Q psy13227        239 VDWSKS  244 (247)
Q Consensus       239 V~~akp  244 (247)
                      |.++.+
T Consensus        92 V~~a~~   97 (118)
T 2db1_A           92 VFKSHR   97 (118)
T ss_dssp             EEEECH
T ss_pred             EEECCH
Confidence            999864

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.74  E-value=1e-18  Score=131.51  Aligned_cols=82  Identities=21%  Similarity=0.295  Sum_probs=76.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+++++++|+++|+.||.|.. .++.++.+|.++|||||+|.+.++|++|++ |||..++|+.|.|.|+
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            45679999999999999999999999999887 677777789999999999999999999999 9999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +++.
T Consensus        93 ~~~~   96 (101)
T 1fj7_A           93 KGRD   96 (101)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            9875

>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=99.73  E-value=9.6e-18  Score=127.42  Aligned_cols=82  Identities=18%  Similarity=0.271  Sum_probs=76.5

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeE-EEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSK-MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~-i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ..+.++|||+|||+++++++|+++|..||.|.. |.|+.+ .+|+++|||||+|.+.++|++||.. |+..++|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            355689999999999999999999999999987 889998 6999999999999999999999997 9999999999999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      ++.++
T Consensus        90 ~~~~~   94 (104)
T 1wg5_A           90 KSSRA   94 (104)
T ss_dssp             EECTT
T ss_pred             ECCHH
Confidence            98865

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.73  E-value=9.3e-18  Score=124.89  Aligned_cols=81  Identities=26%  Similarity=0.378  Sum_probs=73.8

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||.++++++|+++|+.||.|..+     ..++.++|||||+|.+.++|+.|+..|||..++|+.|.|+|
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3456899999999999999999999999988766     24789999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy13227        242 SKSTNQ  247 (247)
Q Consensus       242 akp~~~  247 (247)
                      ++++.+
T Consensus        88 a~~~~~   93 (96)
T 1fjc_A           88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             cCCCCC
Confidence            998753

>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=99.73  E-value=3.5e-18  Score=133.70  Aligned_cols=83  Identities=14%  Similarity=0.206  Sum_probs=76.0

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||+++++++|+++|..||.|..+.++.+..+|.++|||||+|.+.++|+.||. |||..|+|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3556899999999999999999999999999886666666799999999999999999999999 999999999999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      +.++
T Consensus       101 a~~~  104 (124)
T 1wel_A          101 ITKK  104 (124)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8753

>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=99.73  E-value=1.1e-17  Score=127.86  Aligned_cols=79  Identities=19%  Similarity=0.215  Sum_probs=71.9

Q ss_pred             CCCccEEEEeecCC-CCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCc--eeCCeEEE
Q psy13227        162 NDDTTAIRISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGY--GYDHLILS  238 (247)
Q Consensus       162 ~~~~~tl~V~nLp~-~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~--~i~g~~L~  238 (247)
                      .+..++|||+|||+ ++++++|+++|++||.|.++.|+++      +|||||+|.+.++|..|++.||+.  .++|+.|+
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            35678999999999 9999999999999999999999876      479999999999999999999975  49999999


Q ss_pred             EeecCCCC
Q psy13227        239 VDWSKSTN  246 (247)
Q Consensus       239 V~~akp~~  246 (247)
                      |+||++..
T Consensus        86 V~~a~~~~   93 (102)
T 1x4d_A           86 VHLSQKYK   93 (102)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCCC
Confidence            99999653

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.73  E-value=6.8e-18  Score=128.47  Aligned_cols=81  Identities=19%  Similarity=0.396  Sum_probs=74.9

Q ss_pred             CCccEEEEeecCCCC------CHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCe-
Q psy13227        163 DDTTAIRISNLSVNT------SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHL-  235 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~------te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~-  235 (247)
                      ...++|||+|||+.+      ++++|+++|++||.|..+.|+  +.+|.++|||||+|.+.++|+.|+..|||..++|+ 
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            345799999999999      779999999999999999988  36899999999999999999999999999999998 


Q ss_pred             EEEEeecCCC
Q psy13227        236 ILSVDWSKST  245 (247)
Q Consensus       236 ~L~V~~akp~  245 (247)
                      .|.|.|+...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999999764

>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=99.73  E-value=1.7e-17  Score=124.46  Aligned_cols=79  Identities=19%  Similarity=0.398  Sum_probs=73.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||+++++++|+++|++||.|..+.+.++      +|||||+|.+.++|++|++.|||..++|+.|+|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            356689999999999999999999999999999999754      68999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus        86 a~~~~   90 (99)
T 2cpj_A           86 ACHSA   90 (99)
T ss_dssp             SSCCS
T ss_pred             cCCCC
Confidence            99875

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=2e-17  Score=121.91  Aligned_cols=76  Identities=24%  Similarity=0.447  Sum_probs=71.8

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||+|||+++++++|+++|++||.|..+.+.        +|||||+|.+.++|+.|+..|||..++|+.|+|+|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   77 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            556899999999999999999999999999999986        579999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +++.
T Consensus        78 ~~~~   81 (90)
T 2dnq_A           78 KNKS   81 (90)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            9875

>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=99.73  E-value=8.1e-18  Score=125.29  Aligned_cols=82  Identities=21%  Similarity=0.447  Sum_probs=75.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHH----HHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLE----DLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLIL  237 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~----~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L  237 (247)
                      ....++|||+|||+++++++|+    ++|++||.|..+.+..   +|.++|||||+|.+.++|..|+..|||..++|+.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            3556899999999999999999    9999999999998873   57889999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q psy13227        238 SVDWSKSTN  246 (247)
Q Consensus       238 ~V~~akp~~  246 (247)
                      +|.|+++++
T Consensus        82 ~v~~a~~~~   90 (97)
T 1nu4_A           82 RIQYAKTDS   90 (97)
T ss_dssp             EEEECSSCC
T ss_pred             EEEEccCCC
Confidence            999999875

>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=99.73  E-value=2.1e-17  Score=126.14  Aligned_cols=79  Identities=16%  Similarity=0.392  Sum_probs=74.2

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||.++++++|+++|++||.|..|.++.+      +|||||+|.+.++|+.|+..|||..++|+.|+|.|
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            455689999999999999999999999999999999876      68999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      +++++
T Consensus        96 a~~~~  100 (109)
T 1x4g_A           96 GKESP  100 (109)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            99875

>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=99.73  E-value=1.3e-17  Score=126.70  Aligned_cols=80  Identities=16%  Similarity=0.308  Sum_probs=74.5

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+++++++|+++|++||.+ .|.|++++ +|+++|||||+|.+.++|++||. +|+..++++.|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            455799999999999999999999999954 99999997 99999999999999999999996 7999999999999998


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      .+.
T Consensus        90 ~~~   92 (102)
T 1wez_A           90 STA   92 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            865

>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=99.73  E-value=5.5e-18  Score=146.69  Aligned_cols=81  Identities=23%  Similarity=0.303  Sum_probs=77.1

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccC--CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFG--PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG--~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..++|||+||++++++++|+++|+.||  .|.+|.|++++.+|+++|||||+|.+.++|++||+.|||..|+|+.|+|.|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            557999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q psy13227        242 SKS  244 (247)
Q Consensus       242 akp  244 (247)
                      +++
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            875

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.73  E-value=1.2e-17  Score=125.55  Aligned_cols=77  Identities=25%  Similarity=0.349  Sum_probs=72.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||.++++++|+++|+.||.|.++.+.      .++|||||+|.+.++|+.|+..|||..++|+.|+|.|+
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            456899999999999999999999999999999987      35789999999999999999999999999999999999


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      +++
T Consensus        99 ~~~  101 (101)
T 2la4_A           99 KER  101 (101)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            985

>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=99.73  E-value=3.7e-17  Score=124.57  Aligned_cols=79  Identities=14%  Similarity=0.296  Sum_probs=71.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhc--CceeCCeEEEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN--GYGYDHLILSV  239 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~Ln--G~~i~g~~L~V  239 (247)
                      ....++|||+|||+++++++|+++|++||.|..+.++++      +|||||+|.+.++|+.|++.|+  +..++|+.|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            355679999999999999999999999999999988765      7899999999999999999875  67799999999


Q ss_pred             eecCCCC
Q psy13227        240 DWSKSTN  246 (247)
Q Consensus       240 ~~akp~~  246 (247)
                      +|++++.
T Consensus        86 ~~a~~~~   92 (101)
T 2cq1_A           86 QYSNHKE   92 (101)
T ss_dssp             EECSCSS
T ss_pred             EEcCccc
Confidence            9999764

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=2.2e-17  Score=123.52  Aligned_cols=80  Identities=19%  Similarity=0.337  Sum_probs=72.8

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+++++++|+++|+.||.|. +.++.+    .++|||||+|.+.++|+.|+..|||..++|+.|.|+|+
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            4567999999999999999999999999996 666644    57899999999999999999999999999999999999


Q ss_pred             CCCCC
Q psy13227        243 KSTNQ  247 (247)
Q Consensus       243 kp~~~  247 (247)
                      +++.+
T Consensus        92 ~~~~~   96 (97)
T 2e5j_A           92 RQQRD   96 (97)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98763

>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=99.72  E-value=2.3e-17  Score=119.90  Aligned_cols=76  Identities=22%  Similarity=0.366  Sum_probs=71.0

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHh-cCceeCCeEEEEe
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL-NGYGYDHLILSVD  240 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~L-nG~~i~g~~L~V~  240 (247)
                      ....++|||+|||.++++++|+++|++||.|..+.+.++      +|||||+|.+.++|+.|+..| ||..++|+.|+|+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            455679999999999999999999999999999999864      689999999999999999998 9999999999999


Q ss_pred             ecC
Q psy13227        241 WSK  243 (247)
Q Consensus       241 ~ak  243 (247)
                      |++
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            986

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.72  E-value=1.7e-17  Score=131.46  Aligned_cols=81  Identities=19%  Similarity=0.347  Sum_probs=73.6

Q ss_pred             CCccEEEEeecCCCCCHHHHH----HHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEE
Q psy13227        163 DDTTAIRISNLSVNTSENDLE----DLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS  238 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~----~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~  238 (247)
                      ...++|||+|||+.+++++|+    ++|++||.|.+|.+..   ++.++|||||+|.+.++|..|+..|||..+.|+.|+
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            345799999999999999876    6999999999988753   688999999999999999999999999999999999


Q ss_pred             EeecCCCC
Q psy13227        239 VDWSKSTN  246 (247)
Q Consensus       239 V~~akp~~  246 (247)
                      |.||+++.
T Consensus       104 V~~a~~~~  111 (127)
T 2a3j_A          104 ITFSETPQ  111 (127)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCcc
Confidence            99999864

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.56  E-value=4e-19  Score=137.23  Aligned_cols=84  Identities=24%  Similarity=0.391  Sum_probs=80.0

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeE--------EEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSK--------MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH  234 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~--------i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g  234 (247)
                      .+.++|||+|||.++++++|+++|++||.|..        +.++.++.++.++|||||+|.+.++|+.|+..|||..++|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            45679999999999999999999999999998        9999998899999999999999999999999999999999


Q ss_pred             eEEEEeecCCCC
Q psy13227        235 LILSVDWSKSTN  246 (247)
Q Consensus       235 ~~L~V~~akp~~  246 (247)
                      +.|+|+|+++++
T Consensus        85 ~~l~V~~a~~~~   96 (116)
T 2lcw_A           85 NPIKVSFATRRA   96 (116)
Confidence            999999999874

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=6.3e-17  Score=119.72  Aligned_cols=77  Identities=21%  Similarity=0.420  Sum_probs=72.0

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||+++++++|+++|++||.|..+.+.+        +||||+|.+.++|++|+..|||..++|+.|+|+|
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            46678999999999999999999999999999999873        3999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus        79 a~~~~   83 (92)
T 2dgt_A           79 STSRL   83 (92)
T ss_dssp             SSCCC
T ss_pred             ccCCC
Confidence            99874

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.72  E-value=2.3e-17  Score=122.93  Aligned_cols=73  Identities=19%  Similarity=0.240  Sum_probs=69.3

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      +..|||+||++.+++++|+++|.+||+|.++++..      ++|||||+|.+.++|..|++.||+..++|+.|+|++|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            46899999999999999999999999999999865      58999999999999999999999999999999999985

>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=99.72  E-value=2.9e-18  Score=131.70  Aligned_cols=84  Identities=27%  Similarity=0.407  Sum_probs=73.4

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+++++++|+++|+.||.|..+.+..+..+|.++|||||+|.+.++|+.|+..|||..++|+.|.|+|+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            45689999999999999999999999999843322222237899999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +++.
T Consensus       103 ~~~~  106 (115)
T 2cpx_A          103 KNKK  106 (115)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            9764

>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=99.72  E-value=3e-17  Score=125.68  Aligned_cols=79  Identities=16%  Similarity=0.236  Sum_probs=71.3

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCce--eCCeEEEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG--YDHLILSV  239 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~--i~g~~L~V  239 (247)
                      .....+|||+|||+++++++|+++|++||.|..|.++++      ||||||+|.+.++|..|++.||+..  ++|+.|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345679999999999999999999999999999998764      6899999999999999999987754  99999999


Q ss_pred             eecCCCC
Q psy13227        240 DWSKSTN  246 (247)
Q Consensus       240 ~~akp~~  246 (247)
                      +|++++.
T Consensus        86 ~~a~~~~   92 (104)
T 1wex_A           86 NYSTSKR   92 (104)
T ss_dssp             EECSSSS
T ss_pred             EEccCcc
Confidence            9998763

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.72  E-value=1.3e-17  Score=125.36  Aligned_cols=76  Identities=24%  Similarity=0.454  Sum_probs=72.3

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST  245 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp~  245 (247)
                      ++|||+|||+++++++|+++|++||.|..+.++.+     ++|||||+|.+.++|+.|+..|||..++|+.|.|+|++++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            58999999999999999999999999999999877     6899999999999999999999999999999999999876


Q ss_pred             C
Q psy13227        246 N  246 (247)
Q Consensus       246 ~  246 (247)
                      +
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.71  E-value=7.2e-17  Score=129.28  Aligned_cols=82  Identities=23%  Similarity=0.473  Sum_probs=78.8

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.||
T Consensus        85 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  164 (166)
T 3md3_A           85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA  164 (166)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEec
Confidence            45679999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CC
Q psy13227        243 KS  244 (247)
Q Consensus       243 kp  244 (247)
                      ++
T Consensus       165 ~~  166 (166)
T 3md3_A          165 AK  166 (166)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.71  E-value=3.4e-17  Score=125.63  Aligned_cols=77  Identities=26%  Similarity=0.503  Sum_probs=72.5

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||.++++++|+++|++||.|..+.+.        +|||||+|.+.++|+.|+..|||..++|+.|.|.|
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3556899999999999999999999999999999987        68999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      +++++
T Consensus       100 a~~~~  104 (108)
T 2jvo_A          100 SKLPA  104 (108)
T ss_dssp             CSCCC
T ss_pred             ecCCC
Confidence            99875

>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=99.71  E-value=5.9e-17  Score=121.74  Aligned_cols=76  Identities=22%  Similarity=0.302  Sum_probs=71.7

Q ss_pred             CCccEEEEeecCC-CCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        163 DDTTAIRISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~-~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      .+.++|||+|||+ ++++++|+++|+.||.|..+.+.        +|||||+|.+.++|..|+..|||..++|+.|+|+|
T Consensus        20 ~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   91 (97)
T 2xnq_A           20 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEV   91 (97)
T ss_dssp             CTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            5568999999998 99999999999999999999882        78999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      +++++
T Consensus        92 a~~~~   96 (97)
T 2xnq_A           92 SSSNA   96 (97)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            99875

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.71  E-value=3.6e-17  Score=124.73  Aligned_cols=77  Identities=23%  Similarity=0.328  Sum_probs=71.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCce--eCCeEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG--YDHLILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~--i~g~~L~V~  240 (247)
                      ..+.+|||+|||+++++++|+++|++||.|.++.++++      ||||||+|.+.++|..|++.|||..  +.|+.|.|+
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            45679999999999999999999999999999998753      6899999999999999999999886  789999999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      ||+++
T Consensus        93 ~S~~k   97 (100)
T 3r27_A           93 YSTSQ   97 (100)
T ss_dssp             ECSCS
T ss_pred             ecccc
Confidence            99986

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.71  E-value=8.4e-17  Score=129.02  Aligned_cols=82  Identities=24%  Similarity=0.475  Sum_probs=78.7

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      .++|||+|||+++++++|+++|+.||.|..+.+++++.+|.++|||||+|.+.++|..|++.|||..++|+.|.|.|+.|
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            47899999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CC
Q psy13227        245 TN  246 (247)
Q Consensus       245 ~~  246 (247)
                      ..
T Consensus        82 ~~   83 (167)
T 1fxl_A           82 SS   83 (167)
T ss_dssp             CC
T ss_pred             Cc
Confidence            53

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.71  E-value=3e-17  Score=127.27  Aligned_cols=79  Identities=19%  Similarity=0.256  Sum_probs=71.4

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccC-CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFG-PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG-~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ..++|||+|||+++++++|+++|++|| .|..+.+..    +.++|||||+|.+.++|+.||+.|||..++|+.|+|+++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            347999999999999999999999999 899998853    347899999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +.++
T Consensus       103 ~~~p  106 (111)
T 2jvr_A          103 DNPP  106 (111)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            8654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.3e-16  Score=119.52  Aligned_cols=77  Identities=26%  Similarity=0.435  Sum_probs=71.1

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhcc--CCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQF--GPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV  239 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~f--G~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V  239 (247)
                      ....++|||+|||+++++++|+++|++|  |.|.++.+.        +|||||+|.+.++|+.|+..|||..++|+.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            3556899999999999999999999999  899988764        579999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy13227        240 DWSKSTN  246 (247)
Q Consensus       240 ~~akp~~  246 (247)
                      +|++++.
T Consensus        84 ~~a~~~~   90 (99)
T 2cpd_A           84 TLAKPVD   90 (99)
T ss_dssp             ECCCCCC
T ss_pred             EECCCCC
Confidence            9999874

>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=99.71  E-value=7.2e-17  Score=121.96  Aligned_cols=76  Identities=25%  Similarity=0.436  Sum_probs=71.1

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+++++++|+++|++||.|..+.++        +|||||+|.+.++|++|+..|||..++|+.|.|.|+
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            456799999999999999999999999999999986        459999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +++.
T Consensus        81 ~~~~   84 (103)
T 2dgu_A           81 KPPD   84 (103)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            8764

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.71  E-value=7.4e-17  Score=136.84  Aligned_cols=83  Identities=22%  Similarity=0.348  Sum_probs=78.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+++++++|+++|++||.|.+|.|++|+.+|+++|||||+|.+.++|+.|+..||+..+.|+.|++.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      .+.
T Consensus        93 ~~~   95 (213)
T 4f02_A           93 QRD   95 (213)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            764

>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=99.71  E-value=5.7e-17  Score=130.56  Aligned_cols=82  Identities=24%  Similarity=0.495  Sum_probs=78.8

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      .++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|..|++.|||..++|+.|.|.|+.+
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   82 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   82 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCC
Confidence            47999999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CC
Q psy13227        245 TN  246 (247)
Q Consensus       245 ~~  246 (247)
                      ..
T Consensus        83 ~~   84 (168)
T 1b7f_A           83 GG   84 (168)
T ss_dssp             CS
T ss_pred             Cc
Confidence            64

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=4.3e-17  Score=127.99  Aligned_cols=78  Identities=17%  Similarity=0.323  Sum_probs=72.0

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcC--ceeCCeEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG--YGYDHLILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG--~~i~g~~L~V~  240 (247)
                      ...++|||+|||+++++++|+++|++||.|.+|.|+++      +|||||+|.+.++|..|++.|++  ..++|+.|+|+
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            45679999999999999999999999999999999875      68999999999999999999885  57999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      ||+++.
T Consensus       103 ~a~~k~  108 (119)
T 2ad9_A          103 FSNHKE  108 (119)
T ss_dssp             ECSSSS
T ss_pred             EccCCC
Confidence            999864

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.71  E-value=8.9e-18  Score=121.64  Aligned_cols=72  Identities=21%  Similarity=0.475  Sum_probs=67.6

Q ss_pred             cEEEEeecCCCC------CHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCe-EEE
Q psy13227        166 TAIRISNLSVNT------SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHL-ILS  238 (247)
Q Consensus       166 ~tl~V~nLp~~~------te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~-~L~  238 (247)
                      ++|||+|||..+      ++++|+++|++||.|.++.++  +.+|.++|||||+|.+.++|+.|+..|||..++|+ .|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            689999999999      679999999999999999987  35899999999999999999999999999999999 887


Q ss_pred             E
Q psy13227        239 V  239 (247)
Q Consensus       239 V  239 (247)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>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=99.70  E-value=5.7e-18  Score=120.37  Aligned_cols=75  Identities=20%  Similarity=0.317  Sum_probs=72.1

Q ss_pred             EEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       167 tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|+. +++..++|+.|.|.+|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            58999999999999999999999999999999999899999999999999999999999 5999999999999986

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=6.7e-17  Score=120.21  Aligned_cols=80  Identities=19%  Similarity=0.367  Sum_probs=73.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEE-EEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKM-YLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i-~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ...++|||+|||+++++++|+++|+.||.|..+ .++.++.++.    |||+|.+.++|+.|+..|||..++|+.|.|+|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            445789999999999999999999999999999 5888875544    99999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++|+.
T Consensus        89 a~~~~   93 (96)
T 2e44_A           89 IPDEM   93 (96)
T ss_dssp             CCCCC
T ss_pred             cCccc
Confidence            99873

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.70  E-value=1.8e-17  Score=124.74  Aligned_cols=80  Identities=15%  Similarity=0.388  Sum_probs=75.7

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.++ +|.++|||||+|.+.++|+.|+.  ||..++|+.|.|.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            345799999999999999999999999999999999998 99999999999999999999999  999999999999998


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      .++
T Consensus        84 ~~~   86 (102)
T 2xs2_A           84 IRK   86 (102)
T ss_dssp             EEC
T ss_pred             CcC
Confidence            765

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.3e-16  Score=119.30  Aligned_cols=77  Identities=14%  Similarity=0.260  Sum_probs=70.9

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+||  ++++++|+++|++||.|..|.+.      .++|||||+|.+.++|++|+..|||..++|+.|.|.|
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            356689999996  89999999999999999999984      4678999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      +++++
T Consensus        84 a~~~~   88 (97)
T 1x5p_A           84 ARKQP   88 (97)
T ss_dssp             CSSCC
T ss_pred             CCCCC
Confidence            99875

