Psyllid ID: psy4086

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-----
Protein Sequence
MTMQLYHRVSNATSPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADSQLAYEHPMTPIPATIQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHMSQVEVLK
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHHccccEEEEcccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEEcccccccEEEEEEcccHHHHHHHHHHHcccccccccccEEEEEccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHHHcccEEEEEccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEEccccccccEEEEEcccHHHHHHHHHHHccccccccccEEEEEEccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mtmqlyhrvsnatspanthsssssntgsqnggthpittnnvqhngspgtptgpeqlsktnlyirgltqdttdkdlinmcsqygpiistkAILDKttnkcrgygfvdfesGGYALAAVKALQDKGIHAQMARqqeqdptnlyianlplnfkecDLESLLAKYVTVVSTRIlrdnnntskgvgfarleskdKCDQMIQLfngstlpgskepllvkfadsglkkrgagaggpniyrgpgaevrlwgrdsadsqlayehpmtpipatiqyqrftagpggtghipagytpwvptqyvmpaphmsqvevlk
Flexible Loop (DISEMBL)
MTMQLYHRVSNatspanthsssssntgsqnGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVStrilrdnnntskgvgfarleskDKCDQMIQLFngstlpgskepLLVKFADSGLKkrgagaggpniyrgPGAEVRLWGRDSADSQLAYEHPMTPIPATIQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHMSQVEVLK
Low Complexity Region (SEG)
MTMQLYHRVsnatspanthsssssntgsqnggthPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADSQLAYEHPMTPIPATIQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHMSQVEVLK
Disordered region (IsUnstruct)
***********************************************************NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA**********TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGS********LLVKFA**************NIYRGPGAEVRLWGRDSADSQLAYEHPMTPIPATIQYQRFTAGPGGTGHIPAGYTPWVPTQYVM************
Disordered Region (DISOPRED)
************************************************************LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDK*****************YIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF*******************************************************************************************
Disordered Region (DISEMBL)
******************************GGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADSQLAYEHPMTPIPATIQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHMSQVEVLK
Disordered Region (DISPRO)
*****YH**SNAT****T*************************************LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADSQLAYEHPMTPIPATIQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHMSQVEVL*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTMQLYHRVSNATSPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADSQLAYEHPMTPIPATIQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHMSQVEVLK
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	305	2.2.26 [Sep-21-2011]
B4MM23	581	Protein alan shepard OS=D	N/A	N/A	0.773	0.406	0.588	3e-78
B4IX08	609	Protein alan shepard OS=D	N/A	N/A	0.767	0.384	0.593	4e-77
B4LFQ9	595	Protein alan shepard OS=D	N/A	N/A	0.767	0.393	0.593	6e-77
B3NGA1	582	Protein alan shepard OS=D	N/A	N/A	0.767	0.402	0.581	4e-76
B4PIS2	582	Protein alan shepard OS=D	N/A	N/A	0.767	0.402	0.581	5e-76
Q8MSV2	578	Protein alan shepard OS=D	yes	N/A	0.727	0.384	0.594	1e-75
B4HUE4	579	Protein alan shepard OS=D	N/A	N/A	0.727	0.383	0.594	1e-75
B4QRJ0	576	Protein alan shepard OS=D	N/A	N/A	0.721	0.381	0.590	3e-73
B4KX02	592	Protein alan shepard OS=D	N/A	N/A	0.767	0.395	0.561	1e-72
B3M3R5	597	Protein alan shepard OS=D	N/A	N/A	0.760	0.388	0.546	1e-69

>sp|B4MM23|SHEP_DROWI Protein alan shepard OS=Drosophila willistoni GN=shep PE=3 SV=2

 Score =  291 bits (746), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 153/260 (58%), Positives = 188/260 (72%), Gaps = 24/260 (9%)

Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
           EQLSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAILDKTTNKC+GYGFVDFE   YA
Sbjct: 232 EQLSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAYA 291

Query: 114 LAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN 173
             AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++L+KY  VVSTRILRD 
Sbjct: 292 ENAVKGLQAKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLSKYGQVVSTRILRDQ 351

Query: 174 NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYR 233
              SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++
Sbjct: 352 QMNSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFK 404

Query: 234 GPGAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAG 282
            P    R W   SA+   +AY+  +          TPI   + Y RF+A P   G  P  
Sbjct: 405 TPDPNTRAWRDVSAEGIPVAYDPTLQQNGVSVNVGTPI--GVPYSRFSAPP--VGGYPVA 460

Query: 283 YTPWVPTQYVMPAPHMSQVE 302
            + W+P  Y+M  P ++QV+
Sbjct: 461 GSQWIPG-YMMTQP-ITQVD 478

Has a role in the perception of gravity.
Drosophila willistoni (taxid: 7260)

>sp|B4IX08|SHEP_DROGR Protein alan shepard OS=Drosophila grimshawi GN=shep PE=3 SV=1

 Score =  288 bits (736), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 153/258 (59%), Positives = 184/258 (71%), Gaps = 24/258 (9%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           LSKTNLYIRGL Q TTDKDLINMC+QYG IISTKAILDKTTNKC+GYGFVDFE   YA  
Sbjct: 254 LSKTNLYIRGLQQGTTDKDLINMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAYAEG 313

Query: 116 AVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN 175
           AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++LAKY  VVSTRILRD   
Sbjct: 314 AVKGLQAKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLAKYGQVVSTRILRDQQM 373

Query: 176 TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGP 235
            SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++ P
Sbjct: 374 NSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFKTP 426

Query: 236 GAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAGYT 284
               R W   SA+   +AY+  M          TPI   + Y RF  G    G  P   +
Sbjct: 427 DPSARAWRDVSAEGIPVAYDPSMQQNGVSVNVGTPI--GVPYSRF--GAPQVGGYPVAGS 482

Query: 285 PWVPTQYVMPAPHMSQVE 302
            W+P  Y+M  P ++QV+
Sbjct: 483 QWIPG-YMMTQP-ITQVD 498

Has a role in the perception of gravity.