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=8.4e-17  Score=118.57  Aligned_cols=77  Identities=25%  Similarity=0.381  Sum_probs=71.6

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||+++++++|+++|++||.|..+.+++        +||||+|.+.++|+.|+..|||..++|+.|+|+|
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            35668999999999999999999999999999999873        3999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++++.
T Consensus        78 a~~~~   82 (90)
T 2dnp_A           78 STKGQ   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            99764

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.70  E-value=8.6e-17  Score=134.79  Aligned_cols=84  Identities=20%  Similarity=0.396  Sum_probs=80.6

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.|+
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            45679999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      ++++
T Consensus       203 ~~~~  206 (216)
T 2qfj_A          203 VTPP  206 (216)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            9875

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=3.8e-17  Score=126.15  Aligned_cols=79  Identities=18%  Similarity=0.234  Sum_probs=73.8

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+..+|||+|||+++++++|+++|+.| .|..|.|+.++ +|+++|||||+|.+.++|++|| .||+..++|+.|.|..+
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a   90 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPA   90 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            455799999999999999999999999 89999999997 5999999999999999999999 59999999999999888


Q ss_pred             CC
Q psy13227        243 KS  244 (247)
Q Consensus       243 kp  244 (247)
                      .+
T Consensus        91 ~~   92 (109)
T 2dnn_A           91 TE   92 (109)
T ss_dssp             CH
T ss_pred             Cc
Confidence            64

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.70  E-value=4.5e-17  Score=125.15  Aligned_cols=80  Identities=20%  Similarity=0.413  Sum_probs=74.0

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +..++|||+|||+++++++|+++|+.||.|..+.++.+   +.++|||||+|.+.++|..|+..|||..++|+.|.|.|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            34579999999999999999999999999999999876   455999999999999999999999999999999999999


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      +++
T Consensus        83 ~~~   85 (115)
T 3lqv_A           83 NAN   85 (115)
T ss_dssp             CHH
T ss_pred             cCC
Confidence            863

>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=99.70  E-value=3.8e-17  Score=120.99  Aligned_cols=77  Identities=27%  Similarity=0.397  Sum_probs=69.9

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCC-eeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcC-ceeCCeEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGP-TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG-YGYDHLILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~-I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG-~~i~g~~L~V~  240 (247)
                      ...++|||+|||+++++++|+++|++||. |..+.+       .++|||||+|.+.++|+.|+..||| ..++|+.|+|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~-------~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-------LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-------EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE-------cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            45679999999999999999999999999 665555       2578999999999999999999999 99999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      |++++.
T Consensus        79 ~a~~~~   84 (93)
T 2cqh_A           79 YSVSKK   84 (93)
T ss_dssp             ECCCCC
T ss_pred             EccCcc
Confidence            999874

>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=99.70  E-value=1.5e-17  Score=132.86  Aligned_cols=84  Identities=27%  Similarity=0.347  Sum_probs=72.8

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEE--E---eecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEE
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMY--L---SRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLIL  237 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~--l---~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L  237 (247)
                      ...++|||+|||+++++++|+++|+.||.|..+.  +   ++...+|.++|||||+|.+.++|..|+..|||..++|+.|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            4457999999999999999999999999987641  1   1112478999999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q psy13227        238 SVDWSKSTN  246 (247)
Q Consensus       238 ~V~~akp~~  246 (247)
                      .|.|+++..
T Consensus       123 ~V~~a~~~~  131 (143)
T 3egn_A          123 VVQFARSAR  131 (143)
T ss_dssp             EEEECCCSC
T ss_pred             EEEECCCCC
Confidence            999998753

>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=99.70  E-value=3.5e-17  Score=126.71  Aligned_cols=75  Identities=21%  Similarity=0.290  Sum_probs=67.3

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeE-----EE
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLI-----LS  238 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~-----L~  238 (247)
                      ..++|||+|||+++++++|+++|.+||.|..+.|+.+       |||||+|.+.++|+.||+.|||..|+|+.     |+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            3478999999999999999999999999999999766       89999999999999999999999999988     88


Q ss_pred             EeecCCC
Q psy13227        239 VDWSKST  245 (247)
Q Consensus       239 V~~akp~  245 (247)
                      |..+.++
T Consensus        88 v~~~~~~   94 (115)
T 3beg_B           88 VKVDGPR   94 (115)
T ss_dssp             EEECC--
T ss_pred             eccCCCC
Confidence            8887765

>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=7.6e-17  Score=129.74  Aligned_cols=80  Identities=25%  Similarity=0.439  Sum_probs=75.3

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||+++++++|+++|++||.|.++.++.+     ++|||||+|.+.++|..|+..|||..++|+.|+|+|
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  144 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL  144 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            355689999999999999999999999999999999876     589999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++|++
T Consensus       145 a~~~~  149 (150)
T 2i2y_A          145 SNGEK  149 (150)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            99975

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.69  E-value=1.1e-16  Score=132.35  Aligned_cols=85  Identities=25%  Similarity=0.432  Sum_probs=81.1

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||.++++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.|+
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q psy13227        243 KSTNQ  247 (247)
Q Consensus       243 kp~~~  247 (247)
                      +|+.+
T Consensus       192 ~~~~~  196 (198)
T 2yh0_A          192 SVGAK  196 (198)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98753

>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=99.69  E-value=6.9e-18  Score=128.85  Aligned_cols=82  Identities=17%  Similarity=0.187  Sum_probs=76.5

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCC---eeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGP---TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS  238 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~---I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~  238 (247)
                      ..+.++|||+|||+++++++|+++|+.||.   |..|.|+.++. |+++|||||+|.+.++|+.||. |||..++|+.|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            356689999999999999999999999988   89999999986 9999999999999999999999 999999999999


Q ss_pred             EeecCCC
Q psy13227        239 VDWSKST  245 (247)
Q Consensus       239 V~~akp~  245 (247)
                      |.++.++
T Consensus        86 V~~a~~~   92 (107)
T 2lmi_A           86 VYEINNE   92 (107)
T ss_dssp             CEECCHH
T ss_pred             EEECCHH
Confidence            9998753

>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=99.69  E-value=3.6e-17  Score=125.93  Aligned_cols=76  Identities=22%  Similarity=0.357  Sum_probs=70.7

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      +.++|||+|||+++++++|+++|++||.|.+|.|+.      ++|||||+|.+.++|+.|+..|||..++|+.|.|+|++
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            457999999999999999999999999999998864      57899999999999999999999999999999999997


Q ss_pred             CC
Q psy13227        244 ST  245 (247)
Q Consensus       244 p~  245 (247)
                      ..
T Consensus        83 ~~   84 (111)
T 1whx_A           83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.69  E-value=5.5e-17  Score=121.22  Aligned_cols=78  Identities=22%  Similarity=0.286  Sum_probs=70.7

Q ss_pred             CCCCccEEEEeecCC-CCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEE
Q psy13227        161 RNDDTTAIRISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV  239 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~-~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V  239 (247)
                      ..++.++|||+|||+ ++++++|+++|++||.|..+.+.        +|||||+|.+.++|+.|+..|||..++|+.|.|
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   77 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            346678999999998 99999999999999999999883        689999999999999999999999999999999


Q ss_pred             eecCCCC
Q psy13227        240 DWSKSTN  246 (247)
Q Consensus       240 ~~akp~~  246 (247)
                      +|++++.
T Consensus        78 ~~a~~~~   84 (96)
T 2kvi_A           78 EVSSSNA   84 (96)
T ss_dssp             EEEECCC
T ss_pred             EEcCcCC
Confidence            9998653

>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=99.69  E-value=2.7e-16  Score=120.14  Aligned_cols=75  Identities=20%  Similarity=0.365  Sum_probs=70.2

Q ss_pred             CCccEEEEeecCCC-CCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        163 DDTTAIRISNLSVN-TSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~-~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ...++|||+|||++ +++++|+++|++||.|..|.+        ++|||||+|.+.++|+.|+..|||..++|+.|+|+|
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   96 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34579999999999 999999999999999999988        578999999999999999999999999999999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      ++++
T Consensus        97 a~~~  100 (110)
T 1wf1_A           97 AGEP  100 (110)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            9854

>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=99.68  E-value=5.5e-17  Score=130.73  Aligned_cols=82  Identities=15%  Similarity=0.337  Sum_probs=78.4

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ..++|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++ +||..++|+.|.|.||.
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecC
Confidence            45689999999999999999999999999999999998899999999999999999999998 89999999999999999


Q ss_pred             CCC
Q psy13227        244 STN  246 (247)
Q Consensus       244 p~~  246 (247)
                      |++
T Consensus       165 pk~  167 (167)
T 2cjk_A          165 PRH  167 (167)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            974

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=1.8e-16  Score=117.82  Aligned_cols=78  Identities=15%  Similarity=0.264  Sum_probs=70.9

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+++++++|+++|+.||.|..|  +.++.+|.   ||||+|.+.++|+.|+. |||..++|+.|.|+++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            455799999999999999999999999999987  66666666   99999999999999999 9999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      .++.
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            8653

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.68  E-value=9.1e-17  Score=133.83  Aligned_cols=82  Identities=28%  Similarity=0.462  Sum_probs=78.5

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+.+++++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|+.|+..|||..|+|+.|.|+||
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456899999999999999999999999999999999998 9999999999999999999999999999999999999999


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      .+.
T Consensus       165 ~~~  167 (177)
T 2f3j_A          165 ASQ  167 (177)
T ss_dssp             SSG
T ss_pred             cCC
Confidence            864

>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=99.67  E-value=2.9e-16  Score=129.67  Aligned_cols=83  Identities=17%  Similarity=0.308  Sum_probs=77.9

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||+++++++|+++|+.||.|..|.++.++.+|.++|||||+|.+.++|..|+.. ++..++|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~   88 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKR   88 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeec
Confidence            45678999999999999999999999999999999999998999999999999999999999985 99999999999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      +.++
T Consensus        89 ~~~~   92 (196)
T 1l3k_A           89 AVSR   92 (196)
T ss_dssp             CCC-
T ss_pred             ccCc
Confidence            8765

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.67  E-value=3.1e-16  Score=126.92  Aligned_cols=81  Identities=25%  Similarity=0.434  Sum_probs=77.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||.++++++|+++|++||.|..+.+..++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|+||
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            34578999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             C
Q psy13227        243 K  243 (247)
Q Consensus       243 k  243 (247)
                      .
T Consensus       172 s  172 (172)
T 2g4b_A          172 S  172 (172)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=8e-17  Score=125.21  Aligned_cols=78  Identities=22%  Similarity=0.295  Sum_probs=70.2

Q ss_pred             CCccEEEEeecCCC-CCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcC--ceeCCeEEEE
Q psy13227        163 DDTTAIRISNLSVN-TSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG--YGYDHLILSV  239 (247)
Q Consensus       163 ~~~~tl~V~nLp~~-~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG--~~i~g~~L~V  239 (247)
                      ...++|||+|||++ +++++|+++|++||.|.++.|++      ++|||||+|.+.++|+.|++.||+  ..++|+.|+|
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   96 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   96 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            44679999999998 99999999999999999999974      368999999999999999998875  4599999999


Q ss_pred             eecCCCC
Q psy13227        240 DWSKSTN  246 (247)
Q Consensus       240 ~~akp~~  246 (247)
                      +||+++.
T Consensus        97 ~~a~~~~  103 (112)
T 1x4f_A           97 DLSEKYK  103 (112)
T ss_dssp             EEECSCS
T ss_pred             EECcccc
Confidence            9998764

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.67  E-value=4.4e-16  Score=124.67  Aligned_cols=80  Identities=24%  Similarity=0.443  Sum_probs=75.0

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST  245 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp~  245 (247)
                      ++|||+|||.++++++|+++|++||.|.++.++.++ ++.++|||||+|.+.++|..|+..|||..+.|+.|.|.|+.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            479999999999999999999999999999999997 6889999999999999999999999999999999999999765


Q ss_pred             C
Q psy13227        246 N  246 (247)
Q Consensus       246 ~  246 (247)
                      .
T Consensus        80 ~   80 (166)
T 3md3_A           80 Q   80 (166)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.66  E-value=2.3e-16  Score=148.56  Aligned_cols=84  Identities=20%  Similarity=0.392  Sum_probs=80.0

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+.+++++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|+.||..|||..|+|+.|.|.|+
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            44579999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +++.
T Consensus       180 ~~~~  183 (437)
T 3pgw_S          180 RGRT  183 (437)
T ss_pred             CCCC
Confidence            8753

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=6e-17  Score=127.72  Aligned_cols=81  Identities=14%  Similarity=0.213  Sum_probs=74.3

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCe----eEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPT----SKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLIL  237 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I----~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L  237 (247)
                      +.+.++|||+|||+++++++|+++|++||.|    ..|.|+.+. +|+++|||||+|.+.++|++||.. |+..++|+.|
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i   97 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYI   97 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEE
Confidence            3566899999999999999999999999985    689999995 999999999999999999999995 9999999999


Q ss_pred             EEeecCC
Q psy13227        238 SVDWSKS  244 (247)
Q Consensus       238 ~V~~akp  244 (247)
                      .|..+.+
T Consensus        98 ~V~~a~~  104 (123)
T 2dha_A           98 ELFRSTA  104 (123)
T ss_dssp             CCEEECH
T ss_pred             EEEECCH
Confidence            9988764

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.66  E-value=4.3e-16  Score=128.63  Aligned_cols=83  Identities=19%  Similarity=0.287  Sum_probs=76.1

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|.+|+.. +|..++|+.|.|.|+
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA  180 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEEC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEec
Confidence            4457999999999999999999999999999999999988999999999999999999999985 899999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      .|+.
T Consensus       181 ~~k~  184 (196)
T 1l3k_A          181 LSKQ  184 (196)
T ss_dssp             C---
T ss_pred             CChh
Confidence            9874

>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=99.66  E-value=3.4e-16  Score=115.05  Aligned_cols=74  Identities=23%  Similarity=0.379  Sum_probs=69.4

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      .++|||+|||+++++++|+++|++| .|..+.+.      .++|||||+|.+.++|++|++.|||..++|+.|+|+|+..
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A            5 SSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            4689999999999999999999999 99999884      5789999999999999999999999999999999999976


Q ss_pred             C
Q psy13227        245 T  245 (247)
Q Consensus       245 ~  245 (247)
                      .
T Consensus        78 ~   78 (88)
T 1wg1_A           78 D   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            4

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.66  E-value=4.4e-16  Score=132.05  Aligned_cols=80  Identities=26%  Similarity=0.358  Sum_probs=75.4

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ...+|||+|||+++++++|+++|+.||.|..+.|+++.  +.++|||||+|.+.++|++||+.|||..|+|+.|.|.|++
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45689999999999999999999999999999999985  5589999999999999999999999999999999999998


Q ss_pred             CC
Q psy13227        244 ST  245 (247)
Q Consensus       244 p~  245 (247)
                      ++
T Consensus       180 ~~  181 (213)
T 4f02_A          180 SR  181 (213)
T ss_dssp             CH
T ss_pred             CC
Confidence            75

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.65  E-value=7.5e-16  Score=122.70  Aligned_cols=77  Identities=23%  Similarity=0.324  Sum_probs=70.6

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeE-EEEEecCHHHHHHHHHHhcCceeCC--eEEEEe
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF-AYIHFKNKADAAKAIQYLNGYGYDH--LILSVD  240 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGf-aFV~F~s~e~A~~Ai~~LnG~~i~g--~~L~V~  240 (247)
                      ....|||+||++.+++++|+++|++||.|.+|.+..+.     +|| |||+|.+.++|+.|++.|||..|.|  +.|+|+
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~  101 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            34578999999999999999999999999999887642     678 9999999999999999999999988  999999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      ||+++
T Consensus       102 ~ak~~  106 (130)
T 3zzy_A          102 FSKLT  106 (130)
T ss_dssp             ECSCS
T ss_pred             ecCCC
Confidence            99986

>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=99.65  E-value=4.6e-16  Score=115.24  Aligned_cols=76  Identities=12%  Similarity=0.356  Sum_probs=63.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCce--eCCeEEEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG--YDHLILSV  239 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~--i~g~~L~V  239 (247)
                      ....++|||+|||+++++++|+++|++||.|.++.|+++     ++|||||+|.+.++|+.    |+|..  +.|+.|.|
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v   78 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHI   78 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEE
Confidence            355689999999999999999999999999999999875     68999999999999883    56665  45999999


Q ss_pred             eecCCCC
Q psy13227        240 DWSKSTN  246 (247)
Q Consensus       240 ~~akp~~  246 (247)
                      .+++|+.
T Consensus        79 ~~a~~k~   85 (89)
T 3d2w_A           79 SNAEPKH   85 (89)
T ss_dssp             EECC---
T ss_pred             EEcCCCC
Confidence            9999875

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.65  E-value=4e-16  Score=123.96  Aligned_cols=78  Identities=18%  Similarity=0.188  Sum_probs=71.4

Q ss_pred             cEEEEeec----CCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecC----HHH----HHHHHH--HhcCce
Q psy13227        166 TAIRISNL----SVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN----KAD----AAKAIQ--YLNGYG  231 (247)
Q Consensus       166 ~tl~V~nL----p~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s----~e~----A~~Ai~--~LnG~~  231 (247)
                      +.|||+||    |+.+++.+|+++|+.||.|.++.++.|+.||.++|||||+|.+    .++    |.+|+.  .|||..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            58999999    9999999999999999999999999999999999999999996    333    888988  789999


Q ss_pred             eCCeEEEEeecC
Q psy13227        232 YDHLILSVDWSK  243 (247)
Q Consensus       232 i~g~~L~V~~ak  243 (247)
                      |+|+.|+|.+-+
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999754

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.65  E-value=5.7e-16  Score=127.90  Aligned_cols=79  Identities=22%  Similarity=0.239  Sum_probs=71.7

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC--eEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH--LILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g--~~L~V~  240 (247)
                      ....+|||+||++.+++++|+++|++||.|.+|.+..+    .++|||||+|.+.++|+.|++.|||..|.|  +.|+|+
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            33467999999999999999999999999999998654    257999999999999999999999999965  999999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      |++++
T Consensus       120 ~Ak~~  124 (164)
T 1sjr_A          120 FSKLT  124 (164)
T ss_dssp             ECSSS
T ss_pred             EecCC
Confidence            99986

>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=99.64  E-value=5e-17  Score=130.80  Aligned_cols=81  Identities=15%  Similarity=0.264  Sum_probs=74.4

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+++++++|+++|++|| |..|.|++++. |+++|||||+|.+.++|++|| .+|+..++|+.|.|.++
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            4557899999999999999999999999 67999999974 999999999999999999999 68999999999999998


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      .++.
T Consensus       121 ~~~~  124 (139)
T 2hgn_A          121 STTG  124 (139)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            8753

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.64  E-value=4.6e-16  Score=135.87  Aligned_cols=80  Identities=14%  Similarity=0.276  Sum_probs=71.0

Q ss_pred             CCCccEEEEeecCCCC---------CHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCcee
Q psy13227        162 NDDTTAIRISNLSVNT---------SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGY  232 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~---------te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i  232 (247)
                      ....++|||+||+..+         ++++|+++|++||.|.+|.|+.      ++|||||+|.+.++|+.|++.|||..|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            3567899999999998         7999999999999999999985      379999999999999999999999999


Q ss_pred             ------------CCeEEEEeecCCCCC
Q psy13227        233 ------------DHLILSVDWSKSTNQ  247 (247)
Q Consensus       233 ------------~g~~L~V~~akp~~~  247 (247)
                                  .|+.|.|.||++.+|
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             eccccccccccCCCCEEEEEEccCCCC
Confidence                        899999999997654

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.64  E-value=1.4e-15  Score=122.42  Aligned_cols=80  Identities=24%  Similarity=0.408  Sum_probs=76.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC--eEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH--LILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g--~~L~V~  240 (247)
                      ...++|||+|||..+++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|.+|+..|||..++|  +.|+|.
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            345799999999999999999999999999999999998899999999999999999999999999999988  999999


Q ss_pred             ec
Q psy13227        241 WS  242 (247)
Q Consensus       241 ~a  242 (247)
                      ||
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.63  E-value=7.4e-16  Score=129.04  Aligned_cols=83  Identities=17%  Similarity=0.284  Sum_probs=76.0

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||+|||.++++++|+++|+.||.|..|.+++++.+|.++|||||+|.+.++|..|++.|||..++|+.|.|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            45679999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      .+.
T Consensus       106 ~~~  108 (216)
T 2qfj_A          106 SNI  108 (216)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            764

>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=99.63  E-value=1.1e-15  Score=123.61  Aligned_cols=82  Identities=22%  Similarity=0.357  Sum_probs=75.2

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCC--ceeeEEEEEecCHHHHHHHHHHhcCceeC---CeEEE
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNG--LCKGFAYIHFKNKADAAKAIQYLNGYGYD---HLILS  238 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg--~skGfaFV~F~s~e~A~~Ai~~LnG~~i~---g~~L~  238 (247)
                      +.++|||+|||+++++++|+++|++||.|.++.+++++.++  .++|||||+|.+.++|+.|++.|||..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            56899999999999999999999999999999999998776  89999999999999999999999998876   67788


Q ss_pred             EeecCCC
Q psy13227        239 VDWSKST  245 (247)
Q Consensus       239 V~~akp~  245 (247)
                      +.++.+.
T Consensus        82 ~~~~~~~   88 (175)
T 3nmr_A           82 MKPADSE   88 (175)
T ss_dssp             EEECGGG
T ss_pred             Ecccccc
Confidence            8887654

>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=99.63  E-value=2.3e-16  Score=124.91  Aligned_cols=79  Identities=18%  Similarity=0.252  Sum_probs=72.4

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCee--EEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTS--KMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~--~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      .+.++|||+|||+++++++|+++|+.| .|.  .|.|++|+. |+++|||||+|.+.++|++||. +++..++|+.|.|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V~  116 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEVF  116 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEEE
Confidence            445789999999999999999999999 677  899999985 9999999999999999999999 58899999999999


Q ss_pred             ecCC
Q psy13227        241 WSKS  244 (247)
Q Consensus       241 ~akp  244 (247)
                      ++.+
T Consensus       117 ~a~~  120 (126)
T 2hgm_A          117 KSSQ  120 (126)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8864

>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=99.62  E-value=1.4e-15  Score=129.29  Aligned_cols=76  Identities=18%  Similarity=0.201  Sum_probs=71.4

Q ss_pred             CccEEEEeecC-CCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        164 DTTAIRISNLS-VNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       164 ~~~tl~V~nLp-~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +.++|||+||| +.+++++|+++|++||.|.+|.+++++     +|||||+|.+.++|+.||+.|||..+.|+.|+|.|+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            45799999999 899999999999999999999998763     799999999999999999999999999999999999


Q ss_pred             CC
Q psy13227        243 KS  244 (247)
Q Consensus       243 kp  244 (247)
                      +.
T Consensus        78 ~~   79 (205)
T 3tyt_A           78 KQ   79 (205)
T ss_dssp             SC
T ss_pred             cC
Confidence            74

>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=99.62  E-value=1.1e-15  Score=124.24  Aligned_cols=79  Identities=27%  Similarity=0.401  Sum_probs=73.4

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||.++++++|+++|++||.|..+     ..++.++|||||+|.+.++|.+|+..|||..++|+.|.|.|+
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  171 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT  171 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEEC
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEec
Confidence            456799999999999999999999999987765     458999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +|++
T Consensus       172 ~~k~  175 (175)
T 1fje_B          172 GEKG  175 (175)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            9985

>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=99.62  E-value=2.1e-15  Score=120.83  Aligned_cols=79  Identities=24%  Similarity=0.462  Sum_probs=74.7

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeE--EEEee
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLI--LSVDW  241 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~--L~V~~  241 (247)
                      ..++|||+|||.++++++|+++|++||.|..+.+..+..+|.++|||||+|.+.++|.+|+..|||..++|+.  |+|.|
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~  166 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF  166 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEe
Confidence            4468999999999999999999999999999999999889999999999999999999999999999999964  89988


Q ss_pred             c
Q psy13227        242 S  242 (247)
Q Consensus       242 a  242 (247)
                      |
T Consensus       167 A  167 (167)
T 1fxl_A          167 A  167 (167)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.62  E-value=8.4e-16  Score=119.77  Aligned_cols=77  Identities=16%  Similarity=0.358  Sum_probs=69.1

Q ss_pred             CCccEEEE--eecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCcee-----CCe
Q psy13227        163 DDTTAIRI--SNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGY-----DHL  235 (247)
Q Consensus       163 ~~~~tl~V--~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i-----~g~  235 (247)
                      ....+|||  +||++++++++|+++|++||.|.+|.++.+      +|||||+|.+.++|++|++.|||..+     .|+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            44578999  779999999999999999999999987642      78999999999999999999999998     688


Q ss_pred             EEEEeecCCC
Q psy13227        236 ILSVDWSKST  245 (247)
Q Consensus       236 ~L~V~~akp~  245 (247)
                      .|.|.|++..
T Consensus        97 ~l~v~~a~~~  106 (114)
T 2cq2_A           97 TLYLNFVEKV  106 (114)
T ss_dssp             ECEEEEESCC
T ss_pred             EEEEEecccC
Confidence            9999998754

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=7.5e-16  Score=118.74  Aligned_cols=77  Identities=16%  Similarity=0.252  Sum_probs=66.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCC---CceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEE
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTN---GLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV  239 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~t---g~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V  239 (247)
                      .+.++|||+|||+++++++|+++|++||.|. +.++.++.+   |.++|||||+|.+.++|++||+.|+  .++|+.|.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4457899999999999999999999999999 888888777   7999999999999999999999883  355555555


Q ss_pred             eec
Q psy13227        240 DWS  242 (247)
Q Consensus       240 ~~a  242 (247)
                      ..+
T Consensus        83 ~~~   85 (114)
T 2dnl_A           83 VSS   85 (114)
T ss_dssp             ECC
T ss_pred             ccC
Confidence            443

>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=99.61  E-value=2.7e-15  Score=121.20  Aligned_cols=80  Identities=23%  Similarity=0.370  Sum_probs=74.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC---CeEEEE
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD---HLILSV  239 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~---g~~L~V  239 (247)
                      ...++|||+|||.++++++|+++|++||.|.++.++++. +|.++|||||+|.+.++|.+|+..|||..+.   ++.|.|
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V  171 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV  171 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEE
Confidence            356799999999999999999999999999999999996 7999999999999999999999999998776   499999


Q ss_pred             eecC
Q psy13227        240 DWSK  243 (247)
Q Consensus       240 ~~ak  243 (247)
                      .||.
T Consensus       172 ~~ad  175 (175)
T 3nmr_A          172 KFAD  175 (175)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9983

>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=99.61  E-value=3.3e-15  Score=130.85  Aligned_cols=83  Identities=22%  Similarity=0.448  Sum_probs=75.8

Q ss_pred             CCCCccEEEEeecCCCCCHHHHH----HHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeE
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLE----DLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLI  236 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~----~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~  236 (247)
                      .....++|||+|||+++++++|+    ++|+.||.|..|.+.+   +|.++|||||+|.+.++|..|++.|||..+.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            34567899999999999999976    8999999999998875   6889999999999999999999999999999999


Q ss_pred             EEEeecCCCC
Q psy13227        237 LSVDWSKSTN  246 (247)
Q Consensus       237 L~V~~akp~~  246 (247)
                      |+|.|++++.
T Consensus        82 l~v~~a~~~~   91 (282)
T 3pgw_A           82 MRIQYAKTDS   91 (282)
T ss_pred             EEEEEeccCc
Confidence            9999998653

>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=99.61  E-value=1.2e-15  Score=122.86  Aligned_cols=80  Identities=15%  Similarity=0.404  Sum_probs=75.0

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      +.++|||+|||.++++++|+++|+.||.|.++.+++++.+|.++|||||+|.+.++|..|+.  ++..++|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            45799999999999999999999999999999999999899999999999999999999999  5788999999999987


Q ss_pred             CC
Q psy13227        244 ST  245 (247)
Q Consensus       244 p~  245 (247)
                      ++
T Consensus        80 ~~   81 (167)
T 2cjk_A           80 PR   81 (167)
T ss_dssp             CH
T ss_pred             ch
Confidence            64

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.61  E-value=3.4e-15  Score=117.90  Aligned_cols=75  Identities=20%  Similarity=0.298  Sum_probs=68.0

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeE-EEEEecCHHHHHHHHHHhcCceeCC--eEEEEeec
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF-AYIHFKNKADAAKAIQYLNGYGYDH--LILSVDWS  242 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGf-aFV~F~s~e~A~~Ai~~LnG~~i~g--~~L~V~~a  242 (247)
                      ..|||+||++.+++++|+++|++||.|.+|.|.. +     .|| |||+|.+.++|..|++.|||..|.|  +.|+|+||
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            4578999999999999999999999999999865 2     276 9999999999999999999999987  68999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +++.
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            9863

>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=99.60  E-value=2.6e-15  Score=132.13  Aligned_cols=83  Identities=24%  Similarity=0.327  Sum_probs=77.2

Q ss_pred             CCccEEEEeecCCC-CCHHHHHHHhhccCCeeEEEEeecCC-CCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        163 DDTTAIRISNLSVN-TSENDLEDLVKQFGPTSKMYLSRDKT-NGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~-~te~dL~~lF~~fG~I~~i~l~~d~~-tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ...++|||+|||.. +++++|+++|++||.|..+.++.+.. ||.++|||||.|.+.++|.+|+ .|||..++|+.|.|.
T Consensus       208 ~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~  286 (292)
T 2ghp_A          208 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVS  286 (292)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEE
T ss_pred             CCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEE
Confidence            45689999999999 99999999999999999999999875 5999999999999999999999 999999999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      |++|++
T Consensus       287 ~a~~k~  292 (292)
T 2ghp_A          287 LADKKP  292 (292)
T ss_dssp             ECCCCC
T ss_pred             EecCCC
Confidence            999975

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.60  E-value=5e-15  Score=113.39  Aligned_cols=82  Identities=15%  Similarity=0.152  Sum_probs=72.6

Q ss_pred             CCccEEEEeecCC-----CCCHHHHHHHhhccCCeeEEEEeecCCC-CceeeEEEEEecCHHHHHHHHHHhcCceeCCeE
Q psy13227        163 DDTTAIRISNLSV-----NTSENDLEDLVKQFGPTSKMYLSRDKTN-GLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLI  236 (247)
Q Consensus       163 ~~~~tl~V~nLp~-----~~te~dL~~lF~~fG~I~~i~l~~d~~t-g~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~  236 (247)
                      ..+++|+|.||..     +-.+++|+++|++||.|.++.|++++.+ +.++||+||+|.+.++|.+|+..|||..++|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            3457999999963     2367999999999999999999998654 689999999999999999999999999999999


Q ss_pred             EEEeecCC
Q psy13227        237 LSVDWSKS  244 (247)
Q Consensus       237 L~V~~akp  244 (247)
                      |.|.|+.+
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999874

>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=99.60  E-value=7.7e-16  Score=112.90  Aligned_cols=76  Identities=11%  Similarity=0.331  Sum_probs=65.6

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ..++|||+|||+++++++|+++|++||.|..+.++.+     ++|||||+|.+.++|++++.  ....+.++.|.|.|++
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEecC
Confidence            4579999999999999999999999999999998765     68999999999999975432  1334689999999999


Q ss_pred             CCC
Q psy13227        244 STN  246 (247)
Q Consensus       244 p~~  246 (247)
                      |+.
T Consensus        77 ~~~   79 (88)
T 1wf0_A           77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            874

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=3.4e-15  Score=112.41  Aligned_cols=73  Identities=19%  Similarity=0.229  Sum_probs=65.6

Q ss_pred             CccEEEEeecCCCCCHHH----HHHHhhcc-CCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEE
Q psy13227        164 DTTAIRISNLSVNTSEND----LEDLVKQF-GPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS  238 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~d----L~~lF~~f-G~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~  238 (247)
                      ..+.|||+|||+.+++++    |+++|+.| |.|..|       ++   |||||.|.+.++|.+|++.|||..+.|+.|+
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~   77 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            334599999999999988    55899999 599988       34   9999999999999999999999999999999


Q ss_pred             EeecCCCC
Q psy13227        239 VDWSKSTN  246 (247)
Q Consensus       239 V~~akp~~  246 (247)
                      |+||+.+.
T Consensus        78 v~~A~~~s   85 (96)
T 2diu_A           78 VSFTPKNR   85 (96)
T ss_dssp             EESSCCSC
T ss_pred             EEecCCCc
Confidence            99999764

>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=99.59  E-value=3.8e-15  Score=108.38  Aligned_cols=71  Identities=18%  Similarity=0.445  Sum_probs=66.0

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhcc----C-------CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCcee
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQF----G-------PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGY  232 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~f----G-------~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i  232 (247)
                      +.++|||+|||+++++++|+++|+.|    |       .|.++.+.++      +|||||+|.+.++|+.|+ .|||..+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            45799999999999999999999999    8       8999988754      789999999999999999 8999999


Q ss_pred             CCeEEEEee
Q psy13227        233 DHLILSVDW  241 (247)
Q Consensus       233 ~g~~L~V~~  241 (247)
                      +|+.|+|+.
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999974

>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=99.58  E-value=9.3e-15  Score=128.09  Aligned_cols=83  Identities=17%  Similarity=0.210  Sum_probs=78.7

Q ss_pred             CCccEEEEeecCCCC-CHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        163 DDTTAIRISNLSVNT-SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~-te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ...++|||+|||+++ ++++|+++|+.||.|..+.|..+. +|.++|||||.|.+.++|.+|+..|||..++|+.|.|.|
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  260 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF  260 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEE
Confidence            456799999999995 999999999999999999999996 899999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      ++|+.
T Consensus       261 a~~~~  265 (284)
T 3smz_A          261 CAPGP  265 (284)
T ss_dssp             CCSSS
T ss_pred             ecCCC
Confidence            99875

>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=99.58  E-value=9e-15  Score=123.23  Aligned_cols=79  Identities=15%  Similarity=0.297  Sum_probs=73.0

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ..++|||+|||+++++++|+++|++||.|..|.++++. +|.++|||||+|.+.++|+.|+..+ +..++|+.|.|.|++
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKD  185 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhH
Confidence            35799999999999999999999999999999999996 6999999999999999999999865 459999999999986


Q ss_pred             C
Q psy13227        244 S  244 (247)
Q Consensus       244 p  244 (247)
                      .
T Consensus       186 ~  186 (193)
T 2voo_A          186 D  186 (193)
T ss_dssp             T
T ss_pred             H
Confidence            4

>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=99.57  E-value=1.4e-14  Score=126.96  Aligned_cols=82  Identities=24%  Similarity=0.475  Sum_probs=78.5

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ..++|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|||..++|+.|.|.|+.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            44799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CC
Q psy13227        244 ST  245 (247)
Q Consensus       244 p~  245 (247)
                      ++
T Consensus       174 ~~  175 (284)
T 3smz_A          174 AG  175 (284)
T ss_dssp             GG
T ss_pred             CC
Confidence            65

>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=99.57  E-value=2.4e-14  Score=110.03  Aligned_cols=81  Identities=22%  Similarity=0.291  Sum_probs=70.0

Q ss_pred             CCCccEEEEeecCCCCC-----------HHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCc
Q psy13227        162 NDDTTAIRISNLSVNTS-----------ENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGY  230 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~t-----------e~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~  230 (247)
                      ...+.+|+|.||.....           +++|+++|++||.|..|.| .++   .++|||||+|.+.++|++|+..|||.
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCC
Confidence            34567999999954432           5799999999999999965 554   37999999999999999999999999


Q ss_pred             eeCCeEEEEeecCCCC
Q psy13227        231 GYDHLILSVDWSKSTN  246 (247)
Q Consensus       231 ~i~g~~L~V~~akp~~  246 (247)
                      .++|+.|.|.|+.++.
T Consensus        88 ~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           88 WFGGRQITAQAWDGTT  103 (112)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCcEEEEEEeCCCC
Confidence            9999999999998864

>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=99.56  E-value=1.5e-15  Score=123.60  Aligned_cols=83  Identities=20%  Similarity=0.288  Sum_probs=73.3

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ...+.++|||+|||.++++++|+++|..||.+.. .++.+..+|.++|||||+|.+.++|..|++ |||..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEe
Confidence            3456789999999999999999999999998766 344444688999999999999999999995 99999999999999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      |+.++
T Consensus        87 ~~~~~   91 (175)
T 1fje_B           87 KPKGR   91 (175)
T ss_dssp             CCCCS
T ss_pred             cCCCc
Confidence            99875

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.55  E-value=6.6e-14  Score=122.52  Aligned_cols=77  Identities=22%  Similarity=0.349  Sum_probs=72.0

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC-CeEEEEee
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD-HLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~-g~~L~V~~  241 (247)
                      ...++|||+|||.++++++|+++|++||.|.++.++.++     +|||||+|.+.++|.+|+..|||..++ |+.|+|.|
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  279 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISF  279 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEE
Confidence            456889999999999999999999999999999998764     689999999999999999999999999 99999999


Q ss_pred             cCC
Q psy13227        242 SKS  244 (247)
Q Consensus       242 akp  244 (247)
                      ++.
T Consensus       280 akk  282 (282)
T 3pgw_A          280 AKK  282 (282)
T ss_pred             ecC
Confidence            973

>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=99.55  E-value=1.6e-14  Score=123.62  Aligned_cols=79  Identities=20%  Similarity=0.251  Sum_probs=74.0

Q ss_pred             CCCccEEEEeecCC-CCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        162 NDDTTAIRISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       162 ~~~~~tl~V~nLp~-~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ..+.++|||+|||+ ++++++|+++|+.||.|..|.+++++     +|||||+|.+.++|+.|++.|||..+.|+.|.|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~  105 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT  105 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            35668999999999 99999999999999999999999885     7899999999999999999999999999999999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      |+++.
T Consensus       106 ~a~~~  110 (229)
T 2adc_A          106 LSKHQ  110 (229)
T ss_dssp             CCSCC
T ss_pred             EecCc
Confidence            99864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.52  E-value=1.3e-14  Score=120.59  Aligned_cols=76  Identities=21%  Similarity=0.260  Sum_probs=72.0

Q ss_pred             ccEEEEeecCC-CCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        165 TTAIRISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       165 ~~tl~V~nLp~-~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      .++|||+|||+ ++++++|+++|+.||.|..|.+++++     +|||||+|.+.++|..|+..|||..++|+.|.|.|++
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            47999999999 99999999999999999999998875     7899999999999999999999999999999999998


Q ss_pred             CC
Q psy13227        244 ST  245 (247)
Q Consensus       244 p~  245 (247)
                      +.
T Consensus        78 ~~   79 (198)
T 1qm9_A           78 HQ   79 (198)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.49  E-value=6.4e-14  Score=123.23  Aligned_cols=82  Identities=20%  Similarity=0.330  Sum_probs=71.3

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccC-CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFG-PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG-~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ..++|||+|||+++++++|+++|+.|| .|..+.++.++ .|.++|||||+|.+.++|..|+..|||..++|+.|.|.|+
T Consensus       116 ~~~~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          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            457999999999999999999999999 99999999987 4889999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      .|+.
T Consensus       195 ~~~~  198 (292)
T 2ghp_A          195 NPLE  198 (292)
T ss_dssp             CCC-
T ss_pred             CCCc
Confidence            8763

>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=99.49  E-value=2e-14  Score=109.67  Aligned_cols=72  Identities=19%  Similarity=0.353  Sum_probs=64.6

Q ss_pred             EeecCCCCCHHHHHHHh------------hccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEE
Q psy13227        170 ISNLSVNTSENDLEDLV------------KQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLIL  237 (247)
Q Consensus       170 V~nLp~~~te~dL~~lF------------~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L  237 (247)
                      +.||+..+++++|+++|            ++||.|.++.|+++. ++.++|||||.|.+.++|.+|+..|||..++|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56777777777777666            999999999999986 58999999999999999999999999999999999


Q ss_pred             EEeec
Q psy13227        238 SVDWS  242 (247)
Q Consensus       238 ~V~~a  242 (247)
                      .|+|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99987

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.48  E-value=5.6e-14  Score=116.70  Aligned_cols=78  Identities=24%  Similarity=0.325  Sum_probs=72.6

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccC-CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC-CeEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFG-PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD-HLILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG-~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~-g~~L~V~  240 (247)
                      ...++|||+|||..+++++|+++|++|| .|..+.+..+.     +|||||+|.+.++|..|+..|||..++ |+.|+|.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            4568999999999999999999999999 99999987642     789999999999999999999999999 9999999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      |++|+
T Consensus       193 ~a~~~  197 (198)
T 1qm9_A          193 FSKST  197 (198)
T ss_dssp             EECCC
T ss_pred             eeccc
Confidence            99985

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.48  E-value=1.8e-13  Score=119.48  Aligned_cols=77  Identities=22%  Similarity=0.464  Sum_probs=71.8

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||+|||+++++++|+++|+.||.|..|.+.++      +|||||.|.+.++|..|+..|||..++|+.|.|.|+
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            55689999999999999999999999999999998654      689999999999999999999999999999999999


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      .+.
T Consensus        94 ~~~   96 (261)
T 3sde_A           94 THG   96 (261)
T ss_dssp             CCS
T ss_pred             ccC
Confidence            864

>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=99.47  E-value=1.4e-13  Score=117.85  Aligned_cols=78  Identities=24%  Similarity=0.309  Sum_probs=72.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccC-CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC-CeEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFG-PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD-HLILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG-~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~-g~~L~V~  240 (247)
                      ...++|||+|||..+++++|+++|++|| .|..+.++.+     .+|||||+|.+.++|.+|+..|||..++ |+.|+|.
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~  223 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  223 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEE
Confidence            4468999999999999999999999999 9999998653     3689999999999999999999999999 9999999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      |++|+
T Consensus       224 ~a~~~  228 (229)
T 2adc_A          224 FSKST  228 (229)
T ss_dssp             ECSSC
T ss_pred             EecCC
Confidence            99985

>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=99.47  E-value=2.6e-13  Score=118.39  Aligned_cols=81  Identities=27%  Similarity=0.308  Sum_probs=73.7

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhc-CceeC---CeEEEE
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN-GYGYD---HLILSV  239 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~Ln-G~~i~---g~~L~V  239 (247)
                      ..++|||+|||..+++++|+++|+.||.|.++.++.+ .+|.++|||||+|.+.++|.+|+..|| |..+.   ++.|.|
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            4568999999999999999999999999999999999 599999999999999999999999995 44554   899999


Q ss_pred             eecCCC
Q psy13227        240 DWSKST  245 (247)
Q Consensus       240 ~~akp~  245 (247)
                      .|+.+.
T Consensus       174 ~~~~~~  179 (261)
T 3sde_A          174 EPMEQF  179 (261)
T ss_dssp             EECCCE
T ss_pred             eecccc
Confidence            998764

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.46  E-value=1.3e-13  Score=105.39  Aligned_cols=81  Identities=17%  Similarity=0.286  Sum_probs=70.2

Q ss_pred             CccEEEEeec--CCCCC--------HHHHHHHhhccCCeeEEEEeecCCC--CceeeEEEEEecCHHHHHHHHHHhcCce
Q psy13227        164 DTTAIRISNL--SVNTS--------ENDLEDLVKQFGPTSKMYLSRDKTN--GLCKGFAYIHFKNKADAAKAIQYLNGYG  231 (247)
Q Consensus       164 ~~~tl~V~nL--p~~~t--------e~dL~~lF~~fG~I~~i~l~~d~~t--g~skGfaFV~F~s~e~A~~Ai~~LnG~~  231 (247)
                      .++.|.+.|+  +....        ++||+++|++||.|.++.|++++.+  +.++||+||+|.+.++|.+|+..|||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            3468999998  33443        2689999999999999999998754  4689999999999999999999999999


Q ss_pred             eCCeEEEEeecCC
Q psy13227        232 YDHLILSVDWSKS  244 (247)
Q Consensus       232 i~g~~L~V~~akp  244 (247)
                      ++|+.|.|.|+.+
T Consensus        84 f~GR~i~v~~~~~   96 (105)
T 3v4m_A           84 FANRVVVTKYCDP   96 (105)
T ss_dssp             ETTEECEEEEECH
T ss_pred             eCCCEEEEEEeCH
Confidence            9999999999754

>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=99.46  E-value=1.4e-13  Score=116.76  Aligned_cols=78  Identities=13%  Similarity=0.287  Sum_probs=69.0

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCe--eEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCe----E
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPT--SKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHL----I  236 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I--~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~----~  236 (247)
                      ....+|||+|||+++++++|+++|++||.|  .++.+..++  +.++|||||+|.+.++|..||..|||..++|.    .
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p  198 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP  198 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcc
Confidence            345789999999999999999999999999  899988875  55679999999999999999999999999887    4


Q ss_pred             EEEeec
Q psy13227        237 LSVDWS  242 (247)
Q Consensus       237 L~V~~a  242 (247)
                      +.|.|+
T Consensus       199 ~~vk~~  204 (205)
T 3tyt_A          199 YTLKLC  204 (205)
T ss_dssp             EECEEE
T ss_pred             eEEEec
Confidence            666654