Drosophila grimshawi (taxid: 7222)

>sp|B4LFQ9|SHEP_DROVI Protein alan shepard OS=Drosophila virilis GN=shep PE=3 SV=2

 Score =  287 bits (735), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 153/258 (59%), Positives = 184/258 (71%), Gaps = 24/258 (9%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           LSKTNLYIRGL Q TTDKDLINMC+QYG IISTKAILDKTTNKC+GYGFVDFE   YA  
Sbjct: 240 LSKTNLYIRGLQQGTTDKDLINMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAYAEG 299

Query: 116 AVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN 175
           AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++LAKY  VVSTRILRD   
Sbjct: 300 AVKGLQAKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLAKYGQVVSTRILRDQQM 359

Query: 176 TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGP 235
            SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++ P
Sbjct: 360 NSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFKTP 412

Query: 236 GAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAGYT 284
               R W   SA+   +AY+  M          TPI   + Y RF  G    G  P   +
Sbjct: 413 DPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI--GVPYSRF--GAPQVGGYPVAGS 468

Query: 285 PWVPTQYVMPAPHMSQVE 302
            W+P  Y+M  P ++QV+
Sbjct: 469 QWIPG-YMMTQP-ITQVD 484

Has a role in the perception of gravity.

Drosophila virilis (taxid: 7244)

>sp|B3NGA1|SHEP_DROER Protein alan shepard OS=Drosophila erecta GN=shep PE=3 SV=1

 Score =  284 bits (727), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 150/258 (58%), Positives = 185/258 (71%), Gaps = 24/258 (9%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           LSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAILDKTTNKC+GYGFVDFE   +A  
Sbjct: 228 LSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAFAEC 287

Query: 116 AVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN 175
           AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++L+KY  VVSTRILRD   
Sbjct: 288 AVKGLQGKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLSKYGQVVSTRILRDQQM 347

Query: 176 TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGP 235
            SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++ P
Sbjct: 348 NSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFKTP 400

Query: 236 GAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAGYT 284
               R W   SA+   +AY+  M          TPI   + Y RF+A     G  P   +
Sbjct: 401 DPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI--GVPYSRFSA--PQVGGYPVAGS 456

Query: 285 PWVPTQYVMPAPHMSQVE 302
            W+P  Y+M  P ++QV+
Sbjct: 457 QWIPG-YMMTQP-ITQVD 472

Has a role in the perception of gravity.

Drosophila erecta (taxid: 7220)

>sp|B4PIS2|SHEP_DROYA Protein alan shepard OS=Drosophila yakuba GN=shep PE=3 SV=1

 Score =  284 bits (727), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 150/258 (58%), Positives = 185/258 (71%), Gaps = 24/258 (9%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           LSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAILDKTTNKC+GYGFVDFE   +A  
Sbjct: 228 LSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAFAEC 287

Query: 116 AVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN 175
           AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++L+KY  VVSTRILRD   
Sbjct: 288 AVKGLQGKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLSKYGQVVSTRILRDQQM 347

Query: 176 TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGP 235
            SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++ P
Sbjct: 348 NSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFKTP 400

Query: 236 GAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAGYT 284
               R W   SA+   +AY+  M          TPI   + Y RF+A     G  P   +
Sbjct: 401 DPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI--GVPYSRFSA--PQVGGYPVAGS 456

Query: 285 PWVPTQYVMPAPHMSQVE 302
            W+P  Y+M  P ++QV+
Sbjct: 457 QWIPG-YMMTQP-ITQVD 472

Has a role in the perception of gravity.

Drosophila yakuba (taxid: 7245)

>sp|Q8MSV2|SHEP_DROME Protein alan shepard OS=Drosophila melanogaster GN=shep PE=1 SV=1

 Score =  283 bits (724), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 145/244 (59%), Positives = 176/244 (72%), Gaps = 22/244 (9%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           LSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAILDKTTNKC+GYGFVDFE   +A  
Sbjct: 228 LSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAFAEC 287

Query: 116 AVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN 175
           AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++L+KY  VVSTRILRD   
Sbjct: 288 AVKGLQGKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLSKYGQVVSTRILRDQQM 347

Query: 176 TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGP 235
            SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++ P
Sbjct: 348 NSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFKTP 400

Query: 236 GAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAGYT 284
               R W   SA+   +AY+  M          TPI   + Y RF+A     G  P   +
Sbjct: 401 DPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI--GVPYSRFSA--PQVGGYPVAGS 456

Query: 285 PWVP 288
            W+P
Sbjct: 457 QWIP 460

Has a role in the perception of gravity.

Drosophila melanogaster (taxid: 7227)

>sp|B4HUE4|SHEP_DROSE Protein alan shepard OS=Drosophila sechellia GN=shep PE=3 SV=1

 Score =  283 bits (724), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 145/244 (59%), Positives = 176/244 (72%), Gaps = 22/244 (9%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           LSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAILDKTTNKC+GYGFVDFE   +A  
Sbjct: 228 LSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAFAEC 287

Query: 116 AVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN 175
           AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++L+KY  VVSTRILRD   
Sbjct: 288 AVKGLQGKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLSKYGQVVSTRILRDQQM 347

Query: 176 TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGP 235
            SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++ P
Sbjct: 348 NSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFKTP 400

Query: 236 GAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAGYT 284
               R W   SA+   +AY+  M          TPI   + Y RF+A     G  P   +
Sbjct: 401 DPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI--GVPYSRFSA--PQVGGYPVAGS 456

Query: 285 PWVP 288
            W+P
Sbjct: 457 QWIP 460

Has a role in the perception of gravity.

Drosophila sechellia (taxid: 7238)

>sp|B4QRJ0|SHEP_DROSI Protein alan shepard OS=Drosophila simulans GN=shep PE=3 SV=1

 Score =  275 bits (704), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 144/244 (59%), Positives = 174/244 (71%), Gaps = 24/244 (9%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           LSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAILDKTTNKC  YGFVDFE   +A  
Sbjct: 228 LSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAILDKTTNKC--YGFVDFEQPAFAEC 285

Query: 116 AVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN 175
           AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++L+KY  VVSTRILRD   
Sbjct: 286 AVKGLQGKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLSKYGQVVSTRILRDQQM 345

Query: 176 TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGP 235
            SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++ P
Sbjct: 346 NSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFKTP 398

Query: 236 GAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAGYT 284
               R W   SA+   +AY+  M          TPI   + Y RF+A     G  P   +
Sbjct: 399 DPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI--GVPYSRFSA--PQVGGYPVAGS 454

Query: 285 PWVP 288
            W+P
Sbjct: 455 QWIP 458

Has a role in the perception of gravity.

Drosophila simulans (taxid: 7240)

>sp|B4KX02|SHEP_DROMO Protein alan shepard OS=Drosophila mojavensis GN=shep PE=3 SV=1

 Score =  273 bits (698), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 151/269 (56%), Positives = 183/269 (68%), Gaps = 35/269 (13%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           LSKTNLYIRGL Q TTDKDLINMC+QYG IISTKAILDKTTNKC+GYGFVDFE   YA  
Sbjct: 226 LSKTNLYIRGLQQGTTDKDLINMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAYAEG 285

Query: 116 AVKALQDKGIHAQMAR-----------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTV 164
           AVK LQ KG+ AQMA+           QQEQDPTNLYIANLP +FKE DLE++LAK+  V
Sbjct: 286 AVKGLQAKGVQAQMAKVGIWVLHRPAIQQEQDPTNLYIANLPPHFKETDLEAMLAKFGQV 345

Query: 165 VSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGA 224
           VSTRILRD    SKGVGFAR+ES++KC+Q+IQ+FNG+T+ G+K+PLLVKFAD G KK+  
Sbjct: 346 VSTRILRDQQMNSKGVGFARMESREKCEQIIQMFNGNTITGAKDPLLVKFADGGPKKK-- 403

Query: 225 GAGGPNIYRGPGAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGP 273
                N+++ P    R W   SA+   +AY+  M          TPI   + Y RF  G 
Sbjct: 404 -----NLFKTPDPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI--GVPYSRF--GA 454

Query: 274 GGTGHIPAGYTPWVPTQYVMPAPHMSQVE 302
              G  P   + W+P  Y+M  P ++QV+
Sbjct: 455 PQVGGYPVAGSQWIPG-YMMTQP-ITQVD 481

Has a role in the perception of gravity.

Drosophila mojavensis (taxid: 7230)

>sp|B3M3R5|SHEP_DROAN Protein alan shepard OS=Drosophila ananassae GN=shep PE=3 SV=2

 Score =  263 bits (672), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 147/269 (54%), Positives = 182/269 (67%), Gaps = 37/269 (13%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           LSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAILDKTTNKC  YGFVDFE   +A  
Sbjct: 233 LSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAILDKTTNKC--YGFVDFEQPAFAEC 290

Query: 116 AVKALQDKGIHAQMAR-----------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTV 164
           AVK LQ KG+ AQMA+           QQEQDPTNLYIANLP ++KE DLE++L+KY  V
Sbjct: 291 AVKGLQGKGVQAQMAKVGIWVLHRPAIQQEQDPTNLYIANLPPHYKETDLEAMLSKYGQV 350

Query: 165 VSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGA 224
           VSTRILRD    SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG K+PLLVKFAD G KK+  
Sbjct: 351 VSTRILRDQQMNSKGVGFARMESREKCEQIIQMFNGNTIPGGKDPLLVKFADGGPKKK-- 408

Query: 225 GAGGPNIYRGPGAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGP 273
                N+++ P    R W   SA+   +AY+  +          TPI   + Y RF+A  
Sbjct: 409 -----NLFKTPDPNARAWRDVSAEGIPVAYDPTLQQNGVSVNVGTPI--GVPYSRFSA-- 459

Query: 274 GGTGHIPAGYTPWVPTQYVMPAPHMSQVE 302
              G  P   + W+P  Y+M  P ++QV+
Sbjct: 460 PQVGGYPVAGSQWIPG-YMMTQP-ITQVD 486

Has a role in the perception of gravity.

Drosophila ananassae (taxid: 7217)

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	305
195427966	603	GK17327 [Drosophila willistoni] gi|19415	0.773	0.391	0.588	2e-76
251765113	581	RecName: Full=Protein alan shepard	0.773	0.406	0.588	2e-76
195376319	868	GJ12205 [Drosophila virilis] gi|19415410	0.767	0.269	0.593	1e-75
195014142	609	GH15273 [Drosophila grimshawi] gi|251765	0.767	0.384	0.593	3e-75
251765112	595	RecName: Full=Protein alan shepard	0.767	0.393	0.593	4e-75
170045947	416	single-stranded DNA-binding protein mssp	0.665	0.487	0.677	7e-75
158295086	453	AGAP005964-PA [Anopheles gambiae str. PE	0.642	0.432	0.686	1e-74
158295088	365	AGAP005964-PB [Anopheles gambiae str. PE	0.642	0.536	0.686	2e-74
194866955	582	GG14139 [Drosophila erecta] gi|251765066	0.767	0.402	0.581	3e-74
195491940	582	GE20568 [Drosophila yakuba] gi|251765013	0.767	0.402	0.581	3e-74