>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=99.44  E-value=3e-13  Score=109.18  Aligned_cols=75  Identities=16%  Similarity=0.371  Sum_probs=67.2

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhcc----C-------CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCcee
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQF----G-------PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGY  232 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~f----G-------~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i  232 (247)
                      +.++|||+|||.++++++|+++|++|    |       .|.++.+.      .++|||||+|.+.++|+.|+ .|||..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            35799999999999999999999999    6       67777664      34799999999999999999 7999999


Q ss_pred             CCeEEEEeecCCC
Q psy13227        233 DHLILSVDWSKST  245 (247)
Q Consensus       233 ~g~~L~V~~akp~  245 (247)
                      +|+.|.|.++.+.
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999998764

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.43  E-value=2.5e-13  Score=112.04  Aligned_cols=74  Identities=16%  Similarity=0.372  Sum_probs=66.1

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhcc----C-------CeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQF----G-------PTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD  233 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~f----G-------~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~  233 (247)
                      .++|||+|||+++++++|+++|+.|    |       .|..+.+      +.++|||||+|.+.++|+.|+ .|||..++
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            4799999999999999999999999    5       5666554      455899999999999999999 79999999


Q ss_pred             CeEEEEeecCCC
Q psy13227        234 HLILSVDWSKST  245 (247)
Q Consensus       234 g~~L~V~~akp~  245 (247)
                      |+.|.|.|+.+.
T Consensus        77 g~~i~v~~~~~~   88 (198)
T 2yh0_A           77 GQSLKIRRPHDY   88 (198)
T ss_dssp             TEEEEEECCCCC
T ss_pred             CceEEEeCCCCC
Confidence            999999998764

>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=99.43  E-value=6.3e-13  Score=103.86  Aligned_cols=80  Identities=18%  Similarity=0.299  Sum_probs=70.6

Q ss_pred             CccEEEEeecC--CCC---CHHHHHHHhhccCCeeEEEEeecCC----CCceeeEEEEEecCHHHHHHHHHHhcCceeCC
Q psy13227        164 DTTAIRISNLS--VNT---SENDLEDLVKQFGPTSKMYLSRDKT----NGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH  234 (247)
Q Consensus       164 ~~~tl~V~nLp--~~~---te~dL~~lF~~fG~I~~i~l~~d~~----tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g  234 (247)
                      .+++|++.|+-  .++   -++||++.|++||.|.+|.|++++.    ++.++||+||+|.+.++|.+|+..|||..|+|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            56799999983  222   3589999999999999999999864    46789999999999999999999999999999


Q ss_pred             eEEEEeecC
Q psy13227        235 LILSVDWSK  243 (247)
Q Consensus       235 ~~L~V~~ak  243 (247)
                      +.|.|.|+.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999875

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.40  E-value=1.4e-12  Score=99.14  Aligned_cols=75  Identities=21%  Similarity=0.270  Sum_probs=63.5

Q ss_pred             ccEEEEeecC-------CCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEE
Q psy13227        165 TTAIRISNLS-------VNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLIL  237 (247)
Q Consensus       165 ~~tl~V~nLp-------~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L  237 (247)
                      ...|.|.-..       ..+++++|+++|++||.|..|.|+     +.++|||||+|.+.++|+.|++.++  .+.++.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV--GLVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC--BCSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC--CCCCCeE
Confidence            3456665433       568999999999999999999987     3679999999999999999999744  4789999


Q ss_pred             EEeecCCCC
Q psy13227        238 SVDWSKSTN  246 (247)
Q Consensus       238 ~V~~akp~~  246 (247)
                      +|.|+++++
T Consensus        83 ~V~~a~~~~   91 (100)
T 2d9o_A           83 KISWLEGQP   91 (100)
T ss_dssp             EEECSSCCC
T ss_pred             EEEEccCCC
Confidence            999999875

>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=99.29  E-value=5.7e-12  Score=115.27  Aligned_cols=75  Identities=17%  Similarity=0.322  Sum_probs=65.0

Q ss_pred             CCccEEEEee--cCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC---Ce--
Q psy13227        163 DDTTAIRISN--LSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD---HL--  235 (247)
Q Consensus       163 ~~~~tl~V~n--Lp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~---g~--  235 (247)
                      ..+.+|||+|  |+..+++++|+++|++||.|.+|.+..      +||||||+|.+.++|++|++.|||..+.   |+  
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~   89 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCce
Confidence            4567999999  689999999999999999999987753      4799999999999999999999999873   34  


Q ss_pred             EEEEeecC
Q psy13227        236 ILSVDWSK  243 (247)
Q Consensus       236 ~L~V~~ak  243 (247)
                      .|.|.|+.
T Consensus        90 ~ly~~~~~   97 (345)
T 3tht_A           90 TLYLNFVE   97 (345)
T ss_dssp             ECEEEECS
T ss_pred             EEEEEEee
Confidence            57888774

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.23  E-value=1.7e-11  Score=95.18  Aligned_cols=75  Identities=17%  Similarity=0.349  Sum_probs=63.7

Q ss_pred             ccEEEEeecCCCC----------CHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC
Q psy13227        165 TTAIRISNLSVNT----------SENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH  234 (247)
Q Consensus       165 ~~tl~V~nLp~~~----------te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g  234 (247)
                      ++.|.+.|+=..-          -++||++.|++||.|.+|.|.++.    ++||+||.|.+.++|.+|+..|||..++|
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            4578888873211          125789999999999999997663    48999999999999999999999999999


Q ss_pred             eEEEEeecC
Q psy13227        235 LILSVDWSK  243 (247)
Q Consensus       235 ~~L~V~~ak  243 (247)
                      +.|.|.|+.
T Consensus        83 R~i~v~~~~   91 (114)
T 3s6e_A           83 KMITAAYVP   91 (114)
T ss_dssp             EECEEEEEC
T ss_pred             EEEEEEEEc
Confidence            999999985

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.07  E-value=7.7e-10  Score=82.41  Aligned_cols=71  Identities=18%  Similarity=0.283  Sum_probs=62.1

Q ss_pred             cEEEEeecCC----CCCH----HHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEE
Q psy13227        166 TAIRISNLSV----NTSE----NDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLIL  237 (247)
Q Consensus       166 ~tl~V~nLp~----~~te----~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L  237 (247)
                      .||.|..++.    ++-.    .+|.+.|++||.|..++++.++        +||+|.+.++|.+||+ |||..++|+.|
T Consensus         8 ~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr~L   78 (91)
T 2dnr_A            8 GTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNRTI   78 (91)
T ss_dssp             CEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTEEE
T ss_pred             CeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCeEE
Confidence            5888988772    3333    5788999999999999998874        8999999999999999 99999999999


Q ss_pred             EEeecCCC
Q psy13227        238 SVDWSKST  245 (247)
Q Consensus       238 ~V~~akp~  245 (247)
                      +|++++|.
T Consensus        79 kV~lkt~d   86 (91)
T 2dnr_A           79 TIALKSPS   86 (91)
T ss_dssp             EEEECCCS
T ss_pred             EEEeCCCC
Confidence            99999874

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.96  E-value=2.2e-09  Score=84.20  Aligned_cols=75  Identities=16%  Similarity=0.108  Sum_probs=66.0

Q ss_pred             CCCccEEEEeecCCC-CCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecC-HHHHHHHHHHhc--CceeCCeEE
Q psy13227        162 NDDTTAIRISNLSVN-TSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKN-KADAAKAIQYLN--GYGYDHLIL  237 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~-~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s-~e~A~~Ai~~Ln--G~~i~g~~L  237 (247)
                      -...+.|||+||+++ +++++|+++|+.||.|..|.+.++..      .|||.|.+ ..+|..|+..||  +..|.+..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            356689999999999 99999999999999999999988864      59999999 899999999995  677888887


Q ss_pred             EEeec
Q psy13227        238 SVDWS  242 (247)
Q Consensus       238 ~V~~a  242 (247)
                      .++..
T Consensus        89 ~~evL   93 (121)
T 1owx_A           89 TWEVL   93 (121)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            77653

>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=98.94  E-value=2.3e-09  Score=91.01  Aligned_cols=66  Identities=18%  Similarity=0.284  Sum_probs=59.9

Q ss_pred             CHHHHHHHhhccCCeeEEEEeecC----CCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        178 SENDLEDLVKQFGPTSKMYLSRDK----TNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       178 te~dL~~lF~~fG~I~~i~l~~d~----~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      .+++|++.|++||.|.++.|.++.    .++.++|++||+|.+.++|.+|+..|||..++|+.|.+.++.
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            457899999999999999998554    456999999999999999999999999999999999999874

>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=98.83  E-value=1.1e-08  Score=76.60  Aligned_cols=71  Identities=11%  Similarity=0.232  Sum_probs=61.2

Q ss_pred             ccEEEEeecCCC------CCH---HHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCe
Q psy13227        165 TTAIRISNLSVN------TSE---NDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHL  235 (247)
Q Consensus       165 ~~tl~V~nLp~~------~te---~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~  235 (247)
                      ..||.|..++..      .++   .+|.+.|..||.|..++++.++        +||+|.+.++|.+||+ |||..++|+
T Consensus        15 D~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~Gr   85 (95)
T 1ufw_A           15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVKGR   85 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEETTE
T ss_pred             CCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeCCe
Confidence            368999988743      232   4688999999999999999884        9999999999999999 999999999


Q ss_pred             EEEEeecCC
Q psy13227        236 ILSVDWSKS  244 (247)
Q Consensus       236 ~L~V~~akp  244 (247)
                      .|+|.+-.|
T Consensus        86 ~L~V~~k~~   94 (95)
T 1ufw_A           86 AVKISGPSS   94 (95)
T ss_dssp             EEEEECCCC
T ss_pred             EEEEeccCC
Confidence            999998654

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.43  E-value=1.2e-06  Score=67.30  Aligned_cols=73  Identities=23%  Similarity=0.223  Sum_probs=67.2

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhcc-----CCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQF-----GPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLI  236 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~f-----G~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~  236 (247)
                      .++.++|-+-|||+.++...|+.|+.++     |.|..|.+..|.      +-|+|+|.+...|.+|.-.|||..|+|++
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~   91 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKV   91 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeE
Confidence            3456789999999999999999999999     999999998884      47999999999999999999999999999


Q ss_pred             EEEe
Q psy13227        237 LSVD  240 (247)
Q Consensus       237 L~V~  240 (247)
                      |++-
T Consensus        92 Lr~g   95 (117)
T 2l9w_A           92 IRSG   95 (117)
T ss_dssp             EEEE
T ss_pred             EEec
Confidence            9985

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.51  E-value=0.00031  Score=53.25  Aligned_cols=76  Identities=14%  Similarity=0.166  Sum_probs=62.8

Q ss_pred             CccEEEEeecCCCC-CH----HHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEE
Q psy13227        164 DTTAIRISNLSVNT-SE----NDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS  238 (247)
Q Consensus       164 ~~~tl~V~nLp~~~-te----~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~  238 (247)
                      -.++|+|+||+.++ ..    +.++++|..|+++......+.-      .-..|.|.+.++|.+|-..|++..++|..|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            34789999998866 33    4568999999998887766552      1457999999999999999999999999999


Q ss_pred             EeecCCC
Q psy13227        239 VDWSKST  245 (247)
Q Consensus       239 V~~akp~  245 (247)
                      |-|+++.
T Consensus        78 ~YFgq~~   84 (104)
T 1wey_A           78 LYFAQTL   84 (104)
T ss_dssp             EECCCCS
T ss_pred             EEecCCC
Confidence            9998754

>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=97.38  E-value=0.00089  Score=50.15  Aligned_cols=54  Identities=15%  Similarity=0.268  Sum_probs=47.0

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhc
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN  228 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~Ln  228 (247)
                      ..++| ++|..+...||.++|+.||.|. |.++-|.       .|||.|.+++.|..|+..++
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fggv~-I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCCEE-EEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            34555 9999999999999999999654 8888885       89999999999999999764

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.09  E-value=0.0038  Score=46.10  Aligned_cols=78  Identities=18%  Similarity=0.264  Sum_probs=61.1

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCc--eeeEEEEEecCHHHHHHHHHHhcCceeCC-----eEEE
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL--CKGFAYIHFKNKADAAKAIQYLNGYGYDH-----LILS  238 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~--skGfaFV~F~s~e~A~~Ai~~LnG~~i~g-----~~L~  238 (247)
                      +.|-|.+||+.++|+++.+.++....+...+.+..+.+..  .-.-|||.|.+.+++..-.+.++|+.+-+     ....
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            5789999999999999999999998877666655543322  23679999999999999999999998642     1235


Q ss_pred             EeecC
Q psy13227        239 VDWSK  243 (247)
Q Consensus       239 V~~ak  243 (247)
                      |++|-
T Consensus        82 VE~AP   86 (91)
T 1uw4_A           82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            66653

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.02  E-value=0.0033  Score=48.73  Aligned_cols=72  Identities=18%  Similarity=0.251  Sum_probs=58.2

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC-eEEEEe
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH-LILSVD  240 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g-~~L~V~  240 (247)
                      ..+.+.|.|.++|+.. -..+...|++||.|.+.....      ...+-.|.|.++.+|++||. .||..+++ ..|-|.
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~   92 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVK   92 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEE
Confidence            3456789999999885 566778899999999887621      23599999999999999999 69999984 667776


Q ss_pred             e
Q psy13227        241 W  241 (247)
Q Consensus       241 ~  241 (247)
                      +
T Consensus        93 p   93 (119)
T 1wwh_A           93 P   93 (119)
T ss_dssp             E
T ss_pred             E
Confidence            5

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.91  E-value=0.0073  Score=45.58  Aligned_cols=72  Identities=15%  Similarity=0.119  Sum_probs=57.5

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhc-----cCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEE
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQ-----FGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV  239 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~-----fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V  239 (247)
                      ..+|.|.|||+.++++.|.-+|..     -|.|..+....        +-|+|+|.+...|++.++. .-+.+++..|.|
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV   78 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQLSL   78 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEEEE
Confidence            468999999999999999999976     25677776533        4789999999999999882 377888888888


Q ss_pred             eecCCC
Q psy13227        240 DWSKST  245 (247)
Q Consensus       240 ~~akp~  245 (247)
                      .-..++
T Consensus        79 ~P~~~~   84 (104)
T 2dhx_A           79 RPAPPR   84 (104)
T ss_dssp             EECCCC
T ss_pred             EcCCCC
Confidence            655544

>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=96.88  E-value=0.0017  Score=48.68  Aligned_cols=53  Identities=15%  Similarity=0.274  Sum_probs=46.3

Q ss_pred             EEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhc
Q psy13227        167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN  228 (247)
Q Consensus       167 tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~Ln  228 (247)
                      .++| ++|..+...||.++|++||. ..|.++-|.       .|||.|.+++.|..|+..++
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            4555 99999999999999999994 458888885       89999999999999999775

>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=95.61  E-value=0.014  Score=45.90  Aligned_cols=35  Identities=17%  Similarity=0.048  Sum_probs=29.2

Q ss_pred             EEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCc
Q psy13227        194 KMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGY  230 (247)
Q Consensus       194 ~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~  230 (247)
                      .+.|+++.  ..++|||||+|.+.++|++|+..+++.
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhccc
Confidence            35677774  468999999999999999999988753

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.56  E-value=0.016  Score=45.57  Aligned_cols=79  Identities=19%  Similarity=0.228  Sum_probs=55.7

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEE-Eeec------------CCCC-ceeeEEEEEecCHHHHHHHHHHhc
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMY-LSRD------------KTNG-LCKGFAYIHFKNKADAAKAIQYLN  228 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~-l~~d------------~~tg-~skGfaFV~F~s~e~A~~Ai~~Ln  228 (247)
                      ...+.|.|-++|++.. ..+.+.|++||.|..-+ +.++            +.-+ ....+-.|.|.+..+|.+||. .|
T Consensus         5 ~~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~N   82 (132)
T 3p3d_A            5 NGELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-EN   82 (132)
T ss_dssp             ---CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TT
T ss_pred             cCceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hC
Confidence            3446788889977654 55667899999987622 1110            0001 134688999999999999999 69


Q ss_pred             CceeCCeEEEEeecC
Q psy13227        229 GYGYDHLILSVDWSK  243 (247)
Q Consensus       229 G~~i~g~~L~V~~ak  243 (247)
                      |..++|..|-|.+..
T Consensus        83 G~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           83 GAVFNGVLLGVIPYT   97 (132)
T ss_dssp             TCEETTEECEEEECC
T ss_pred             CeEeCcEEEEEEECC
Confidence            999999988887654

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=95.44  E-value=0.011  Score=46.33  Aligned_cols=41  Identities=22%  Similarity=0.138  Sum_probs=37.8

Q ss_pred             CCceeeEEEEEecCHHHHHHHHHHh-cCceeCCeEEEEeecCC
Q psy13227        203 NGLCKGFAYIHFKNKADAAKAIQYL-NGYGYDHLILSVDWSKS  244 (247)
Q Consensus       203 tg~skGfaFV~F~s~e~A~~Ai~~L-nG~~i~g~~L~V~~akp  244 (247)
                      ....+|+++|+|.+.++|++|+..| ||..++| .+.++++.+
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            4567899999999999999999999 9999999 999999875

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=94.87  E-value=0.043  Score=40.87  Aligned_cols=80  Identities=16%  Similarity=0.213  Sum_probs=56.6

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCC--ceeeEEEEEecCHHHHHHHHHHhcCceeCCe-----E
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNG--LCKGFAYIHFKNKADAAKAIQYLNGYGYDHL-----I  236 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg--~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~-----~  236 (247)
                      .+-.|-|..||+.++|+++.+.++.+-.+...+.+....+.  ..-.-|||.|.+.++...-.+.++|+.+-+.     .
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~   87 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYP   87 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEee
Confidence            34579999999999999999888876554333332222221  1225689999999999999999999986432     3


Q ss_pred             EEEeecC
Q psy13227        237 LSVDWSK  243 (247)
Q Consensus       237 L~V~~ak  243 (247)
                      -.|++|-
T Consensus        88 a~VE~AP   94 (97)
T 2l08_A           88 AVVEFAP   94 (97)
T ss_dssp             EEEEECC
T ss_pred             eEEEecC
Confidence            4566653

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=94.54  E-value=0.027  Score=53.08  Aligned_cols=59  Identities=22%  Similarity=0.367  Sum_probs=43.7

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHH
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ  225 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~  225 (247)
                      +....++|+|. .+..+++.+|.+.|++||+|.++.+-.+.  |   -||.|+|.+.+++..++.
T Consensus        49 ~~qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g---~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           49 REQAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G---LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHHHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S---EEEEEECC---CCHHHHS
T ss_pred             HHHhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C---eEEEEEeCCHHHHHHHHh
Confidence            34555799997 79999999999999999999999886653  3   599999999998887654

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=91.19  E-value=0.063  Score=33.46  Aligned_cols=21  Identities=33%  Similarity=0.760  Sum_probs=18.0

Q ss_pred             eeeeeeccC-CccccCCCCccc
Q psy13227         77 FISCRTCKG-AHFTNNCPFKDS   97 (247)
Q Consensus        77 ~~~Cr~C~g-~h~t~~CP~k~~   97 (247)
                      .++|++|+. +||...||-+..
T Consensus        10 ~~~C~~Cgk~GH~ardCP~~~~   31 (40)
T 1a6b_B           10 RDQCAYCKEKGHWAKDCPKKPR   31 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSCC
T ss_pred             CCeeeECCCCCcchhhCcCCcc
Confidence            578999954 999999998765

>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=87.26  E-value=1.6  Score=41.22  Aligned_cols=55  Identities=15%  Similarity=0.253  Sum_probs=45.7

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG  229 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG  229 (247)
                      ..++|+ ++..+...+|.++|+.||.+ .|.++.+.       .|||.|.+.+.|..++..++.
T Consensus       441 ~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt-------~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          441 HVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             GEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSS-------EEEEECSCHHHHHHHHHHHTT
T ss_pred             cEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCC-------eEEEEECCHHHHHHHHHHHHh
Confidence            456665 99999999999999999954 57766654       799999999999999998854

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=87.17  E-value=0.19  Score=33.62  Aligned_cols=21  Identities=33%  Similarity=0.760  Sum_probs=18.0

Q ss_pred             eeeeeeccC-CccccCCCCccc
Q psy13227         77 FISCRTCKG-AHFTNNCPFKDS   97 (247)
Q Consensus        77 ~~~Cr~C~g-~h~t~~CP~k~~   97 (247)
                      ..+|++|+. +||...||-+..
T Consensus        23 ~~~C~~Cge~GH~ardCp~~~~   44 (56)
T 1u6p_A           23 RDQCAYCKEKGHWAKDCPKKPR   44 (56)
T ss_dssp             TTBCSSSCCBSSCGGGCTTCCC
T ss_pred             CCcceeCCCCCcccccCcCCcc
Confidence            578999965 999999998755

---

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	247
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	5e-16
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	5e-15
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-14
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-14
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-13
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	6e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	7e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	8e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	5e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	6e-12
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	7e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	7e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-11
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-11
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	7e-11
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-10
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-06
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	4e-10
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-10
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	6e-10
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-10
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	7e-10
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	8e-10
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	9e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-09
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-09
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	7e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-08
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-08
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-08
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-08
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-08
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-07
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-07
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-07
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-07
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	4e-07
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	7e-07
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-06
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-06
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	8e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-05
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	9e-05
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	2e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.001
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	0.002
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.003

>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 = 69.3 bits (169), Expect = 5e-16
 Identities = 48/88 (54%), Positives = 67/88 (76%), Gaps = 1/88 (1%)

Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           RR DD   IR++NLS +T E DL++L + FG  S++YL++DKT G  KGFA+I F  + D
Sbjct: 3   RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 62

Query: 220 AAKAIQYLNGYGYDHLILSVDWSK-STN 246
           AA+AI  ++G+GYDHLIL+V+W+K STN
Sbjct: 63  AARAIAGVSGFGYDHLILNVEWAKPSTN 90

>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 = 66.5 bits (162), Expect = 5e-15
 Identities = 23/82 (28%), Positives = 41/82 (50%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
             +  + + NLS  T+E  + +L  + G   K+ +  DK      GF ++ + ++ADA  
Sbjct: 5   KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 64

Query: 223 AIQYLNGYGYDHLILSVDWSKS 244
           A++Y+NG   D  I+  DW   
Sbjct: 65  AMRYINGTRLDDRIIRTDWDAG 86

>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 = 64.6 bits (157), Expect = 3e-14
 Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTN-GLCKGFAYIHFKNKAD 219
           +   T+ I + N+    ++ ++ +L   FG    + L +  T  G  +GF ++ F  K D
Sbjct: 4   KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 63