>gi|195427966|ref|XP_002062046.1| GK17327 [Drosophila willistoni] gi|194158131|gb|EDW73032.1| GK17327 [Drosophila willistoni]

 Score =  291 bits (746), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 153/260 (58%), Positives = 188/260 (72%), Gaps = 24/260 (9%)

Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
           EQLSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAILDKTTNKC+GYGFVDFE   YA
Sbjct: 254 EQLSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAYA 313

Query: 114 LAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN 173
             AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++L+KY  VVSTRILRD 
Sbjct: 314 ENAVKGLQAKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLSKYGQVVSTRILRDQ 373

Query: 174 NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYR 233
              SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++
Sbjct: 374 QMNSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFK 426

Query: 234 GPGAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAG 282
            P    R W   SA+   +AY+  +          TPI   + Y RF+A P   G  P  
Sbjct: 427 TPDPNTRAWRDVSAEGIPVAYDPTLQQNGVSVNVGTPI--GVPYSRFSAPP--VGGYPVA 482

Query: 283 YTPWVPTQYVMPAPHMSQVE 302
            + W+P  Y+M  P ++QV+
Sbjct: 483 GSQWIPG-YMMTQP-ITQVD 500

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|251765113|sp|B4MM23.2|SHEP_DROWI RecName: Full=Protein alan shepard

 Score =  291 bits (746), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 153/260 (58%), Positives = 188/260 (72%), Gaps = 24/260 (9%)

Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
           EQLSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAILDKTTNKC+GYGFVDFE   YA
Sbjct: 232 EQLSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAYA 291

Query: 114 LAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN 173
             AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++L+KY  VVSTRILRD 
Sbjct: 292 ENAVKGLQAKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLSKYGQVVSTRILRDQ 351

Query: 174 NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYR 233
              SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++
Sbjct: 352 QMNSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFK 404

Query: 234 GPGAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAG 282
            P    R W   SA+   +AY+  +          TPI   + Y RF+A P   G  P  
Sbjct: 405 TPDPNTRAWRDVSAEGIPVAYDPTLQQNGVSVNVGTPI--GVPYSRFSAPP--VGGYPVA 460

Query: 283 YTPWVPTQYVMPAPHMSQVE 302
            + W+P  Y+M  P ++QV+
Sbjct: 461 GSQWIPG-YMMTQP-ITQVD 478

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195376319|ref|XP_002046944.1| GJ12205 [Drosophila virilis] gi|194154102|gb|EDW69286.1| GJ12205 [Drosophila virilis]

 Score =  289 bits (740), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 153/258 (59%), Positives = 184/258 (71%), Gaps = 24/258 (9%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           LSKTNLYIRGL Q TTDKDLINMC+QYG IISTKAILDKTTNKC+GYGFVDFE   YA  
Sbjct: 513 LSKTNLYIRGLQQGTTDKDLINMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAYAEG 572

Query: 116 AVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN 175
           AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++LAKY  VVSTRILRD   
Sbjct: 573 AVKGLQAKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLAKYGQVVSTRILRDQQM 632

Query: 176 TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGP 235
            SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++ P
Sbjct: 633 NSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFKTP 685

Query: 236 GAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAGYT 284
               R W   SA+   +AY+  M          TPI   + Y RF  G    G  P   +
Sbjct: 686 DPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI--GVPYSRF--GAPQVGGYPVAGS 741

Query: 285 PWVPTQYVMPAPHMSQVE 302
            W+P  Y+M  P ++QV+
Sbjct: 742 QWIPG-YMMTQP-ITQVD 757

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195014142|ref|XP_001983966.1| GH15273 [Drosophila grimshawi] gi|251765067|sp|B4IX08.1|SHEP_DROGR RecName: Full=Protein alan shepard gi|193897448|gb|EDV96314.1| GH15273 [Drosophila grimshawi]

 Score =  288 bits (736), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 153/258 (59%), Positives = 184/258 (71%), Gaps = 24/258 (9%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           LSKTNLYIRGL Q TTDKDLINMC+QYG IISTKAILDKTTNKC+GYGFVDFE   YA  
Sbjct: 254 LSKTNLYIRGLQQGTTDKDLINMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAYAEG 313

Query: 116 AVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN 175
           AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++LAKY  VVSTRILRD   
Sbjct: 314 AVKGLQAKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLAKYGQVVSTRILRDQQM 373

Query: 176 TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGP 235
            SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++ P
Sbjct: 374 NSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFKTP 426

Query: 236 GAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAGYT 284
               R W   SA+   +AY+  M          TPI   + Y RF  G    G  P   +
Sbjct: 427 DPSARAWRDVSAEGIPVAYDPSMQQNGVSVNVGTPI--GVPYSRF--GAPQVGGYPVAGS 482

Query: 285 PWVPTQYVMPAPHMSQVE 302
            W+P  Y+M  P ++QV+
Sbjct: 483 QWIPG-YMMTQP-ITQVD 498

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|251765112|sp|B4LFQ9.2|SHEP_DROVI RecName: Full=Protein alan shepard

 Score =  287 bits (735), Expect = 4e-75,   Method: Compositional matrix adjust.
 Identities = 153/258 (59%), Positives = 184/258 (71%), Gaps = 24/258 (9%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           LSKTNLYIRGL Q TTDKDLINMC+QYG IISTKAILDKTTNKC+GYGFVDFE   YA  
Sbjct: 240 LSKTNLYIRGLQQGTTDKDLINMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAYAEG 299

Query: 116 AVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN 175
           AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++LAKY  VVSTRILRD   
Sbjct: 300 AVKGLQAKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLAKYGQVVSTRILRDQQM 359

Query: 176 TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGP 235
            SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++ P
Sbjct: 360 NSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFKTP 412