Query: 220 AAKAIQYL-NGYGYDHLILSVDWSKS 244
           A KA   L +        L ++W+ S
Sbjct: 64  AKKAFNALCHSTHLYGRRLVLEWADS 89

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.4 bits (154), Expect = 5e-14
 Identities = 18/76 (23%), Positives = 36/76 (47%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + +L  + +E  L +     GP   + + RD       G+AY++F+  ADA +A+  +
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 228 NGYGYDHLILSVDWSK 243
           N        + + WS+
Sbjct: 63  NFDVIKGKPVRIMWSQ 78

>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 = 61.7 bits (149), Expect = 3e-13
 Identities = 20/78 (25%), Positives = 36/78 (46%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + ++ L  N ++ +   L    G      L RDK  G   G+ ++++ +  DA KAI 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 226 YLNGYGYDHLILSVDWSK 243
            LNG       + V +++
Sbjct: 63  TLNGLRLQTKTIKVSYAR 80

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.4 bits (146), Expect = 6e-13
 Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 170 ISNLSVNTSENDLEDLVKQFGP---TSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQY 226
           I NL+ +T+E  L+ +  + G     +           L  GF ++ +K    A KA++ 
Sbjct: 3   IKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ 62

Query: 227 LNGYGYDHLILSVDWSKSTNQ 247
           L G+  D   L V  S+   +
Sbjct: 63  LQGHTVDGHKLEVRISERATK 83

>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 = 60.8 bits (147), Expect = 7e-13
 Identities = 23/92 (25%), Positives = 45/92 (48%), Gaps = 1/92 (1%)

Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
           G  + RN D T + +  L    SE  L +L  Q GP    ++ +D+  G  +G+ ++ F 
Sbjct: 1   GPISERNQDAT-VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFL 59

Query: 216 NKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
           ++ DA  AI+ ++        + V+ + + N+
Sbjct: 60  SEEDADYAIKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 61.2 bits (148), Expect = 8e-13
 Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           +    + I NL    +  ++ D+  ++GP  ++           +G AY+ +++  DA  
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKN 61

Query: 223 AIQYLNGYGYDHLILSVDWSKS 244
           A  +L+G+   +  L V +  +
Sbjct: 62  ACDHLSGFNVCNRYLVVLYYNA 83

>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 = 60.0 bits (145), Expect = 1e-12
 Identities = 20/78 (25%), Positives = 42/78 (53%)

Query: 166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ 225
           T + ++ L  + ++ +L  L +  GP +   + RD   G   G+A++ F ++ D+ +AI+
Sbjct: 3   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 226 YLNGYGYDHLILSVDWSK 243
            LNG    +  L V +++
Sbjct: 63  VLNGITVRNKRLKVSYAR 80

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 59.2 bits (143), Expect = 2e-12
 Identities = 19/80 (23%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
             T + ++NL    +++ L+ +  ++G   +  + RDK  G  +G A++ +  + +A +A
Sbjct: 5   KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 224 IQYLNGYGYD--HLILSVDW 241
           I  LN    +     LSV  
Sbjct: 65  ISALNNVIPEGGSQPLSVRL 84

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 58.2 bits (140), Expect = 5e-12
 Identities = 17/84 (20%), Positives = 40/84 (47%)

Query: 161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADA 220
           R+ +   + ++++     E+++++    +G    ++L+ D+  G  KG+A + ++    A
Sbjct: 3   RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQA 62

Query: 221 AKAIQYLNGYGYDHLILSVDWSKS 244
             A + LNG       + VDW   
Sbjct: 63  LAAKEALNGAEIMGQTIQVDWCFV 86

>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 = 57.6 bits (139), Expect = 6e-12
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + +SNL    S+ D+++L  +FG   K  +  D++     G A +HF+ KADA KA++  
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGR-SLGTADVHFERKADALKAMKQY 61

Query: 228 NGYGYDHLILSVDWSKS 244
           NG   D   +++    S
Sbjct: 62  NGVPLDGRPMNIQLVTS 78

>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 = 57.7 bits (139), Expect = 7e-12
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 2/83 (2%)

Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
           +     + + NLS + +E  +  L  Q GP     +  + T+     F  + F    DAA
Sbjct: 5   DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCF--VEFYEHRDAA 62

Query: 222 KAIQYLNGYGYDHLILSVDWSKS 244
            A+  +NG       + V+W+ +
Sbjct: 63  AALAAMNGRKILGKEVKVNWATT 85

>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 = 57.8 bits (139), Expect = 7e-12
 Identities = 24/95 (25%), Positives = 43/95 (45%), Gaps = 6/95 (6%)

Query: 150 GGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGF 209
           GG  + G     +     I + NL  +    D+ED+  ++G    + L   +       F
Sbjct: 2   GGGVIRGPAGNND---CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG---GPPF 55

Query: 210 AYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
           A++ F++  DA  A+   +GY YD   L V++ +S
Sbjct: 56  AFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS 90

>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 = 56.1 bits (135), Expect = 3e-11
 Identities = 18/85 (21%), Positives = 31/85 (36%), Gaps = 2/85 (2%)

Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           R    T+ + +  L   T+E DL++    FG    + + +D   G  KGF ++ F     
Sbjct: 3   RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 62

Query: 220 AAKAIQYLNGYGYDHLILSVDWSKS 244
             K +     +  D          S
Sbjct: 63  QVKVMS--QRHMIDGRWCDCKLPNS 85

>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 = 56.2 bits (135), Expect = 3e-11
 Identities = 17/76 (22%), Positives = 32/76 (42%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + +  L+    +  L      FG  + + +  D      +GFA++ F+   DAA AI  +
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67

Query: 228 NGYGYDHLILSVDWSK 243
           N        + V+ +K
Sbjct: 68  NESELFGRTIRVNLAK 83

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 3e-11
 Identities = 20/75 (26%), Positives = 34/75 (45%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I  L    +++ +++L+  FGP     L +D   GL KG+A+  + +     +AI  LNG
Sbjct: 6   IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 65

Query: 230 YGYDHLILSVDWSKS 244
                  L V  +  
Sbjct: 66  MQLGDKKLLVQRASV 80

>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 = 55.8 bits (134), Expect = 5e-11
 Identities = 21/86 (24%), Positives = 43/86 (50%), Gaps = 5/86 (5%)

Query: 159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
           +++      +   NLS N +E++L+++ +       + +     +G  KG AYI FK++A
Sbjct: 10  SKKVRAARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEA 64

Query: 219 DAAKAIQYLNGYGYDHLILSVDWSKS 244
           DA K ++   G   D   +S+ ++  
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGE 90

>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 = 55.1 bits (132), Expect = 6e-11
 Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 2/81 (2%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
               + +S L    ++ +LE L  Q+G      +  D+  G+ +G  +I F  + +A +A
Sbjct: 5   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

Query: 224 IQYLNGYGYD--HLILSVDWS 242
           I+ LNG         ++V ++
Sbjct: 65  IKGLNGQKPSGATEPITVKFA 85

>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 = 55.5 bits (133), Expect = 7e-11
 Identities = 11/82 (13%), Positives = 29/82 (35%), Gaps = 4/82 (4%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKM--YLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I  +       ++ + + +           +        +GFA++ +++   AA A + L
Sbjct: 6   IGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKL 65

Query: 228 NGYGY--DHLILSVDWSKSTNQ 247
                      ++VDW++    
Sbjct: 66  MPGRIQLWGHQIAVDWAEPEID 87

>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 = 54.3 bits (130), Expect = 1e-10
 Identities = 22/77 (28%), Positives = 43/77 (55%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           D    + +  LS+ T+E DL ++  ++GP + + +  D+ +   +GFA+++F+N  DA +
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 223 AIQYLNGYGYDHLILSV 239
           A +  NG   D   + V
Sbjct: 67  AKERANGMELDGRRIRV 83

>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 = 54.6 bits (131), Expect = 1e-10
 Identities = 13/86 (15%), Positives = 33/86 (38%), Gaps = 6/86 (6%)

Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           + +     +    ++   ++  +      FG   ++ +         KG++++ F     
Sbjct: 13  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFP------EKGYSFVRFSTHES 66

Query: 220 AAKAIQYLNGYGYDHLILSVDWSKST 245
           AA AI  +NG   +  ++   W K +
Sbjct: 67  AAHAIVSVNGTTIEGHVVKCYWGKES 92

>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 = 54.3 bits (130), Expect = 2e-10
 Identities = 26/100 (26%), Positives = 39/100 (39%), Gaps = 6/100 (6%)

Query: 148 GPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
           G  G + EG       +   + I +L     + DL  +   FG      +  DK   L K
Sbjct: 7   GAAGSQKEG------PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 60

Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
            F ++ + N   A  AIQ +NG+      L V   +S N 
Sbjct: 61  CFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND 100

>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 = 54.3 bits (130), Expect = 2e-10
 Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           R  +    + I  LS  T+E  L +  +Q+G  +   + RD  +   +GF ++ F + A+
Sbjct: 15  REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 74

Query: 220 AAKAIQYLNGYGYDHLILSVDWSKS 244
              A+     +  D  ++    + +
Sbjct: 75  VDAAMA-ARPHSIDGRVVEPKRAVA 98

>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 = 54.1 bits (130), Expect = 2e-10
 Identities = 15/84 (17%), Positives = 36/84 (42%), Gaps = 9/84 (10%)

Query: 162 NDDTTAIRISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADA 220
               + + I NL+     ++D+E +  ++G      +         KGFA++ + N+ +A
Sbjct: 12  RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNA 63

Query: 221 AKAIQYLNGYGYDHLILSVDWSKS 244
             A+   +G      +L ++ +  
Sbjct: 64  RAAVAGEDGRMIAGQVLDINLAAE 87

>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 = 53.5 bits (128), Expect = 3e-10
 Identities = 13/76 (17%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQ-FGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
           I+NL+    +++L+  +   F    ++       +   +G A++ FK  + A  A++ + 
Sbjct: 8   INNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQ 67

Query: 229 GYGYDHLILSVDWSKS 244
           G+ +    + + ++K+
Sbjct: 68  GFPFYDKPMRIQYAKT 83

>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 = 55.8 bits (133), Expect = 3e-10
 Identities = 17/95 (17%), Positives = 38/95 (40%), Gaps = 1/95 (1%)

Query: 153 RVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYI 212
           R +      +     I +  +  +T E+ L D  +Q+G    + +  D+ +G  +GFA++
Sbjct: 85  REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 144

Query: 213 HFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
            F +     K +     +  +     V  + S  +
Sbjct: 145 TFDDHDSVDKIVI-QKYHTVNGHNCEVRKALSKQE 178

>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 = 44.6 bits (104), Expect = 2e-06
 Identities = 12/65 (18%), Positives = 24/65 (36%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I  LS  T++  L    +Q+G  +   + RD      +GF ++ +    +   A+     
Sbjct: 11  IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPH 70

Query: 230 YGYDH 234
                
Sbjct: 71  KVDGR 75

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.7 bits (126), Expect = 4e-10
 Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I  LS  T++  L +   QFG   +  + RD      +GF ++ F ++A   K +   + 
Sbjct: 5   IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSR 63

Query: 230 YGYDHLILSVDW 241
           +  D   +    
Sbjct: 64  HELDSKTIDPKV 75

>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 = 52.9 bits (126), Expect = 4e-10
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 1/80 (1%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
           + T + ++N   + ++ ++ DL++     +             + FAYI   +K DA   
Sbjct: 1   ECT-LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 59

Query: 224 IQYLNGYGYDHLILSVDWSK 243
           ++ LNG   +   L    S 
Sbjct: 60  VEKLNGLKIEGYTLVTKVSN 79

>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 = 53.2 bits (127), Expect = 4e-10
 Identities = 21/95 (22%), Positives = 43/95 (45%), Gaps = 8/95 (8%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGP--------TSKMYLSRDKTNGLCKGF 209
           +   + D +AI +  L+ + + +DL D  KQ G            +++  DK  G  KG 
Sbjct: 1   DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 60

Query: 210 AYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
           A + +++   A  A+++ +G  +    L V  ++ 
Sbjct: 61  ATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>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 = 53.1 bits (127), Expect = 5e-10
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 6/81 (7%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I + NL    + + L  +  +FG   K+           +  A + + +   A  A   L
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL 65

Query: 228 NGY--GYDHLILSVDWSKSTN 246
           +G         L +D+SK T+
Sbjct: 66  DGQNIYNACCTLRIDFSKLTS 86

>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 = 52.8 bits (126), Expect = 5e-10
 Identities = 25/82 (30%), Positives = 39/82 (47%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
             +  + + NLS  +SE DLE L   +GP S+++   D      KGFA++ F     A K
Sbjct: 6   SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 223 AIQYLNGYGYDHLILSVDWSKS 244
           A   ++G  +   +L V  S  
Sbjct: 66  AYAEVDGQVFQGRMLHVLPSTI 87

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 6e-10
 Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + I NLS   + +DL  L           +       L  G+A++ + ++  A +AI+ L
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQV------LLKSGYAFVDYPDQNWAIRAIETL 57

Query: 228 NG-YGYDHLILSVDWSKSTNQ 247
           +G       I+ VD+S S   
Sbjct: 58  SGKVELHGKIMEVDYSVSKKL 78

>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 = 52.3 bits (125), Expect = 6e-10
 Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + + NL  + +E ++  L +++G   +++          KGF +I  + +  A  A   L
Sbjct: 11  LFVGNLPPDITEEEMRKLFEKYGKAGEVF------IHKDKGFGFIRLETRTLAEIAKVEL 64

Query: 228 NGYGYDHLILSVDWSKS 244
           +        L V ++  
Sbjct: 65  DNMPLRGKQLRVRFACH 81

>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 = 52.4 bits (125), Expect = 7e-10
 Identities = 20/87 (22%), Positives = 41/87 (47%), Gaps = 2/87 (2%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
           N+        + +SN+     + DL  +  QFG    + +  ++     KGF ++ F+N 
Sbjct: 4   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENS 61

Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKS 244
           ADA +A + L+G   +   + V+ + +
Sbjct: 62  ADADRAREKLHGTVVEGRKIEVNNATA 88

>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 = 52.1 bits (124), Expect = 8e-10
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 1/76 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMY-LSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN 228
           I NL     E  L D    FG   +   + RD   G  KG+A+I+F +   +  AI+ +N
Sbjct: 3   IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN 62

Query: 229 GYGYDHLILSVDWSKS 244
           G    +  ++V ++  
Sbjct: 63  GQYLCNRPITVSYAFK 78

>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 = 53.4 bits (127), Expect = 9e-10
 Identities = 19/85 (22%), Positives = 41/85 (48%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
           D    + ++ +     E  L  L +++GP   + +  D+     +G+ ++ F++ + A +
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

Query: 223 AIQYLNGYGYDHLILSVDWSKSTNQ 247
           AI  LNG+   +  L V  + S +Q
Sbjct: 100 AIAGLNGFNILNKRLKVALAASGHQ 124

>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 = 52.0 bits (124), Expect = 1e-09
 Identities = 13/77 (16%), Positives = 30/77 (38%)

Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
            T I++ N+    S +++ D    +         +    G+  G A + F+++ +A  A+
Sbjct: 9   PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 68

Query: 225 QYLNGYGYDHLILSVDW 241
             LN        + +  
Sbjct: 69  IDLNDRPIGSRKVKLVL 85

>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 = 51.7 bits (123), Expect = 1e-09
 Identities = 22/83 (26%), Positives = 44/83 (53%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
           D   + +  LS +T+E  LE +  ++G  S++ + +D+     +GF ++ F+N  DA  A
Sbjct: 4   DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 224 IQYLNGYGYDHLILSVDWSKSTN 246
           +  +NG   D   + VD +  ++
Sbjct: 64  MMAMNGKSVDGRQIRVDQAGKSS 86

>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 = 52.0 bits (124), Expect = 1e-09
 Identities = 16/90 (17%), Positives = 40/90 (44%), Gaps = 1/90 (1%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
            ++++   T I +  L  +T++  L    + FG   +  +  D+  G  +G+ ++   ++
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
           A A +A +  N    D    +V+ +    +
Sbjct: 63  AAAERACKDPNPI-IDGRKANVNLAYLGAK 91

>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 = 51.3 bits (122), Expect = 3e-09
 Identities = 20/83 (24%), Positives = 40/83 (48%)

Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
           +    ++ + N+    +E  L+D+  + GP     L  D+  G  KG+ +  ++++  A 
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 222 KAIQYLNGYGYDHLILSVDWSKS 244
            A++ LNG  +    L VD + S
Sbjct: 65  SAMRNLNGREFSGRALRVDNAAS 87

>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 = 50.8 bits (121), Expect = 3e-09
 Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 2/86 (2%)

Query: 159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
           + R      I I NL  +     L D    FG      +  D+       + ++HF+ + 
Sbjct: 2   SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQE 59

Query: 219 DAAKAIQYLNGYGYDHLILSVDWSKS 244
            A +AI+ +NG   +   + V   KS
Sbjct: 60  AAERAIEKMNGMLLNDRKVFVGRFKS 85

>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 = 49.0 bits (116), Expect = 7e-09
 Identities = 19/64 (29%), Positives = 29/64 (45%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I  L   T++ DL  L + +G         DKT   CKG+ ++ F + + A KA+  L  
Sbjct: 3   IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA 62

Query: 230 YGYD 233
            G  
Sbjct: 63  SGVQ 66

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.4 bits (115), Expect = 1e-08
 Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 4/64 (6%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI----Q 225
           +  LS +T E  + +    FG    + L  D      +GF +I FK +    K +     
Sbjct: 4   VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYH 63

Query: 226 YLNG 229
            +  
Sbjct: 64  NVGL 67

>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 = 48.9 bits (116), Expect = 2e-08
 Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 1/81 (1%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
           D   +    L+      DLED     G    + +  D+ +   KG AY+ F        A
Sbjct: 17  DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA 76

Query: 224 IQYLNGYGYDHLILSVDWSKS 244
           I  L G     + + V  S++
Sbjct: 77  IG-LTGQRLLGVPIIVQASQA 96

>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 = 47.9 bits (113), Expect = 3e-08
 Identities = 20/91 (21%), Positives = 38/91 (41%), Gaps = 6/91 (6%)

Query: 163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAK 222
            +   + I NLS ++ E  L ++++QFG    + +         KG A+  F  +  A K
Sbjct: 6   TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 65

Query: 223 AIQYLN------GYGYDHLILSVDWSKSTNQ 247
            +   +      G   D   L VD + + ++
Sbjct: 66  CLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 96

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 4e-08
 Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 7/81 (8%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
            ++ I + NL  +++  ++ DL+K +                 K  A++   N   A  A
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDR-------NKRTAFVTLLNGEQAQNA 56

Query: 224 IQYLNGYGYDHLILSVDWSKS 244
           IQ  + Y +    L V    +
Sbjct: 57  IQMFHQYSFRGKDLIVQLQPT 77

>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 = 46.9 bits (111), Expect = 5e-08
 Identities = 17/70 (24%), Positives = 30/70 (42%), Gaps = 1/70 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I  LS +T++ DL+D   +FG      L  D   G  +GF ++ FK      K +     
Sbjct: 4   IGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKE 62

Query: 230 YGYDHLILSV 239
           +  +  ++  
Sbjct: 63  HKLNGKVIDP 72

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.5 bits (112), Expect = 6e-08
 Identities = 13/89 (14%), Positives = 32/89 (35%), Gaps = 8/89 (8%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
           +  +   +  + +  L  +  E DL + +++FG    + +         K  A + F+N 
Sbjct: 8   SHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQALVEFENI 61

Query: 218 ADAAKAIQYLNGYGY--DHLILSVDWSKS 244
             A + + +               ++S S
Sbjct: 62  DSAKECVTFAADVPVYIAGQQAFFNYSTS 90

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 6e-08
 Identities = 14/75 (18%), Positives = 30/75 (40%), Gaps = 1/75 (1%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I  LS  T++  L    +Q+G  +   + RD      +GF ++ +    +   A+     
Sbjct: 11  IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARP 69

Query: 230 YGYDHLILSVDWSKS 244
           +  D  ++    + S
Sbjct: 70  HKVDGRVVEPKRAVS 84

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 1e-07
 Identities = 23/87 (26%), Positives = 39/87 (44%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
           +    +    + + NLS   +E DL  L  +F       +      G  +G A+I F NK
Sbjct: 11  SYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNK 70

Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSKS 244
             A +A+  +NGY     IL +++ K+
Sbjct: 71  EIAWQALHLVNGYKLYGKILVIEFGKN 97

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.8 bits (108), Expect = 2e-07
 Identities = 22/86 (25%), Positives = 36/86 (41%), Gaps = 8/86 (9%)

Query: 161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADA 220
           + + TT + +  L  NTS   L     +FG    +       +     FAYI +++   A
Sbjct: 13  KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTID------HVKGDSFAYIQYESLDAA 66

Query: 221 AKAIQYLNGY--GYDHLILSVDWSKS 244
             A   + G+  G     L VD++KS
Sbjct: 67  QAACAKMRGFPLGGPDRRLRVDFAKS 92

>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 = 45.8 bits (108), Expect = 2e-07
 Identities = 13/79 (16%), Positives = 32/79 (40%), Gaps = 1/79 (1%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
             + + +        E    ++ +++G   +M +  +       G  Y+ F+ + DA KA
Sbjct: 26  AVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKA 84

Query: 224 IQYLNGYGYDHLILSVDWS 242
           +  LN   ++   +  + S
Sbjct: 85  VIDLNNRWFNGQPIHAELS 103

>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 = 45.6 bits (107), Expect = 2e-07
 Identities = 13/86 (15%), Positives = 28/86 (32%), Gaps = 1/86 (1%)

Query: 158 NARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK 217
           N+    +   +R+  L    S+ ++                     G   G A++ F ++
Sbjct: 8   NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQ 67

Query: 218 ADAAKAIQYLNGYGYDHLILSVDWSK 243
             A KA+   +     H  + +  S 
Sbjct: 68  EIAEKAL-KKHKERIGHRYIEIFKSS 92

>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 = 45.5 bits (107), Expect = 3e-07
 Identities = 16/100 (16%), Positives = 32/100 (32%), Gaps = 7/100 (7%)

Query: 148 GPGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCK 207
           G  G R+               + NL  + +E  +++  +    ++             K
Sbjct: 4   GSSGSRLPKSPPYT------AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLK 57

Query: 208 GFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTNQ 247
           GF Y  F++      A+  LN     +  + VD +     
Sbjct: 58  GFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVADQAQD 96

>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 = 45.0 bits (106), Expect = 3e-07
 Identities = 8/83 (9%), Positives = 29/83 (34%), Gaps = 7/83 (8%)

Query: 162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAA 221
           +  ++ + +   + + +E++L +   Q+G                + FA++ F +   A 
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDV-----MDVFIPKPFRAFAFVTFADDQIAQ 56

Query: 222 KAIQYLNGYGYDHLILSVDWSKS 244
                        + + +  ++ 
Sbjct: 57  SLCG--EDLIIKGISVHISNAEP 77

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.1 bits (106), Expect = 4e-07
 Identities = 10/79 (12%), Positives = 26/79 (32%), Gaps = 6/79 (7%)

Query: 152 KRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAY 211
           +            +  +    L    S N L  ++++ G    +           K +++
Sbjct: 7   RHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL------MPPNKPYSF 60

Query: 212 IHFKNKADAAKAIQYLNGY 230
             ++   ++ +A   LNG 
Sbjct: 61  ARYRTTEESKRAYVTLNGK 79

>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 = 44.3 bits (104), Expect = 4e-07
 Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 1/74 (1%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           I +  LSVNT+  D++   +QFG      L  DKT    +GF ++ F+++    K  + +
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60

Query: 228 NGYGYDHLILSVDW 241
           + +  ++ ++    
Sbjct: 61  HFHEINNKMVECKK 74

>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 = 44.9 bits (106), Expect = 4e-07
 Identities = 16/72 (22%), Positives = 27/72 (37%), Gaps = 4/72 (5%)

Query: 172 NLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG 231
            L +N    DL     +FG   K+ L          G A + F++  +A   IQ L+G  
Sbjct: 26  PLVLNEIREDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDGRW 81

Query: 232 YDHLILSVDWSK 243
           +    ++     
Sbjct: 82  FGGRQITAQAWD 93

>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 = 43.9 bits (103), Expect = 7e-07
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 6/78 (7%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           + NL ++TSE  +E       P +   +         + +A++HF N+ DA +A++ LNG
Sbjct: 13  VRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKALNG 66

Query: 230 YGYDHLILSVDWSKSTNQ 247
              D   + V  +K  ++
Sbjct: 67  KVLDGSPIEVTLAKPVDK 84

>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 = 43.6 bits (102), Expect = 1e-06
 Identities = 13/90 (14%), Positives = 30/90 (33%), Gaps = 3/90 (3%)

Query: 155 EGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHF 214
              ++ ++     + +  L    +END+ +      P           +G   G A + F
Sbjct: 5   SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IGPDGRVTGEADVEF 62

Query: 215 KNKADAAKAIQYLNGYGYDHLILSVDWSKS 244
               DA  A+   +     H  + +  + +
Sbjct: 63  ATHEDAVAAMA-KDKANMQHRYVELFLNST 91

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 2e-06
 Identities = 17/84 (20%), Positives = 35/84 (41%), Gaps = 1/84 (1%)

Query: 160 RRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           ++  D T + ISNL ++  E +LE+++K FG           ++G  +G  +   ++   
Sbjct: 13  QQEQDPTNLYISNLPLSMDEQELENMLKPFGQV-ISTRILRDSSGTSRGVGFARMESTEK 71

Query: 220 AAKAIQYLNGYGYDHLILSVDWSK 243
               I + NG            ++
Sbjct: 72  CEAVIGHFNGKFIKTPPGVSAPTE 95

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (99), Expect = 2e-06
 Identities = 12/76 (15%), Positives = 29/76 (38%), Gaps = 8/76 (10%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + +    +  +   L      FG         D +    +  A++ ++    A +A+  L
Sbjct: 8   LYVYGEDM--TPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAVAEL 59

Query: 228 NGYGYDHLILSVDWSK 243
           NG   + + L V+ ++
Sbjct: 60  NGTQVESVQLKVNIAR 75

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.5 bits (99), Expect = 3e-06
 Identities = 9/87 (10%), Positives = 29/87 (33%), Gaps = 11/87 (12%)

Query: 165 TTAIRISNLSV-----NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKAD 219
           ++ +     +      + +    E L + +   +     +            I+F N   
Sbjct: 5   SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLS 58

Query: 220 AAKAIQYLNGYGYDHLILSVDWSKSTN 246
           AA A   L+   +    + + ++++ +
Sbjct: 59  AADARLRLHKTEFLGKEMKLYFAQTLH 85

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.5 bits (97), Expect = 7e-06
 Identities = 12/75 (16%), Positives = 28/75 (37%), Gaps = 2/75 (2%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL--CKGFAYIHFKNKADAAKAIQYL 227
           + +        D+ D   ++G    + + R          G  ++ F +  D  KA+Q L
Sbjct: 19  LDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGL 78

Query: 228 NGYGYDHLILSVDWS 242
            G  + + ++   + 
Sbjct: 79  TGRKFANRVVVTKYC 93

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.2 bits (96), Expect = 8e-06
 Identities = 16/88 (18%), Positives = 25/88 (28%), Gaps = 9/88 (10%)

Query: 160 RRNDDTTAIRISNL-SVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKA 218
            R +    + I +          L  LV+ FG  S   +            A+I      
Sbjct: 3   GRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN------KINEAFIEMATTE 56

Query: 219 DAAKAIQY--LNGYGYDHLILSVDWSKS 244
           DA  A+ Y            + V  S+ 
Sbjct: 57  DAQAAVDYYTTTPALVFGKPVRVHLSQK 84

>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 = 40.5 bits (94), Expect = 1e-05
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
           +  + +SN+  + SE DL+ L    G      +   K     +  A I   +  +A +A+
Sbjct: 10  SATLHLSNIPPSVSEEDLKVLFSSNGG----VVKGFKFFQKDRKMALIQMGSVEEAVQAL 65

Query: 225 QYLNGYG-YDHLILSVDWSKST 245
             L+ +   ++  L V +SKST
Sbjct: 66  IDLHNHDLGENHHLRVSFSKST 87

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.8 bits (92), Expect = 2e-05
 Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 168 IRISNLSVNTSENDL---EDLVKQFGPTSKMYLSRDKTNGLC---KGFAYIHFKNKADAA 221
           + +  LS   ++ ++    +   +FG   K+ ++   +          AY+ +    DA 
Sbjct: 11  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 70

Query: 222 KAIQYLNGYGYDHLILSV 239
           +AIQ +N    D   L  
Sbjct: 71  RAIQCVNNVVVDGRTLKA 88

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.9 bits (92), Expect = 3e-05
 Identities = 17/89 (19%), Positives = 34/89 (38%), Gaps = 6/89 (6%)

Query: 156 GYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFK 215
           G +       T I   NL   T   ++++   +FG   ++              A + F 
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVL------LPEGGITAIVEFL 54

Query: 216 NKADAAKAIQYLNGYGYDHLILSVDWSKS 244
              +A KA ++L    + H+ L ++W+  
Sbjct: 55  EPLEARKAFRHLAYSKFHHVPLYLEWAPI 83

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.3 bits (91), Expect = 3e-05
 Identities = 13/90 (14%), Positives = 30/90 (33%), Gaps = 12/90 (13%)

Query: 159 ARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSR-----DKTNGLCKGFAYIH 213
           ARR      + + N+    +E  + D          +  +             K FA++ 
Sbjct: 1   ARR------LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 54

Query: 214 FKNKADAAKAIQYLNGYGYDHLILSVDWSK 243
           F++  +  +A+   +G  +    L +    
Sbjct: 55  FRSVDETTQAM-AFDGIIFQGQSLKIRRPH 83

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.8 bits (92), Expect = 3e-05
 Identities = 12/76 (15%), Positives = 28/76 (36%), Gaps = 7/76 (9%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + +S L  + S  DL+D +++ G      +          G   + +  K D   A++ L
Sbjct: 18  VLVSGLPPSGSWQDLKDHMREAGDVCYADVQ-------KDGMGMVEYLRKEDMEYALRKL 70

Query: 228 NGYGYDHLILSVDWSK 243
           +   +        + +
Sbjct: 71  DDTKFRSHEGETSYIR 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 = 38.7 bits (89), Expect = 9e-05
 Identities = 14/82 (17%), Positives = 26/82 (31%), Gaps = 1/82 (1%)

Query: 149 PGGKRVEGYNARRNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKG 208
           P G++     +        + +  L        + D  K+              NG   G
Sbjct: 3   PSGQKRSRSRSPHEAGFC-VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATG 61

Query: 209 FAYIHFKNKADAAKAIQYLNGY 230
             ++ F+N+AD   A+     Y
Sbjct: 62  EGFVEFRNEADYKAALCRHKQY 83

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 2e-04
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 166 TAIRISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAI 224
           + + +SNL+    +   L  L   +G   ++ +  +      K  A +   +   A  A+
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAM 57

Query: 225 QYLNGYGYDHLILSVDWSKSTN 246
            +LNG+      + +  SK  N
Sbjct: 58  SHLNGHKLHGKPIRITLSKHQN 79

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.5 bits (78), Expect = 0.001
 Identities = 14/75 (18%), Positives = 24/75 (32%), Gaps = 7/75 (9%)

Query: 170 ISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNG 229
           I  L  + +  ++ DL+  +                 KG A++   N   A  AI   + 
Sbjct: 3   IRGLPGDVTNQEVHDLLSDYELKYCF-------VDKYKGTAFVTLLNGEQAEAAINTFHQ 55

Query: 230 YGYDHLILSVDWSKS 244
                  LSV    +
Sbjct: 56  SRLRERELSVQLQPT 70

>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 = 33.8 bits (77), Expect = 0.002
 Identities = 8/65 (12%), Positives = 21/65 (32%), Gaps = 7/65 (10%)

Query: 164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKA 223
           D T + +      ++   L    +       +  +          + +I +++K  A KA
Sbjct: 3   DDTWVTVFGFPQASASYILLQFAQYGNILKHVMSNT-------GNWMHIRYQSKLQARKA 55

Query: 224 IQYLN 228
           +    
Sbjct: 56  LSKDG 60

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.7 bits (76), Expect = 0.003
 Identities = 11/79 (13%), Positives = 25/79 (31%), Gaps = 8/79 (10%)

Query: 168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL 227
           + I  L    +E ++  L   FG  + +           K  A++    +  A   + Y 
Sbjct: 11  LHIRKLPGEVTETEVIALGLPFGKVTNIL------MLKGKNQAFLELATEEAAITMVNYY 64

Query: 228 NGYGYDHL--ILSVDWSKS 244
           +          + + +S  
Sbjct: 65  SAVTPHLRNQPIYIQYSNH 83

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	247
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.89
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.87
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.87
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.86
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.86
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.86
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.85
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.85
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.84
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.83
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.83
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.83
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.83
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.83
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.82
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.82
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.82
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.82
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.82
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.81
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.81
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.81
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.81
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.81
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.8
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.79
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.78
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.78
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.77
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.77
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.77
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.76
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.76
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.76
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.75
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.75
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.75
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.75
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.75
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.74
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.74
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.74
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.73
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.73
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.73
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.73
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.73
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.72
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.72
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.72
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.72
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.72
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.7
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.7
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.7
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.69
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.68
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.68
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.67
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.67
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.64
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.64
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.63
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.63
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.62
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.59
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	99.55
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.55
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.48
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.41
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.41
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.39
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.32
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.21
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.14
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.91
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.78
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.36
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	88.89

>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=99.89  E-value=4.9e-23  Score=151.90  Aligned_cols=87  Identities=51%  Similarity=0.960  Sum_probs=83.4

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      +.++.++|||+|||.++++++|+++|+.||.|.++.|+.++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|+
T Consensus         4 ~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~   83 (90)
T d2cq0a1           4 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   83 (90)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45677899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCCCC
Q psy13227        241 WSKSTNQ  247 (247)
Q Consensus       241 ~akp~~~  247 (247)
                      ||+|+.|
T Consensus        84 ~akp~~n   90 (90)
T d2cq0a1          84 WAKPSTN   90 (90)
T ss_dssp             ESSCCCC
T ss_pred             eeeCCCC
Confidence            9999875

>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=99.87  E-value=4.6e-22  Score=146.07  Aligned_cols=85  Identities=19%  Similarity=0.395  Sum_probs=80.5

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||.++++++|+++|+.||.|.++.+++|+.+|.++|||||+|.+.++|++|+..|||..++|+.|+|+|
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~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45668999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      |.++.
T Consensus        84 a~~kG   88 (88)
T d1rk8a_          84 CFVKG   88 (88)
T ss_dssp             SEECC
T ss_pred             ecCCC
Confidence            99863

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.87  E-value=3.2e-22  Score=144.57  Aligned_cols=80  Identities=25%  Similarity=0.510  Sum_probs=77.9

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      .++|||+|||.++++++|+++|++||.|.++.+++++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|+||+|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999998

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=9.6e-22  Score=141.88  Aligned_cols=80  Identities=25%  Similarity=0.483  Sum_probs=77.8

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST  245 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp~  245 (247)
                      ++|||+|||.++++++|+++|++||.|.++.++++..+|.++|||||+|.+.++|+.|++.|||..++|+.|+|+||+|.
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkPs   82 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPS   82 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeCc
Confidence            68999999999999999999999999999999999989999999999999999999999999999999999999999984

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=7e-22  Score=146.64  Aligned_cols=85  Identities=21%  Similarity=0.355  Sum_probs=81.2

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      .+..++|||+|||.++++++|+++|++||.|.++.|++++.||.++|||||+|.+.++|+.|++.|||..++|+.|+|+|
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34557999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      |+++.
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            99975

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=7.2e-22  Score=145.22  Aligned_cols=83  Identities=20%  Similarity=0.319  Sum_probs=79.7

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ..++|||+|||+++++++|+++|++||.|.++.+++|+.+|.++|||||+|.+.++|+.|+..|||..++|+.|+|+||+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCC
Q psy13227        244 STN  246 (247)
Q Consensus       244 p~~  246 (247)
                      |+.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            875

>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=99.85  E-value=3e-21  Score=145.46  Aligned_cols=84  Identities=26%  Similarity=0.393  Sum_probs=80.6

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ++.++|||+|||+++++++|+++|+.||.|.++.++.++.+|.++|||||+|.+.++|+.||+.|||..|+|+.|+|+|+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            45578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +|+.
T Consensus        96 ~~k~   99 (102)
T d2cpza1          96 RSKN   99 (102)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            9985

>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=99.85  E-value=3.2e-21  Score=143.01  Aligned_cols=83  Identities=28%  Similarity=0.549  Sum_probs=79.7

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ..+++|||+|||.++++++|+++|++||.|.+|.+++++.+|.++|||||+|.+.++|+.|++.|||..++|+.|+|+|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            46689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      .+.
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            754

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=3.6e-21  Score=138.73  Aligned_cols=78  Identities=23%  Similarity=0.385  Sum_probs=76.0

Q ss_pred             EEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       167 tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      +|||+|||+++++++|+++|++||+|.++.|++|+.||.++|||||+|.+.++|..|++.|||..++|+.|+|.||+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            699999999999999999999999999999999999999999999999999999999999999999999999999963

>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=99.84  E-value=2.8e-20  Score=147.04  Aligned_cols=84  Identities=21%  Similarity=0.424  Sum_probs=79.8

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +..++|||+|||+++++++|+++|+.||.|.+|.|++++.||+++|||||+|.+.++|..||+.|||+.|+|+.|+|+||
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a  119 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +++.
T Consensus       120 ~~~~  123 (139)
T d1u6fa1         120 ASGH  123 (139)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8653

>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=99.84  E-value=6.8e-21  Score=142.49  Aligned_cols=84  Identities=30%  Similarity=0.394  Sum_probs=80.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||+|||+++++++|+++|.+||.|.++.|++++.+|.++|||||+|.+.++|+.||+.|||..|+|+.|+|.|+
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +++.
T Consensus        86 ~~~~   89 (99)
T d1whwa_          86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            9864

>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=99.83  E-value=9.2e-21  Score=140.76  Aligned_cols=85  Identities=24%  Similarity=0.463  Sum_probs=78.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecC-CCCceeeEEEEEecCHHHHHHHHHHh-cCceeCCeEEEE
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDK-TNGLCKGFAYIHFKNKADAAKAIQYL-NGYGYDHLILSV  239 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~-~tg~skGfaFV~F~s~e~A~~Ai~~L-nG~~i~g~~L~V  239 (247)
                      +...++|||+|||+++++++|+++|+.||.|.++.|++++ .+|.++|||||+|.+.++|..||..| ||..++|+.|.|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            3556789999999999999999999999999999999885 48999999999999999999999998 899999999999


Q ss_pred             eecCCCC
Q psy13227        240 DWSKSTN  246 (247)
Q Consensus       240 ~~akp~~  246 (247)
                      +||+++.
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9999864

>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=99.83  E-value=6.8e-21  Score=137.26  Aligned_cols=79  Identities=19%  Similarity=0.292  Sum_probs=70.3

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      ++|||+|||+++++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|++|++.|||..++|+.|+|+||+|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6999999999999999999999999999998888888999999999999999999999999999999999999999998

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.83  E-value=1.5e-20  Score=136.79  Aligned_cols=80  Identities=24%  Similarity=0.408  Sum_probs=75.9

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC--eEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH--LILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g--~~L~V~  240 (247)
                      .+.++|||+|||.++++++|+++|++||.|.++.+++++.+|.++|||||+|.+.++|..|++.|||..+.|  +.|.|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            345789999999999999999999999999999999999999999999999999999999999999999976  889999


Q ss_pred             ec
Q psy13227        241 WS  242 (247)
Q Consensus       241 ~a  242 (247)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            97

>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=99.83  E-value=2.9e-20  Score=137.24  Aligned_cols=82  Identities=21%  Similarity=0.352  Sum_probs=77.0

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||+++++++|+++|+.||.|.++.|++|+.||.++|||||+|.+.++|++||+  +.+.++|+.|.|.++
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~--~~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh--cCCccCCEEeEEEeC
Confidence            445789999999999999999999999999999999999999999999999999999999998  556899999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      .++.
T Consensus        84 ~~k~   87 (90)
T d2cqga1          84 NSKQ   87 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            9875

>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=99.83  E-value=5.1e-21  Score=139.64  Aligned_cols=81  Identities=25%  Similarity=0.424  Sum_probs=78.2

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKST  245 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp~  245 (247)
                      ..|||+|||.++++++|+++|++||+|.++.|++|+.||.++|||||+|.+.++|..|+..|||..++|+.|.|+||++.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            36999999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             C
Q psy13227        246 N  246 (247)
Q Consensus       246 ~  246 (247)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1e-20  Score=138.95  Aligned_cols=84  Identities=26%  Similarity=0.485  Sum_probs=79.6

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+..+|||+|||+++++++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|+.|+..|||+.++|+.|+|+||
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34567999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      .++.
T Consensus        83 ~~~~   86 (90)
T d1x5sa1          83 GKSS   86 (90)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            8874

>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=99.83  E-value=3.3e-20  Score=136.46  Aligned_cols=84  Identities=21%  Similarity=0.401  Sum_probs=77.4

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||.++++++|+++|+.||.|.++.++.++.++  +|||||+|.+.++|..|+..|||..++|+.|+|.|
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   82 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   82 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456799999999999999999999999999999999987554  78999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy13227        242 SKSTNQ  247 (247)
Q Consensus       242 akp~~~  247 (247)
                      |+++.+
T Consensus        83 a~~~~~   88 (90)
T d2cqia1          83 ATTPSS   88 (90)
T ss_dssp             CCCTTC
T ss_pred             cCCCCC
Confidence            998753

>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=99.82  E-value=2.3e-20  Score=135.98  Aligned_cols=78  Identities=24%  Similarity=0.454  Sum_probs=74.4

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC--eEEEEeec
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH--LILSVDWS  242 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g--~~L~V~~a  242 (247)
                      .++|||+|||+++++++|+++|++||.|.++.+++|+.+|.++|||||+|.+.++|+.|++.|||..++|  +.|.|.||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            4689999999999999999999999999999999999999999999999999999999999999999997  55999997

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=9.3e-21  Score=137.14  Aligned_cols=80  Identities=28%  Similarity=0.372  Sum_probs=75.9

Q ss_pred             EEEeecCCCCCHHHHHHHhhccCCeeE-EEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCCCC
Q psy13227        168 IRISNLSVNTSENDLEDLVKQFGPTSK-MYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTN  246 (247)
Q Consensus       168 l~V~nLp~~~te~dL~~lF~~fG~I~~-i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp~~  246 (247)
                      |||+|||+++++++|+++|++||.|.+ +.+++++.+|+++|||||+|.+.++|+.|++.|||..++|+.|+|+||.|+.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            799999999999999999999999866 4789999999999999999999999999999999999999999999999876


Q ss_pred             C
Q psy13227        247 Q  247 (247)
Q Consensus       247 ~  247 (247)
                      +
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.2e-20  Score=142.15  Aligned_cols=82  Identities=24%  Similarity=0.476  Sum_probs=78.6

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      .++|||+|||.++++++|+++|++||.|.++.|++++.||+++|||||+|.+.++|+.|++.|||..++|+.|+|+||.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q psy13227        245 TN  246 (247)
Q Consensus       245 ~~  246 (247)
                      +.
T Consensus        88 ~~   89 (104)
T d1p1ta_          88 EK   89 (104)
T ss_dssp             TT
T ss_pred             CC
Confidence            63

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=3.4e-20  Score=138.56  Aligned_cols=86  Identities=24%  Similarity=0.402  Sum_probs=79.5

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCee--------EEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeC
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTS--------KMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYD  233 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~--------~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~  233 (247)
                      ..+.++|||+|||.++++++|+++|+.||.|.        .+.+..++.+|.++|||||+|.+.++|..||+.|||..|+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            45678999999999999999999999999873        5677888889999999999999999999999999999999


Q ss_pred             CeEEEEeecCCCCC
Q psy13227        234 HLILSVDWSKSTNQ  247 (247)
Q Consensus       234 g~~L~V~~akp~~~  247 (247)
                      |+.|+|+||+++++
T Consensus        85 gr~i~V~~a~~~~p   98 (101)
T d2cpea1          85 GSKLKVSLARKKPP   98 (101)
T ss_dssp             TEECEEECSSCCCC
T ss_pred             CEEEEEEEcCCCCC
Confidence            99999999998764

>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=99.82  E-value=2.5e-20  Score=136.07  Aligned_cols=82  Identities=27%  Similarity=0.361  Sum_probs=72.5

Q ss_pred             CccEEEEeecCCCCC-HHHHHHHhhccCCeeEEEEeec-CCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        164 DTTAIRISNLSVNTS-ENDLEDLVKQFGPTSKMYLSRD-KTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       164 ~~~tl~V~nLp~~~t-e~dL~~lF~~fG~I~~i~l~~d-~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      +.++|||+|||++++ +++|+++|++||.|.++.|+.+ +.++.++|||||+|.+.++|+.|++ |||..++|+.|+|+|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            457999999999875 5679999999999999998764 5789999999999999999999996 999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      |+|+|
T Consensus        82 a~~kP   86 (86)
T d2ghpa3          82 ADKKP   86 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            99986