Query: 236 GAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAGYT 284
               R W   SA+   +AY+  M          TPI   + Y RF  G    G  P   +
Sbjct: 413 DPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI--GVPYSRF--GAPQVGGYPVAGS 468

Query: 285 PWVPTQYVMPAPHMSQVE 302
            W+P  Y+M  P ++QV+
Sbjct: 469 QWIPG-YMMTQP-ITQVD 484

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170045947|ref|XP_001850551.1| single-stranded DNA-binding protein mssp-1 [Culex quinquefasciatus] gi|167868784|gb|EDS32167.1| single-stranded DNA-binding protein mssp-1 [Culex quinquefasciatus]

 Score =  286 bits (732), Expect = 7e-75,   Method: Compositional matrix adjust.
 Identities = 143/211 (67%), Positives = 163/211 (77%), Gaps = 8/211 (3%)

Query: 38  TNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTN 97
           TN     G   TP   EQLSKTNLYIRGL Q TTDKDLINMC+QYG IISTKAILDKTTN
Sbjct: 49  TNTNNTMGPSNTPQQTEQLSKTNLYIRGLQQGTTDKDLINMCAQYGTIISTKAILDKTTN 108

Query: 98  KCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESL 157
           KC+GYGFVDFES   A  AVK LQ KGI AQMA+QQEQDPTNLYIANLPLN+KE D+E+L
Sbjct: 109 KCKGYGFVDFESPACAEGAVKGLQAKGIQAQMAKQQEQDPTNLYIANLPLNYKETDVENL 168

Query: 158 LAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
           L+KY  V+STRILRD N  SKGVGFAR+ES++KC+Q+IQ+FNG+ L G+KEPLLVKFAD 
Sbjct: 169 LSKYGQVISTRILRDQNAQSKGVGFARMESREKCEQIIQIFNGTQLQGAKEPLLVKFADG 228

Query: 218 GLKKRGAGAGGPNIYRGPGAEVRLWGRDSAD 248
           G KK+       N ++ P    R W RD A+
Sbjct: 229 GSKKK-------NPFKSPDPNARTW-RDGAE 251

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158295086|ref|XP_001688763.1| AGAP005964-PA [Anopheles gambiae str. PEST] gi|157015867|gb|EDO63769.1| AGAP005964-PA [Anopheles gambiae str. PEST]

 Score =  285 bits (730), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 140/204 (68%), Positives = 161/204 (78%), Gaps = 8/204 (3%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           G   TP   EQLSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAILDKTTNKC+GYGF
Sbjct: 90  GPSNTPQQTEQLSKTNLYIRGLQQGTTDKDLVNMCAQYGNIISTKAILDKTTNKCKGYGF 149

Query: 105 VDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTV 164
           VDFES   A  AVK LQ KGI AQMA+QQEQDPTNLYIANLPLN+KE D+E+LL+KY  V
Sbjct: 150 VDFESPSCAEGAVKGLQAKGIQAQMAKQQEQDPTNLYIANLPLNYKETDVENLLSKYGQV 209

Query: 165 VSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGA 224
           +STRILRD N  SKGVGFAR+ES+DKC+Q+IQ+FNG+ LP +KEPLLVKFAD G KK+  
Sbjct: 210 ISTRILRDQNAQSKGVGFARMESRDKCEQIIQIFNGTLLPNAKEPLLVKFADGGSKKK-- 267

Query: 225 GAGGPNIYRGPGAEVRLWGRDSAD 248
                N ++ P    R W R+ A+
Sbjct: 268 -----NPFKSPDPNTRTW-REGAE 285

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158295088|ref|XP_316007.4| AGAP005964-PB [Anopheles gambiae str. PEST] gi|157015868|gb|EAA10943.4| AGAP005964-PB [Anopheles gambiae str. PEST]

 Score =  285 bits (728), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 140/204 (68%), Positives = 161/204 (78%), Gaps = 8/204 (3%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           G   TP   EQLSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAILDKTTNKC+GYGF
Sbjct: 2   GPSNTPQQTEQLSKTNLYIRGLQQGTTDKDLVNMCAQYGNIISTKAILDKTTNKCKGYGF 61

Query: 105 VDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTV 164
           VDFES   A  AVK LQ KGI AQMA+QQEQDPTNLYIANLPLN+KE D+E+LL+KY  V
Sbjct: 62  VDFESPSCAEGAVKGLQAKGIQAQMAKQQEQDPTNLYIANLPLNYKETDVENLLSKYGQV 121

Query: 165 VSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGA 224
           +STRILRD N  SKGVGFAR+ES+DKC+Q+IQ+FNG+ LP +KEPLLVKFAD G KK+  
Sbjct: 122 ISTRILRDQNAQSKGVGFARMESRDKCEQIIQIFNGTLLPNAKEPLLVKFADGGSKKK-- 179

Query: 225 GAGGPNIYRGPGAEVRLWGRDSAD 248
                N ++ P    R W R+ A+
Sbjct: 180 -----NPFKSPDPNTRTW-REGAE 197

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194866955|ref|XP_001971976.1| GG14139 [Drosophila erecta] gi|251765066|sp|B3NGA1.1|SHEP_DROER RecName: Full=Protein alan shepard gi|190653759|gb|EDV51002.1| GG14139 [Drosophila erecta]

 Score =  284 bits (727), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 150/258 (58%), Positives = 185/258 (71%), Gaps = 24/258 (9%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           LSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAILDKTTNKC+GYGFVDFE   +A  
Sbjct: 228 LSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAFAEC 287

Query: 116 AVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN 175
           AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++L+KY  VVSTRILRD   
Sbjct: 288 AVKGLQGKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLSKYGQVVSTRILRDQQM 347

Query: 176 TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGP 235
            SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++ P
Sbjct: 348 NSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFKTP 400