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=5.7e-20  Score=133.00  Aligned_cols=77  Identities=29%  Similarity=0.505  Sum_probs=73.8

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEE
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSV  239 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V  239 (247)
                      +..++|||+|||+++++++|+++|++||.|.++.|++++.+|.++|||||+|.+.++|+.|+..|||..++|+.|+|
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.82  E-value=4e-20  Score=134.30  Aligned_cols=78  Identities=28%  Similarity=0.464  Sum_probs=73.7

Q ss_pred             EEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCC---ceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNG---LCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       168 l~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg---~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      |||+|||+++++++|+++|++||.|.++.|++++.++   .++|||||+|.+.++|++|++.|||..++|+.|+|+||++
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999999987665   5799999999999999999999999999999999999976


Q ss_pred             C
Q psy13227        245 T  245 (247)
Q Consensus       245 ~  245 (247)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            5

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=4.6e-20  Score=136.95  Aligned_cols=85  Identities=24%  Similarity=0.357  Sum_probs=79.6

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhc------CceeCCe
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN------GYGYDHL  235 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~Ln------G~~i~g~  235 (247)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++.||      |..++|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            3566799999999999999999999999999999999999999999999999999999999999987      6778999


Q ss_pred             EEEEeecCCCC
Q psy13227        236 ILSVDWSKSTN  246 (247)
Q Consensus       236 ~L~V~~akp~~  246 (247)
                      .|+|+||+++.
T Consensus        85 ~l~v~~a~~k~   95 (98)
T d1x4ha1          85 QLKVDLAVTRD   95 (98)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999999875

>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=99.82  E-value=3.5e-20  Score=139.81  Aligned_cols=83  Identities=19%  Similarity=0.314  Sum_probs=77.1

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      +.+.++|||+|||+++++++|+++|+.||.|.++.|++++.||.++|||||+|.+.++|++||+.+|+ .++|+.|.|+|
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~   85 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   85 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEE
Confidence            34557899999999999999999999999999999999999999999999999999999999998876 79999999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      +.++
T Consensus        86 a~~~   89 (103)
T d2cqda1          86 AYLG   89 (103)
T ss_dssp             STTT
T ss_pred             cCCC
Confidence            8753

>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=99.81  E-value=7.7e-20  Score=133.04  Aligned_cols=80  Identities=18%  Similarity=0.316  Sum_probs=75.8

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      +.++|||+|||+++++++|+++|+.||.|..+.|++|+.+|.++|||||+|.+.++|++|++ ++++.|+|+.|+|..|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            44689999999999999999999999999999999999999999999999999999999998 69999999999999886


Q ss_pred             C
Q psy13227        244 S  244 (247)
Q Consensus       244 p  244 (247)
                      +
T Consensus        84 s   84 (84)
T d1l3ka1          84 S   84 (84)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.81  E-value=1.2e-19  Score=134.33  Aligned_cols=83  Identities=23%  Similarity=0.374  Sum_probs=77.1

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ....++|||+|||+++++++|+++|+.||.|.++.++.++  +.++|||||+|.+.++|.+|+..|||..++|+.|+|+|
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            3556789999999999999999999999999999999986  34699999999999999999999999999999999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      |+|+.
T Consensus        86 A~~r~   90 (93)
T d2cq3a1          86 ATARV   90 (93)
T ss_dssp             CCSSC
T ss_pred             cCcCC
Confidence            99985

>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=99.81  E-value=6.7e-20  Score=131.41  Aligned_cols=77  Identities=32%  Similarity=0.499  Sum_probs=74.2

Q ss_pred             EEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       167 tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      .|||+|||+++++++|+++|++||.|.++.|..++ +|+++|||||+|.+.++|+.|++.|||..++|+.|+|+++.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            59999999999999999999999999999999996 899999999999999999999999999999999999999863

>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=99.81  E-value=5.9e-20  Score=138.85  Aligned_cols=82  Identities=20%  Similarity=0.342  Sum_probs=78.2

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      +.++|||+|||+++++++|+++|++||.|..+.|++|+.++.++|||||+|.+.++|++|++ +||+.|+|+.|.|.+|+
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            44789999999999999999999999999999999999999999999999999999999997 79999999999999999


Q ss_pred             CCC
Q psy13227        244 STN  246 (247)
Q Consensus       244 p~~  246 (247)
                      |+.
T Consensus        98 ~ke  100 (103)
T d1x4ba1          98 ARE  100 (103)
T ss_dssp             SCC
T ss_pred             ccC
Confidence            874

>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=99.81  E-value=9.5e-21  Score=142.75  Aligned_cols=81  Identities=23%  Similarity=0.331  Sum_probs=77.1

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      +.++|||+|||.++++++|+++|+.||.|.++.|++++.+|+++|||||+|.+.++|..|+. |||..|+|+.|.|.+++
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            34689999999999999999999999999999999999999999999999999999999996 99999999999999987


Q ss_pred             CC
Q psy13227        244 ST  245 (247)
Q Consensus       244 p~  245 (247)
                      ++
T Consensus        96 ~~   97 (101)
T d2cq4a1          96 AE   97 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            65

>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=99.80  E-value=4.2e-20  Score=135.62  Aligned_cols=81  Identities=26%  Similarity=0.357  Sum_probs=75.9

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ...+|||+|||+++++++|+++|+.||.|.++.|+.++  +.++|||||+|.+.++|++|++.|||..++|+.|.|+|++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34689999999999999999999999999999999986  4578999999999999999999999999999999999999


Q ss_pred             CCC
Q psy13227        244 STN  246 (247)
Q Consensus       244 p~~  246 (247)
                      ++.
T Consensus        85 ~~~   87 (89)
T d1cvja2          85 SRK   87 (89)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            875

>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=99.80  E-value=2.3e-20  Score=133.91  Aligned_cols=76  Identities=21%  Similarity=0.359  Sum_probs=73.4

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ++|||+|||+++++++|+++|++||.|.++.|++|+.||+++|||||+|.+.++|++|++ +|++.++|+.|+|.+|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999999999999999999999999999999998 7999999999999986

>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=99.79  E-value=1.8e-19  Score=135.32  Aligned_cols=83  Identities=23%  Similarity=0.362  Sum_probs=77.9

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ...+.++|||+|||.++++++|+++|+.||.|..+.+..+. ++.++|||||+|.+.++|.+|++.|||..|.|+.|.|.
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~   92 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   92 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccC
Confidence            34566899999999999999999999999999999999885 89999999999999999999999999999999999999


Q ss_pred             ecCC
Q psy13227        241 WSKS  244 (247)
Q Consensus       241 ~akp  244 (247)
                      +++|
T Consensus        93 ~~~P   96 (101)
T d1x5oa1          93 PTEP   96 (101)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            9887

>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=99.78  E-value=3.4e-19  Score=132.75  Aligned_cols=79  Identities=16%  Similarity=0.392  Sum_probs=74.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +..++|||+|||.++++++|+++|++||.|.+|.++.+      +|||||+|.+.++|..|+..|||..++|+.|+|.|+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            44578999999999999999999999999999999876      689999999999999999999999999999999999


Q ss_pred             CCCCC
Q psy13227        243 KSTNQ  247 (247)
Q Consensus       243 kp~~~  247 (247)
                      +++++
T Consensus        90 k~~p~   94 (96)
T d1x4ga1          90 KESPD   94 (96)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            98764

>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=99.78  E-value=2.2e-19  Score=127.83  Aligned_cols=75  Identities=23%  Similarity=0.409  Sum_probs=71.7

Q ss_pred             EEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       167 tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .|||+|||+++++++|+++|++||.|..+.|++++.+++++|||||+|.+.++|+.||+ ++++.++|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            38999999999999999999999999999999999999999999999999999999998 7999999999999754

>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=99.78  E-value=8.4e-19  Score=125.38  Aligned_cols=76  Identities=20%  Similarity=0.327  Sum_probs=73.1

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+|||+|||+++++++|+++|++||.|..+.+..++.++.++|||||+|.+.+++.+|+. |||+.|+|+.|+|+.|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            589999999999999999999999999999999999999999999999999999999986 8999999999999976

>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=99.77  E-value=1.6e-18  Score=128.58  Aligned_cols=81  Identities=26%  Similarity=0.479  Sum_probs=73.9

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .+.++|||+|||+++++++|+++|+.||.|..+.+..+   +.++|||||+|.+.++|+.||+.|||+.|+|+.|+|+||
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            44578999999999999999999999999999887654   457899999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      ++..
T Consensus        89 ~~~r   92 (95)
T d1x4aa1          89 RSGR   92 (95)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9753

>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=99.77  E-value=6.5e-20  Score=137.33  Aligned_cols=84  Identities=27%  Similarity=0.407  Sum_probs=79.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +.+++|||+|||.++++++|+++|+.||.|..+.+..+..+|.++|||||.|.+.++|+.|++.|||..++|+.|+|+||
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            34579999999999999999999999999999988888889999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      +++.
T Consensus        96 k~k~   99 (102)
T d2cpxa1          96 KNKK   99 (102)
T ss_dssp             CCCS
T ss_pred             CCcc
Confidence            9874

>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=99.77  E-value=9.7e-20  Score=134.52  Aligned_cols=81  Identities=20%  Similarity=0.287  Sum_probs=75.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ....+|||+|||+++++++|+++|+.||.|..+.|+.+ .+|+++|||||+|.+.++|++||+ |||..++|+.|+|+||
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            45568999999999999999999999999998888766 589999999999999999999996 9999999999999999


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      +++
T Consensus        89 k~k   91 (91)
T d1fjeb1          89 KGR   91 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            875

>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=99.76  E-value=4.9e-19  Score=125.18  Aligned_cols=75  Identities=24%  Similarity=0.388  Sum_probs=72.4

Q ss_pred             EEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       167 tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .|||+|||.++++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|+.|++ |||+.++|+.|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            38999999999999999999999999999999999999999999999999999999997 9999999999999986

>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=99.76  E-value=2.8e-19  Score=127.62  Aligned_cols=75  Identities=20%  Similarity=0.317  Sum_probs=71.5

Q ss_pred             EEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       167 tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      .|||+|||+++++++|+++|++||.|.++.|+.++.|++++|||||+|.+.++|++||+ ++++.++|+.|.|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            48999999999999999999999999999999999999999999999999999999998 5888999999999875

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.76  E-value=1.2e-18  Score=129.44  Aligned_cols=81  Identities=26%  Similarity=0.370  Sum_probs=73.7

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ..+.++|||+|||.++++++|+++|+.||.|..+.     .++.++|||||+|.+.++|+.|++.|||..++|+.|+|+|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568999999999999999999999999876654     3788999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q psy13227        242 SKSTNQ  247 (247)
Q Consensus       242 akp~~~  247 (247)
                      +.|+.+
T Consensus        88 a~~k~~   93 (96)
T d1fjca_          88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             eCCCCC
Confidence            999753

>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=99.76  E-value=1.6e-18  Score=132.25  Aligned_cols=78  Identities=21%  Similarity=0.376  Sum_probs=72.5

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      .+++|||+|||.++++++|+++|++||.|.+|.+..+   +.++|||||+|.+.++|..||+.|||..|+|+.|.|.|+.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3468999999999999999999999999999998754   5678999999999999999999999999999999999987


Q ss_pred             C
Q psy13227        244 S  244 (247)
Q Consensus       244 p  244 (247)
                      +
T Consensus        83 ~   83 (114)
T d2f9da1          83 A   83 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=3.4e-18  Score=124.43  Aligned_cols=77  Identities=16%  Similarity=0.309  Sum_probs=72.9

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      .++|||+|||.++++++|+++|+.||.|..+.|..+. +|.++|||||+|.+.++|++||+ ++|..++|+.|.|.|+.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            4689999999999999999999999999999998885 89999999999999999999997 79999999999999974

>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=99.75  E-value=2.7e-18  Score=124.86  Aligned_cols=77  Identities=26%  Similarity=0.418  Sum_probs=70.8

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ...+|||+|||+++++++|+++|+.||.|..+.+.      .++|||||+|.+.++|..|+..|||..|+|+.|.|+||+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            34689999999999999999999999998877663      457899999999999999999999999999999999999


Q ss_pred             CCC
Q psy13227        244 STN  246 (247)
Q Consensus       244 p~~  246 (247)
                      |+.
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            975

>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=99.75  E-value=3.4e-18  Score=127.77  Aligned_cols=75  Identities=20%  Similarity=0.380  Sum_probs=68.6

Q ss_pred             CCccEEEEeecC-CCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        163 DDTTAIRISNLS-VNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp-~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      ...++|||+||+ ..+++++|+++|++||.|.++.|        ++|||||+|.+.++|++||+.|||..|+|+.|+|+|
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            444679999997 56888999999999999999988        478999999999999999999999999999999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      ++++
T Consensus        85 a~~~   88 (98)
T d1wf2a_          85 AAEP   88 (98)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            9865

>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=99.75  E-value=3.9e-18  Score=128.08  Aligned_cols=81  Identities=20%  Similarity=0.340  Sum_probs=72.7

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecC-CCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDK-TNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~-~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ..++|||+|||+++++++|+++|+.|| +..+.++.+. .++.++|||||+|.+.++|++|+. ||+..|+|+.|+|+||
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEEC
Confidence            457999999999999999999999998 7777777664 478999999999999999987775 9999999999999999


Q ss_pred             CCCC
Q psy13227        243 KSTN  246 (247)
Q Consensus       243 kp~~  246 (247)
                      .++.
T Consensus        92 ~~~~   95 (104)
T d1wi8a_          92 DQAQ   95 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9764

>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=99.75  E-value=1.3e-18  Score=129.13  Aligned_cols=81  Identities=14%  Similarity=0.205  Sum_probs=73.7

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCC-eeEEEEeecC-CCCceeeEEEEEecCHHHHHHHHHHhcCc--eeCCeEEEEee
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGP-TSKMYLSRDK-TNGLCKGFAYIHFKNKADAAKAIQYLNGY--GYDHLILSVDW  241 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~-I~~i~l~~d~-~tg~skGfaFV~F~s~e~A~~Ai~~LnG~--~i~g~~L~V~~  241 (247)
                      +.|||+|||.++++++|+++|+.||. |..+.++.+. .+|+++|||||+|.+.++|..|++.|++.  .++|+.|+|+|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            68999999999999999999999996 8999999885 46899999999999999999999998754  46799999999


Q ss_pred             cCCCC
Q psy13227        242 SKSTN  246 (247)
Q Consensus       242 akp~~  246 (247)
                      |+|+.
T Consensus        82 A~p~~   86 (96)
T d2disa1          82 AEPEI   86 (96)
T ss_dssp             SCSSC
T ss_pred             cCCCC
Confidence            99874

>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=99.74  E-value=2.1e-18  Score=123.79  Aligned_cols=74  Identities=15%  Similarity=0.284  Sum_probs=69.1

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      .++|||+||+  +++++|+++|++||.|.++.+.++      +|||||+|.+.++|..|+..|||..++|+.|+|+|++|
T Consensus         5 ~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   76 (79)
T d2bz2a1           5 GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARK   76 (79)
T ss_dssp             CCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCS
T ss_pred             CCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecC
Confidence            4689999996  899999999999999999998754      57999999999999999999999999999999999999


Q ss_pred             CC
Q psy13227        245 TN  246 (247)
Q Consensus       245 ~~  246 (247)
                      +|
T Consensus        77 ~P   78 (79)
T d2bz2a1          77 QP   78 (79)
T ss_dssp             SC
T ss_pred             CC
Confidence            76

>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=99.74  E-value=3.6e-18  Score=124.55  Aligned_cols=77  Identities=19%  Similarity=0.422  Sum_probs=72.0

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ..++|||+|||.++++++|+++|++||.|.++.+.++      +|||||+|.+.++|+.|+..|||..++|+.|+|+||.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3468999999999999999999999999999999765      5799999999999999999999999999999999999


Q ss_pred             CCC
Q psy13227        244 STN  246 (247)
Q Consensus       244 p~~  246 (247)
                      +..
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            865

>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=99.74  E-value=1.6e-18  Score=124.82  Aligned_cols=76  Identities=25%  Similarity=0.327  Sum_probs=68.8

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCc-eeCCeEEEEeecCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGY-GYDHLILSVDWSKS  244 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~-~i~g~~L~V~~akp  244 (247)
                      ++|||+|||+++++++|+++|++||.|..+.+..      ++|||||+|.+.++|.+|++.|||. .++|+.|+|+||.|
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            5799999999999999999999999987766544      4789999999999999999999996 69999999999999


Q ss_pred             CCC
Q psy13227        245 TNQ  247 (247)
Q Consensus       245 ~~~  247 (247)
                      +.+
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            853

>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=99.73  E-value=4.4e-18  Score=127.77  Aligned_cols=83  Identities=16%  Similarity=0.305  Sum_probs=74.9

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      +.....+|||+|||++++++||+++|..||. ..+.++.+. ++.++|||||+|.+.++|++|++ ||+..|+|+.|+|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            3456679999999999999999999999984 578888885 78999999999999999999997 89999999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      |+.+++
T Consensus        88 ~s~~~~   93 (102)
T d1weza_          88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             EcCCCC
Confidence            998764

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.73  E-value=7.7e-18  Score=121.77  Aligned_cols=77  Identities=19%  Similarity=0.333  Sum_probs=70.5

Q ss_pred             CCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCcee-CCeEEEEe
Q psy13227        162 NDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGY-DHLILSVD  240 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i-~g~~L~V~  240 (247)
                      .+.+++|||+|||.++++++|.++|+.||.|.++.+++++     +|||||+|.+.++|..|+..|||..+ +|+.|+|.
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            3556799999999999999999999999999999997653     68999999999999999999999988 46899999


Q ss_pred             ecC
Q psy13227        241 WSK  243 (247)
Q Consensus       241 ~ak  243 (247)
                      ||+
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            997

>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=99.73  E-value=6.5e-18  Score=123.96  Aligned_cols=78  Identities=19%  Similarity=0.290  Sum_probs=70.7

Q ss_pred             CCccEEEEeecCCCCCHHHH---HHHhhccCCeeEEEEeecCCCCce---eeEEEEEecCHHHHHHHHHHhcCceeCCeE
Q psy13227        163 DDTTAIRISNLSVNTSENDL---EDLVKQFGPTSKMYLSRDKTNGLC---KGFAYIHFKNKADAAKAIQYLNGYGYDHLI  236 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL---~~lF~~fG~I~~i~l~~d~~tg~s---kGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~  236 (247)
                      .+.++|||+|||+++++++|   .++|++||.|.+|.+++++.++.+   +|||||+|.+.++|..|++.|||..++|+.
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEE
Confidence            34468999999999999999   678999999999999999877655   499999999999999999999999999999


Q ss_pred             EEEe
Q psy13227        237 LSVD  240 (247)
Q Consensus       237 L~V~  240 (247)
                      |+|.
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9984

>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=99.73  E-value=4.8e-18  Score=123.38  Aligned_cols=79  Identities=18%  Similarity=0.264  Sum_probs=71.4

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEE-EEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEee
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKM-YLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i-~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~  241 (247)
                      +..++|||+|||.+++++||+++|+.||.+... .+..+ .+|.++|||||+|.+.++|.+|+..|||..++|+.|+|.+
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~-~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeC-CCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            445789999999999999999999999998764 45554 6899999999999999999999999999999999999987


Q ss_pred             c
Q psy13227        242 S  242 (247)
Q Consensus       242 a  242 (247)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=1.4e-18  Score=122.14  Aligned_cols=71  Identities=27%  Similarity=0.473  Sum_probs=68.6

Q ss_pred             EEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEE
Q psy13227        168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILS  238 (247)
Q Consensus       168 l~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~  238 (247)
                      |||+|||.++++++|+++|++||.|..+.+.+++.++.++|||||+|.+.++|++|+..|||..++|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999999999999999999999999999999999999999999998764

>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=99.72  E-value=6.3e-18  Score=127.64  Aligned_cols=76  Identities=21%  Similarity=0.260  Sum_probs=70.5

Q ss_pred             ccEEEEeecCC-CCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        165 TTAIRISNLSV-NTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       165 ~~tl~V~nLp~-~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      +++|||+||++ .+++++|+++|+.||.|.++.|++++     +|||||+|.+.++|.+|++.|||..|+|+.|+|+|++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            46899999965 59999999999999999999998875     7899999999999999999999999999999999997


Q ss_pred             CC
Q psy13227        244 ST  245 (247)
Q Consensus       244 p~  245 (247)
                      .+
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.72  E-value=4.6e-18  Score=128.69  Aligned_cols=76  Identities=22%  Similarity=0.357  Sum_probs=69.9

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ..++|||+|||.++++++|+++|+.||.|.+|.|..      ++|||||+|.+.++|.+|++.|||..|+|+.|.|+|+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            347999999999999999999999999999998743      47899999999999999999999999999999999986


Q ss_pred             CC
Q psy13227        244 ST  245 (247)
Q Consensus       244 p~  245 (247)
                      ..
T Consensus        83 ~~   84 (111)
T d1whxa_          83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=1e-17  Score=122.23  Aligned_cols=79  Identities=25%  Similarity=0.295  Sum_probs=70.7

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCcee-CCeEEEEee
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGY-DHLILSVDW  241 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i-~g~~L~V~~  241 (247)
                      +.+++|||+|||+++++++|+++|++||.|..+.+..+    .++|||||+|.+.++|.+|+..|||..+ +|+.|+|+|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            34579999999999999999999999999988776543    4578999999999999999999999988 589999999


Q ss_pred             cCCC
Q psy13227        242 SKST  245 (247)
Q Consensus       242 akp~  245 (247)
                      |+++
T Consensus        84 sk~~   87 (88)
T d2adca2          84 SKST   87 (88)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            9975

>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=99.72  E-value=5.7e-18  Score=124.53  Aligned_cols=79  Identities=22%  Similarity=0.465  Sum_probs=71.9

Q ss_pred             ccEEEEeecCCCCCHHHHH----HHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        165 TTAIRISNLSVNTSENDLE----DLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~----~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      +++|||+|||++++++||+    ++|++||.|.+|.+..   ++.++|||||+|.+.++|..|++.|||..++|+.|+|.
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3689999999999999986    4689999999988754   57789999999999999999999999999999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      ||+++.
T Consensus        80 ~ak~~~   85 (91)
T d1nu4a_          80 YAKTDS   85 (91)
T ss_dssp             ECSSCC
T ss_pred             EeCCCc
Confidence            999875

>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=99.72  E-value=2.2e-17  Score=122.83  Aligned_cols=79  Identities=27%  Similarity=0.384  Sum_probs=71.8