Query: 236 GAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAGYT 284
               R W   SA+   +AY+  M          TPI   + Y RF+A     G  P   +
Sbjct: 401 DPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI--GVPYSRFSA--PQVGGYPVAGS 456

Query: 285 PWVPTQYVMPAPHMSQVE 302
            W+P  Y+M  P ++QV+
Sbjct: 457 QWIPG-YMMTQP-ITQVD 472

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195491940|ref|XP_002093780.1| GE20568 [Drosophila yakuba] gi|251765013|sp|B4PIS2.1|SHEP_DROYA RecName: Full=Protein alan shepard gi|194179881|gb|EDW93492.1| GE20568 [Drosophila yakuba]

 Score =  284 bits (727), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 150/258 (58%), Positives = 185/258 (71%), Gaps = 24/258 (9%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           LSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAILDKTTNKC+GYGFVDFE   +A  
Sbjct: 228 LSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAILDKTTNKCKGYGFVDFEQPAFAEC 287

Query: 116 AVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN 175
           AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE DLE++L+KY  VVSTRILRD   
Sbjct: 288 AVKGLQGKGVQAQMAKQQEQDPTNLYIANLPPHFKETDLEAMLSKYGQVVSTRILRDQQM 347

Query: 176 TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGP 235
            SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLVKFAD G KK+       N+++ P
Sbjct: 348 NSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLVKFADGGPKKK-------NLFKTP 400

Query: 236 GAEVRLWGRDSADS-QLAYEHPM----------TPIPATIQYQRFTAGPGGTGHIPAGYT 284
               R W   SA+   +AY+  M          TPI   + Y RF+A     G  P   +
Sbjct: 401 DPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI--GVPYSRFSA--PQVGGYPVAGS 456

Query: 285 PWVPTQYVMPAPHMSQVE 302
            W+P  Y+M  P ++QV+
Sbjct: 457 QWIPG-YMMTQP-ITQVD 472

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

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	305
UNIPROTKB|B4MM23	581	shep "Protein alan shepard" [D	0.836	0.438	0.566	1.6e-72
UNIPROTKB|B4IX08	609	shep "Protein alan shepard" [D	0.836	0.418	0.578	2e-72
UNIPROTKB|B4LFQ9	595	shep "Protein alan shepard" [D	0.836	0.428	0.578	2e-72
UNIPROTKB|B3NGA1	582	shep "Protein alan shepard" [D	0.836	0.438	0.567	2.5e-72
UNIPROTKB|B4PIS2	582	shep "Protein alan shepard" [D	0.836	0.438	0.567	2.5e-72
FB|FBgn0052423	578	shep "alan shepard" [Drosophil	0.809	0.427	0.575	2.3e-71
UNIPROTKB|B4HUE4	579	shep "Protein alan shepard" [D	0.809	0.426	0.575	2.3e-71
UNIPROTKB|B4QRJ0	576	shep "Protein alan shepard" [D	0.803	0.425	0.571	2.4e-69
UNIPROTKB|B4KX02	592	shep "Protein alan shepard" [D	0.836	0.430	0.549	4.4e-68
UNIPROTKB|B3M3R5	597	shep "Protein alan shepard" [D	0.829	0.423	0.534	1.7e-66

UNIPROTKB|B4MM23 shep "Protein alan shepard" [Drosophila willistoni (taxid:7260)]

 Score = 733 (263.1 bits), Expect = 1.6e-72, P = 1.6e-72
 Identities = 158/279 (56%), Positives = 196/279 (70%)

Query:    37 TTNNVQHNGSPGTPT----GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAIL 92
             T  N+  NG+         G EQLSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAIL
Sbjct:   211 TNTNMGPNGTAQNQNQQGGGGEQLSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAIL 270

Query:    93 DKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKEC 152
             DKTTNKC+GYGFVDFE   YA  AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE 
Sbjct:   271 DKTTNKCKGYGFVDFEQPAYAENAVKGLQAKGVQAQMAKQQEQDPTNLYIANLPPHFKET 330

Query:   153 DLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV 212
             DLE++L+KY  VVSTRILRD    SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLLV
Sbjct:   331 DLEAMLSKYGQVVSTRILRDQQMNSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLLV 390

Query:   213 KFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADS-QLAYEHPMTP--------IPAT 263
             KFAD G KK+       N+++ P    R W   SA+   +AY+  +           P  
Sbjct:   391 KFADGGPKKK-------NLFKTPDPNTRAWRDVSAEGIPVAYDPTLQQNGVSVNVGTPIG 443

Query:   264 IQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHMSQVE 302
             + Y RF+A P G G+  AG + W+P  Y+M  P ++QV+
Sbjct:   444 VPYSRFSAPPVG-GYPVAG-SQWIPG-YMMTQP-ITQVD 478

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0009629 "response to gravity" evidence=ISS

UNIPROTKB|B4IX08 shep "Protein alan shepard" [Drosophila grimshawi (taxid:7222)]

 Score = 732 (262.7 bits), Expect = 2.0e-72, P = 2.0e-72
 Identities = 162/280 (57%), Positives = 194/280 (69%)

Query:    37 TTNNVQHNGSPGTPT-----GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI 91
             TTN     G  GT       G EQLSKTNLYIRGL Q TTDKDLINMC+QYG IISTKAI
Sbjct:   230 TTNTNTTMGPNGTAQNQNQQGGEQLSKTNLYIRGLQQGTTDKDLINMCAQYGTIISTKAI 289

Query:    92 LDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKE 151
             LDKTTNKC+GYGFVDFE   YA  AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE
Sbjct:   290 LDKTTNKCKGYGFVDFEQPAYAEGAVKGLQAKGVQAQMAKQQEQDPTNLYIANLPPHFKE 349

Query:   152 CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL 211
              DLE++LAKY  VVSTRILRD    SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLL
Sbjct:   350 TDLEAMLAKYGQVVSTRILRDQQMNSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLL 409

Query:   212 VKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADS-QLAYEHPMTP--------IPA 262
             VKFAD G KK+       N+++ P    R W   SA+   +AY+  M           P 
Sbjct:   410 VKFADGGPKKK-------NLFKTPDPSARAWRDVSAEGIPVAYDPSMQQNGVSVNVGTPI 462

Query:   263 TIQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHMSQVE 302
              + Y RF A   G G+  AG + W+P  Y+M  P ++QV+
Sbjct:   463 GVPYSRFGAPQVG-GYPVAG-SQWIPG-YMMTQP-ITQVD 498

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0009629 "response to gravity" evidence=ISS

UNIPROTKB|B4LFQ9 shep "Protein alan shepard" [Drosophila virilis (taxid:7244)]

 Score = 732 (262.7 bits), Expect = 2.0e-72, P = 2.0e-72
 Identities = 162/280 (57%), Positives = 194/280 (69%)

Query:    37 TTNNVQHNGSPGTPT-----GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI 91
             TTN     G  GT       G EQLSKTNLYIRGL Q TTDKDLINMC+QYG IISTKAI
Sbjct:   216 TTNTNTTMGPNGTAQNQNQQGGEQLSKTNLYIRGLQQGTTDKDLINMCAQYGTIISTKAI 275

Query:    92 LDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKE 151
             LDKTTNKC+GYGFVDFE   YA  AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE
Sbjct:   276 LDKTTNKCKGYGFVDFEQPAYAEGAVKGLQAKGVQAQMAKQQEQDPTNLYIANLPPHFKE 335

Query:   152 CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL 211
              DLE++LAKY  VVSTRILRD    SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLL
Sbjct:   336 TDLEAMLAKYGQVVSTRILRDQQMNSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLL 395

Query:   212 VKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADS-QLAYEHPMTP--------IPA 262
             VKFAD G KK+       N+++ P    R W   SA+   +AY+  M           P 
Sbjct:   396 VKFADGGPKKK-------NLFKTPDPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI 448

Query:   263 TIQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHMSQVE 302
              + Y RF A   G G+  AG + W+P  Y+M  P ++QV+
Sbjct:   449 GVPYSRFGAPQVG-GYPVAG-SQWIPG-YMMTQP-ITQVD 484

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0009629 "response to gravity" evidence=ISS

UNIPROTKB|B3NGA1 shep "Protein alan shepard" [Drosophila erecta (taxid:7220)]

 Score = 731 (262.4 bits), Expect = 2.5e-72, P = 2.5e-72
 Identities = 159/280 (56%), Positives = 196/280 (70%)

Query:    37 TTNNVQHNGSPGT-----PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI 91
             TTN   + G  GT       G EQLSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAI
Sbjct:   204 TTNTNTNMGPNGTVQNQNQQGGEQLSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAI 263

Query:    92 LDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKE 151
             LDKTTNKC+GYGFVDFE   +A  AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE
Sbjct:   264 LDKTTNKCKGYGFVDFEQPAFAECAVKGLQGKGVQAQMAKQQEQDPTNLYIANLPPHFKE 323

Query:   152 CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL 211
              DLE++L+KY  VVSTRILRD    SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLL
Sbjct:   324 TDLEAMLSKYGQVVSTRILRDQQMNSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLL 383

Query:   212 VKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADS-QLAYEHPMTP--------IPA 262
             VKFAD G KK+       N+++ P    R W   SA+   +AY+  M           P 
Sbjct:   384 VKFADGGPKKK-------NLFKTPDPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI 436

Query:   263 TIQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHMSQVE 302
              + Y RF+A   G G+  AG + W+P  Y+M  P ++QV+
Sbjct:   437 GVPYSRFSAPQVG-GYPVAG-SQWIPG-YMMTQP-ITQVD 472

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0009629 "response to gravity" evidence=ISS

UNIPROTKB|B4PIS2 shep "Protein alan shepard" [Drosophila yakuba (taxid:7245)]

 Score = 731 (262.4 bits), Expect = 2.5e-72, P = 2.5e-72
 Identities = 159/280 (56%), Positives = 196/280 (70%)

Query:    37 TTNNVQHNGSPGT-----PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI 91
             TTN   + G  GT       G EQLSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAI
Sbjct:   204 TTNTNTNMGPNGTVQNQNQQGGEQLSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAI 263

Query:    92 LDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKE 151
             LDKTTNKC+GYGFVDFE   +A  AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE
Sbjct:   264 LDKTTNKCKGYGFVDFEQPAFAECAVKGLQGKGVQAQMAKQQEQDPTNLYIANLPPHFKE 323

Query:   152 CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL 211
              DLE++L+KY  VVSTRILRD    SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLL
Sbjct:   324 TDLEAMLSKYGQVVSTRILRDQQMNSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLL 383

Query:   212 VKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADS-QLAYEHPMTP--------IPA 262
             VKFAD G KK+       N+++ P    R W   SA+   +AY+  M           P 
Sbjct:   384 VKFADGGPKKK-------NLFKTPDPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI 436

Query:   263 TIQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHMSQVE 302
              + Y RF+A   G G+  AG + W+P  Y+M  P ++QV+
Sbjct:   437 GVPYSRFSAPQVG-GYPVAG-SQWIPG-YMMTQP-ITQVD 472

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0009629 "response to gravity" evidence=ISS

FB|FBgn0052423 shep "alan shepard" [Drosophila melanogaster (taxid:7227)]

 Score = 722 (259.2 bits), Expect = 2.3e-71, P = 2.3e-71
 Identities = 156/271 (57%), Positives = 190/271 (70%)

Query:    37 TTNNVQHNGSPGT-----PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI 91
             TTN   + G  GT       G EQLSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAI
Sbjct:   204 TTNTNTNMGPNGTVQNQNQQGGEQLSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAI 263