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCC--eEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDH--LILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g--~~L~V~  240 (247)
                      ...++|||+|||+++++++|+++|++||.|..+.+.++      ++||||+|.+.++|+.|++.|||..|+|  +.|+|+
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            34578999999999999999999999999999998765      5799999999999999999999999986  589999


Q ss_pred             ecCCCCC
Q psy13227        241 WSKSTNQ  247 (247)
Q Consensus       241 ~akp~~~  247 (247)
                      ||++.+.
T Consensus        89 ~ak~~~~   95 (97)
T d1whya_          89 FAKSGPS   95 (97)
T ss_dssp             ECCCCCC
T ss_pred             eCCCCCC
Confidence            9998763

>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=99.72  E-value=1.5e-17  Score=125.05  Aligned_cols=84  Identities=14%  Similarity=0.184  Sum_probs=76.2

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ..++..+|||+|||++++++||+++|..||.+....++.+..++.++|||||+|.+.++|++|++ +|+..|+|+.|+|.
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIF   89 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEE
Confidence            34556689999999999999999999999999887677776799999999999999999999997 89999999999999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      +++++
T Consensus        90 ~~~~~   94 (104)
T d1wg5a_          90 KSSRA   94 (104)
T ss_dssp             EECTT
T ss_pred             ECCHH
Confidence            99875

>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=99.70  E-value=8.4e-18  Score=122.94  Aligned_cols=76  Identities=11%  Similarity=0.307  Sum_probs=69.3

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      .+++|||+|||+++++++|+++|++||.|.++.+.     ..++|||||+|.+.++|+.|+.  +++.++|+.|+|+|++
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            45799999999999999999999999999998764     3468999999999999999986  8899999999999999


Q ss_pred             CCC
Q psy13227        244 STN  246 (247)
Q Consensus       244 p~~  246 (247)
                      |+.
T Consensus        77 ~k~   79 (88)
T d1wf0a_          77 PKH   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            875

>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=99.70  E-value=4.4e-17  Score=115.79  Aligned_cols=74  Identities=20%  Similarity=0.190  Sum_probs=68.4

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ++|||+|||+++++++|+++|+.||.|..+.+..++.+  .+|||||+|.+.++|++|+. +|+..|+|+.|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            58999999999999999999999999999999998643  45799999999999999996 8999999999999865

>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=99.70  E-value=2.3e-17  Score=123.16  Aligned_cols=75  Identities=16%  Similarity=0.242  Sum_probs=69.1

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ...+|||+|||+++++++|+++|+.||.|.++.+.+       +|||||+|.+.++|++||+.|||..++|+.|+|.|++
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            346899999999999999999999999999998853       4799999999999999999999999999999999987


Q ss_pred             CC
Q psy13227        244 ST  245 (247)
Q Consensus       244 p~  245 (247)
                      ++
T Consensus        87 ~~   88 (98)
T d1wg4a_          87 VY   88 (98)
T ss_dssp             EE
T ss_pred             cC
Confidence            54

>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=99.69  E-value=1.7e-17  Score=121.38  Aligned_cols=74  Identities=23%  Similarity=0.381  Sum_probs=65.7

Q ss_pred             ccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        165 TTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       165 ~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      +++|||+|||++++++||+++|.+|| +..+.+      +.++|||||+|.+.++|+.|++.|||+.++|+.|+|+|+++
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999 222332      45689999999999999999999999999999999999986


Q ss_pred             C
Q psy13227        245 T  245 (247)
Q Consensus       245 ~  245 (247)
                      +
T Consensus        78 ~   78 (88)
T d1wg1a_          78 D   78 (88)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1e-17  Score=122.19  Aligned_cols=71  Identities=21%  Similarity=0.283  Sum_probs=66.2

Q ss_pred             EEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        167 AIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       167 tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      .|||+|||+++++++|+++|+.||.|.++.+..+       |||||+|.+.++|+.||..|||..|+|+.|+|.++++
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            5999999999999999999999999999998654       7999999999999999999999999999998888754

>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=99.68  E-value=4.4e-17  Score=123.33  Aligned_cols=79  Identities=22%  Similarity=0.255  Sum_probs=72.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCcee--CCeEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGY--DHLILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i--~g~~L~V~  240 (247)
                      ....+|||+|||+.+++++|+++|++||.|.++.+..++    ++|||||+|.+.++|+.|+..|||..+  .++.|+|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            445689999999999999999999999999999998774    489999999999999999999999998  57899999


Q ss_pred             ecCCC
Q psy13227        241 WSKST  245 (247)
Q Consensus       241 ~akp~  245 (247)
                      |++++
T Consensus        81 ~s~~~   85 (108)
T d2adba1          81 FSKLT   85 (108)
T ss_dssp             ECSSC
T ss_pred             ecCCc
Confidence            99875

>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=99.67  E-value=4.5e-17  Score=122.10  Aligned_cols=80  Identities=19%  Similarity=0.181  Sum_probs=71.0

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ...+|||+|||+++++++|+++|..||.|..+.++....+|.++|||||+|.+.++|++||+ |||..|+|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            34689999999999999999999999998764444444699999999999999999999997 99999999999999875


Q ss_pred             C
Q psy13227        244 S  244 (247)
Q Consensus       244 p  244 (247)
                      +
T Consensus        86 ~   86 (103)
T d2cpya1          86 L   86 (103)
T ss_dssp             H
T ss_pred             H
Confidence            3

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=1.5e-16  Score=113.00  Aligned_cols=72  Identities=21%  Similarity=0.312  Sum_probs=64.7

Q ss_pred             EEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecCCCC
Q psy13227        168 IRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSKSTN  246 (247)
Q Consensus       168 l~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~akp~~  246 (247)
                      |||+|||+++++++|+++|++|| +..+.+      ++++|||||+|.+.++|++|+..|||..++|+.|+|+|++..+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 444443      4568999999999999999999999999999999999997653

>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=99.64  E-value=4.7e-16  Score=126.28  Aligned_cols=82  Identities=20%  Similarity=0.288  Sum_probs=78.0

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|.+|+. ++++.++|+.|+|.||
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A  173 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA  173 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEEC
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEec
Confidence            455789999999999999999999999999999999999999999999999999999999998 7999999999999999


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      .|+
T Consensus       174 ~~k  176 (183)
T d1u1qa_         174 LSK  176 (183)
T ss_dssp             CCH
T ss_pred             CCc
Confidence            886

>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=99.64  E-value=6.9e-16  Score=112.37  Aligned_cols=78  Identities=14%  Similarity=0.284  Sum_probs=70.2

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHh--cCceeCCeEEEEe
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL--NGYGYDHLILSVD  240 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~L--nG~~i~g~~L~V~  240 (247)
                      ..+++|||+|||.++++++|+++|++||.|..+.+..+      +|||||+|.+.++|++|++.+  ++..+.|+.|+|.
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            45679999999999999999999999999999988765      479999999999999999865  5678999999999


Q ss_pred             ecCCCC
Q psy13227        241 WSKSTN  246 (247)
Q Consensus       241 ~akp~~  246 (247)
                      |++.+.
T Consensus        80 ~sk~~~   85 (88)
T d2cq1a1          80 YSNHKE   85 (88)
T ss_dssp             ECSCSS
T ss_pred             ECCCCC
Confidence            998763

>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=99.63  E-value=9.8e-16  Score=115.06  Aligned_cols=79  Identities=16%  Similarity=0.221  Sum_probs=70.2

Q ss_pred             CCCCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHh--cCceeCCeEEE
Q psy13227        161 RNDDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL--NGYGYDHLILS  238 (247)
Q Consensus       161 ~~~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~L--nG~~i~g~~L~  238 (247)
                      ....+.+|||+|||+.+++++|.++|.+||.|.++.+.++      +|||||+|.+.++|+.|+..|  ++..++|+.|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            3456779999999999999999999999999999998754      579999999999999999987  45668899999


Q ss_pred             EeecCCC
Q psy13227        239 VDWSKST  245 (247)
Q Consensus       239 V~~akp~  245 (247)
                      |.|++.+
T Consensus        85 v~~s~~~   91 (104)
T d1wexa_          85 FNYSTSK   91 (104)
T ss_dssp             EEECSSS
T ss_pred             EEEcCCC
Confidence            9999864

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=5.5e-16  Score=115.70  Aligned_cols=78  Identities=22%  Similarity=0.316  Sum_probs=70.0

Q ss_pred             CCccEEEEeecCCC-CCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHH--HhcCceeCCeEEEE
Q psy13227        163 DDTTAIRISNLSVN-TSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQ--YLNGYGYDHLILSV  239 (247)
Q Consensus       163 ~~~~tl~V~nLp~~-~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~--~LnG~~i~g~~L~V  239 (247)
                      ..+++|||+|||.+ +++++|.++|++||.|.++.+.++      +|||||+|.+.++|.+|++  .+++..++|+.|+|
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            45679999999975 899999999999999999999765      5799999999999999998  47888899999999


Q ss_pred             eecCCCC
Q psy13227        240 DWSKSTN  246 (247)
Q Consensus       240 ~~akp~~  246 (247)
                      .||+.+.
T Consensus        90 ~~s~~~~   96 (99)
T d1x4fa1          90 DLSEKYK   96 (99)
T ss_dssp             EEECSCS
T ss_pred             EEcCCcc
Confidence            9998764

>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=99.62  E-value=1.6e-16  Score=121.05  Aligned_cols=81  Identities=15%  Similarity=0.206  Sum_probs=72.3

Q ss_pred             CCccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        163 DDTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      ....+|||+|||+++++++|+++|+.||.+..+.++.+..+|.++|||||+|.+.++|++|+. |||..|+|+.|.|.++
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            455689999999999999999999999998765555555699999999999999999999997 9999999999999987


Q ss_pred             CC
Q psy13227        243 KS  244 (247)
Q Consensus       243 kp  244 (247)
                      .+
T Consensus        95 ~~   96 (112)
T d1wela1          95 TK   96 (112)
T ss_dssp             CH
T ss_pred             Ch
Confidence            64

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=1.6e-15  Score=110.98  Aligned_cols=79  Identities=19%  Similarity=0.210  Sum_probs=70.0

Q ss_pred             CCCccEEEEeecCCC-CCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHh--cCceeCCeEEE
Q psy13227        162 NDDTTAIRISNLSVN-TSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYL--NGYGYDHLILS  238 (247)
Q Consensus       162 ~~~~~tl~V~nLp~~-~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~L--nG~~i~g~~L~  238 (247)
                      .+.+.+|||+|||.. ++++||.++|++||.|.++.+..+      +++|||.|.+.++|..|++.|  ++..++|+.|+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            355679999999986 789999999999999999999766      369999999999999999966  67789999999


Q ss_pred             EeecCCCC
Q psy13227        239 VDWSKSTN  246 (247)
Q Consensus       239 V~~akp~~  246 (247)
                      |+||++..
T Consensus        79 V~~s~~~~   86 (89)
T d1x4da1          79 VHLSQKYK   86 (89)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCcc
Confidence            99998653

>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=99.59  E-value=6.4e-16  Score=116.55  Aligned_cols=78  Identities=14%  Similarity=0.169  Sum_probs=68.7

Q ss_pred             CCccEEEEeecCCCC-CH----HHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEE
Q psy13227        163 DDTTAIRISNLSVNT-SE----NDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLIL  237 (247)
Q Consensus       163 ~~~~tl~V~nLp~~~-te----~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L  237 (247)
                      ...++|||+||+.++ ++    ++|+++|+.||.|.++.+.+.      +|||||+|.+.++|.+|+..|||..++|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            345789999999986 43    458899999999999998753      6799999999999999999999999999999


Q ss_pred             EEeecCCCC
Q psy13227        238 SVDWSKSTN  246 (247)
Q Consensus       238 ~V~~akp~~  246 (247)
                      +|.|++++.
T Consensus        77 ~v~~a~~~~   85 (104)
T d1weya_          77 KLYFAQTLH   85 (104)
T ss_dssp             EEECCCCSS
T ss_pred             EEeecccCC
Confidence            999998764

>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=99.55  E-value=4.7e-16  Score=117.29  Aligned_cols=76  Identities=17%  Similarity=0.301  Sum_probs=72.1

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeec
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWS  242 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~a  242 (247)
                      +.++|.++..+++|++|+++|++||.|.+|.|+++. +|.++|||||.|.+.++|.+|+..|||..|+|+.|.|+|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            468889999999999999999999999999999884 8999999999999999999999999999999999999986

>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=99.55  E-value=5.2e-17  Score=118.85  Aligned_cols=78  Identities=13%  Similarity=0.250  Sum_probs=68.4

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEe-----ecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEe
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLS-----RDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVD  240 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~-----~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~  240 (247)
                      ++|||+|||.++++++|+++|+.||.+..+.+.     .+..++.++|||||+|.+.++|+.|+. |||..++|+.|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            479999999999999999999999987665443     344678899999999999999999996 99999999999998


Q ss_pred             ecCC
Q psy13227        241 WSKS  244 (247)
Q Consensus       241 ~akp  244 (247)
                      .++.
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            7654

>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=99.48  E-value=6.9e-14  Score=113.20  Aligned_cols=81  Identities=17%  Similarity=0.312  Sum_probs=73.5

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      +.++|||+|||+++++++|+++|++||.|.++.++++..+|.++|||||.|.+.++|..|+. +++..++++.+.+.+..
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhh
Confidence            44799999999999999999999999999999999999999999999999999999999998 56777888888887765


Q ss_pred             CC
Q psy13227        244 ST  245 (247)
Q Consensus       244 p~  245 (247)
                      ++
T Consensus        84 ~~   85 (183)
T d1u1qa_          84 SR   85 (183)
T ss_dssp             CT
T ss_pred             hc
Confidence            44

>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=99.41  E-value=1.1e-13  Score=105.37  Aligned_cols=73  Identities=21%  Similarity=0.153  Sum_probs=64.1

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCH-HHHHHHHHHhcCceeCCeEEEEeecCC
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNK-ADAAKAIQYLNGYGYDHLILSVDWSKS  244 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~-e~A~~Ai~~LnG~~i~g~~L~V~~akp  244 (247)
                      ..+||+|||+.+++++|+++|++||.|.+|.|+++      +|||||.|.+. ++|..|+..||+..+.++.+.|.|+.+
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            45699999999999999999999999999999754      68999999985 789999999999998877777776644

>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=99.41  E-value=3.9e-13  Score=99.99  Aligned_cols=80  Identities=21%  Similarity=0.305  Sum_probs=68.6

Q ss_pred             CCccEEEEeec--CCCCC---------HHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCce
Q psy13227        163 DDTTAIRISNL--SVNTS---------ENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYG  231 (247)
Q Consensus       163 ~~~~tl~V~nL--p~~~t---------e~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~  231 (247)
                      ..+.+|+|.||  |.++.         ++||++.|++||.|..+.+..+    ..+||+||.|.+.++|.+|+..|||..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            45579999999  54432         2578899999999999988665    357999999999999999999999999


Q ss_pred             eCCeEEEEeecCCCC
Q psy13227        232 YDHLILSVDWSKSTN  246 (247)
Q Consensus       232 i~g~~L~V~~akp~~  246 (247)
                      ++|+.|.|+|+.++.
T Consensus        82 ~~gr~i~v~~~~g~~   96 (99)
T d2dita1          82 FGGRQITAQAWDGTT   96 (99)
T ss_dssp             ETTEECEEEECCSCC
T ss_pred             ECCEEEEEEEeCCcC
Confidence            999999999988764

>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=99.39  E-value=3.5e-13  Score=100.64  Aligned_cols=64  Identities=19%  Similarity=0.380  Sum_probs=57.4

Q ss_pred             CCccEEEEee--cCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCcee
Q psy13227        163 DDTTAIRISN--LSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGY  232 (247)
Q Consensus       163 ~~~~tl~V~n--Lp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i  232 (247)
                      ....+|+|.|  ||.++++++|+++|++||.|..+.+..+      +|||||+|.+.++|..|+..|||..+
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            3456788855  9999999999999999999999988765      57999999999999999999999986

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.32  E-value=1.3e-12  Score=93.80  Aligned_cols=74  Identities=19%  Similarity=0.223  Sum_probs=62.2

Q ss_pred             CccEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCe-EEEEeec
Q psy13227        164 DTTAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHL-ILSVDWS  242 (247)
Q Consensus       164 ~~~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~-~L~V~~a  242 (247)
                      +.+.|+|.+||++.+++.| ++|++||.|.++.+.      ..+|||||.|.++++|++||+ +||..++|+ +|.|...
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            3467999999999886555 579999999999874      346899999999999999997 999999997 5678776


Q ss_pred             CCC
Q psy13227        243 KST  245 (247)
Q Consensus       243 kp~  245 (247)
                      ..+
T Consensus        75 ~~k   77 (81)
T d1wwha1          75 IDK   77 (81)
T ss_dssp             CCH
T ss_pred             CCh
Confidence            543

>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=99.21  E-value=6e-12  Score=94.09  Aligned_cols=80  Identities=18%  Similarity=0.292  Sum_probs=68.1

Q ss_pred             ccEEEEeec--CCCCC--------HHHHHHHhhccCCeeEEEEeecCCCC--ceeeEEEEEecCHHHHHHHHHHhcCcee
Q psy13227        165 TTAIRISNL--SVNTS--------ENDLEDLVKQFGPTSKMYLSRDKTNG--LCKGFAYIHFKNKADAAKAIQYLNGYGY  232 (247)
Q Consensus       165 ~~tl~V~nL--p~~~t--------e~dL~~lF~~fG~I~~i~l~~d~~tg--~skGfaFV~F~s~e~A~~Ai~~LnG~~i  232 (247)
                      +..|.|.|+  +..+.        .+||++.|++||.|.+|.|+++..+.  ...|++||.|.+.++|.+|+..|||..+
T Consensus         4 s~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f   83 (104)
T d1o0pa_           4 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF   83 (104)
T ss_dssp             CSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCS
T ss_pred             CcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEE
Confidence            568999999  55443        25688999999999999998876443  3468999999999999999999999999


Q ss_pred             CCeEEEEeecCC
Q psy13227        233 DHLILSVDWSKS  244 (247)
Q Consensus       233 ~g~~L~V~~akp  244 (247)
                      +|+.|.|.|..+
T Consensus        84 ~gR~v~v~f~~~   95 (104)
T d1o0pa_          84 ANRVVVTKYCDP   95 (104)
T ss_dssp             SSSCCEEEEECH
T ss_pred             CCeEEEEEEcCH
Confidence            999999999764

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.14  E-value=0.0014  Score=46.73  Aligned_cols=77  Identities=18%  Similarity=0.270  Sum_probs=61.8

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCc--eeeEEEEEecCHHHHHHHHHHhcCceeCC-----eEEE
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGL--CKGFAYIHFKNKADAAKAIQYLNGYGYDH-----LILS  238 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~--skGfaFV~F~s~e~A~~Ai~~LnG~~i~g-----~~L~  238 (247)
                      +.|-|.+||+.++|+++.+.++..|.+...+....+.+..  .-.-|||.|.+.++...-.+.++|+.+.+     .+-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            6799999999999999999999999988877766544332  23679999999999999999999998642     1335


Q ss_pred             Eeec
Q psy13227        239 VDWS  242 (247)
Q Consensus       239 V~~a  242 (247)
                      |++|
T Consensus        82 VE~A   85 (91)
T d1uw4a_          82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            6665

>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=96.91  E-value=0.0019  Score=45.84  Aligned_cols=70  Identities=11%  Similarity=0.220  Sum_probs=55.8

Q ss_pred             cEEEEeecCCCC------CH---HHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeE
Q psy13227        166 TAIRISNLSVNT------SE---NDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLI  236 (247)
Q Consensus       166 ~tl~V~nLp~~~------te---~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~  236 (247)
                      .||-|.=.+++.      ++   .+|.+.|..||.|.-++++.+        -.+|+|.+-+.|..|+. |+|..+.|+.
T Consensus        16 gTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G~~   86 (95)
T d1ufwa_          16 ATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKGRA   86 (95)
T ss_dssp             CEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETTEE
T ss_pred             cEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcceE
Confidence            467776555333      33   356778899999998988877        58999999999999999 8999999999


Q ss_pred             EEEeecCC
Q psy13227        237 LSVDWSKS  244 (247)
Q Consensus       237 L~V~~akp  244 (247)
                      |.|....|
T Consensus        87 l~It~~~~   94 (95)
T d1ufwa_          87 VKISGPSS   94 (95)
T ss_dssp             EEEECCCC
T ss_pred             EEEecCCC
Confidence            99876443

>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=96.78  E-value=0.0044  Score=41.90  Aligned_cols=65  Identities=20%  Similarity=0.225  Sum_probs=53.1

Q ss_pred             CCCHHHH----HHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhcCceeCCeEEEEeecC
Q psy13227        176 NTSENDL----EDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLNGYGYDHLILSVDWSK  243 (247)
Q Consensus       176 ~~te~dL----~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~LnG~~i~g~~L~V~~ak  243 (247)
                      ..++.+|    ...|.+++.|.++.+.... .|.  -.|-|...+.++|.-|+..|+.+.+++++|.|.++.
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~-dg~--~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHT-DYQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCC-STT--CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEecc-CCc--EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            3445554    4678999999999886553 333  378999999999999999999999999999999875

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.36  E-value=0.01  Score=42.49  Aligned_cols=55  Identities=15%  Similarity=0.206  Sum_probs=47.3

Q ss_pred             cEEEEeecCCCCCHHHHHHHhhccCCeeEEEEeecCCCCceeeEEEEEecCHHHHHHHHHHhc
Q psy13227        166 TAIRISNLSVNTSENDLEDLVKQFGPTSKMYLSRDKTNGLCKGFAYIHFKNKADAAKAIQYLN  228 (247)
Q Consensus       166 ~tl~V~nLp~~~te~dL~~lF~~fG~I~~i~l~~d~~tg~skGfaFV~F~s~e~A~~Ai~~Ln  228 (247)
                      ..||.-.+|..+...||.++|++||.|. |.++-+.       -|||...++++++.++..++
T Consensus        16 dHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          16 DHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             ceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            4689999999999999999999999976 5555553       79999999999999988655

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=88.89  E-value=0.068  Score=31.28  Aligned_cols=19  Identities=37%  Similarity=0.899  Sum_probs=15.9

Q ss_pred             eeeeeccC-CccccCCCCcc
Q psy13227         78 ISCRTCKG-AHFTNNCPFKD   96 (247)
Q Consensus        78 ~~Cr~C~g-~h~t~~CP~k~   96 (247)
                      -.|-+|++ .||...||-+-
T Consensus        11 DQCAyCke~GHW~~dCPkkp   30 (40)
T d1a6bb_          11 DQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             SSCSSSCCTTCCTTSCSSSC
T ss_pred             hhhHHHhhcCchhhhCccCC
Confidence            46999976 89999999653