Query:    92 LDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKE 151
             LDKTTNKC+GYGFVDFE   +A  AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE
Sbjct:   264 LDKTTNKCKGYGFVDFEQPAFAECAVKGLQGKGVQAQMAKQQEQDPTNLYIANLPPHFKE 323

Query:   152 CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL 211
              DLE++L+KY  VVSTRILRD    SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLL
Sbjct:   324 TDLEAMLSKYGQVVSTRILRDQQMNSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLL 383

Query:   212 VKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADS-QLAYEHPMTP--------IPA 262
             VKFAD G KK+       N+++ P    R W   SA+   +AY+  M           P 
Sbjct:   384 VKFADGGPKKK-------NLFKTPDPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI 436

Query:   263 TIQYQRFTAGPGGTGHIPAGYTPWVPTQYVM 293
              + Y RF+A   G G+  AG + W+P  Y+M
Sbjct:   437 GVPYSRFSAPQVG-GYPVAG-SQWIPG-YMM 464

GO:0003729 "mRNA binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0042332 "gravitaxis" evidence=IMP

GO:0009629 "response to gravity" evidence=IMP

UNIPROTKB|B4HUE4 shep "Protein alan shepard" [Drosophila sechellia (taxid:7238)]

 Score = 722 (259.2 bits), Expect = 2.3e-71, P = 2.3e-71
 Identities = 156/271 (57%), Positives = 190/271 (70%)

Query:    37 TTNNVQHNGSPGT-----PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI 91
             TTN   + G  GT       G EQLSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAI
Sbjct:   204 TTNTNTNMGPNGTVQNQNQQGGEQLSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAI 263

Query:    92 LDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKE 151
             LDKTTNKC+GYGFVDFE   +A  AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE
Sbjct:   264 LDKTTNKCKGYGFVDFEQPAFAECAVKGLQGKGVQAQMAKQQEQDPTNLYIANLPPHFKE 323

Query:   152 CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL 211
              DLE++L+KY  VVSTRILRD    SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLL
Sbjct:   324 TDLEAMLSKYGQVVSTRILRDQQMNSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLL 383

Query:   212 VKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADS-QLAYEHPMTP--------IPA 262
             VKFAD G KK+       N+++ P    R W   SA+   +AY+  M           P 
Sbjct:   384 VKFADGGPKKK-------NLFKTPDPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI 436

Query:   263 TIQYQRFTAGPGGTGHIPAGYTPWVPTQYVM 293
              + Y RF+A   G G+  AG + W+P  Y+M
Sbjct:   437 GVPYSRFSAPQVG-GYPVAG-SQWIPG-YMM 464

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0009629 "response to gravity" evidence=ISS

UNIPROTKB|B4QRJ0 shep "Protein alan shepard" [Drosophila simulans (taxid:7240)]

 Score = 703 (252.5 bits), Expect = 2.4e-69, P = 2.4e-69
 Identities = 155/271 (57%), Positives = 188/271 (69%)

Query:    37 TTNNVQHNGSPGT-----PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI 91
             TTN   + G  GT       G EQLSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAI
Sbjct:   204 TTNTNTNMGPNGTVQNQNQQGGEQLSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAI 263

Query:    92 LDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKE 151
             LDKTTNKC  YGFVDFE   +A  AVK LQ KG+ AQMA+QQEQDPTNLYIANLP +FKE
Sbjct:   264 LDKTTNKC--YGFVDFEQPAFAECAVKGLQGKGVQAQMAKQQEQDPTNLYIANLPPHFKE 321

Query:   152 CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL 211
              DLE++L+KY  VVSTRILRD    SKGVGFAR+ES++KC+Q+IQ+FNG+T+PG+K+PLL
Sbjct:   322 TDLEAMLSKYGQVVSTRILRDQQMNSKGVGFARMESREKCEQIIQMFNGNTIPGAKDPLL 381

Query:   212 VKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADS-QLAYEHPMTP--------IPA 262
             VKFAD G KK+       N+++ P    R W   SA+   +AY+  M           P 
Sbjct:   382 VKFADGGPKKK-------NLFKTPDPNARAWRDVSAEGIPVAYDPTMQQNGVSVNVGTPI 434

Query:   263 TIQYQRFTAGPGGTGHIPAGYTPWVPTQYVM 293
              + Y RF+A   G G+  AG + W+P  Y+M
Sbjct:   435 GVPYSRFSAPQVG-GYPVAG-SQWIPG-YMM 462

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0009629 "response to gravity" evidence=ISS

UNIPROTKB|B4KX02 shep "Protein alan shepard" [Drosophila mojavensis (taxid:7230)]

 Score = 691 (248.3 bits), Expect = 4.4e-68, P = 4.4e-68
 Identities = 160/291 (54%), Positives = 193/291 (66%)

Query:    37 TTNNVQHNGSPGTPT-----GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI 91
             TTN     G  GT       G EQLSKTNLYIRGL Q TTDKDLINMC+QYG IISTKAI
Sbjct:   202 TTNTNTTMGPNGTAQNQNQQGGEQLSKTNLYIRGLQQGTTDKDLINMCAQYGTIISTKAI 261

Query:    92 LDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR-----------QQEQDPTNL 140
             LDKTTNKC+GYGFVDFE   YA  AVK LQ KG+ AQMA+           QQEQDPTNL
Sbjct:   262 LDKTTNKCKGYGFVDFEQPAYAEGAVKGLQAKGVQAQMAKVGIWVLHRPAIQQEQDPTNL 321

Query:   141 YIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNG 200
             YIANLP +FKE DLE++LAK+  VVSTRILRD    SKGVGFAR+ES++KC+Q+IQ+FNG
Sbjct:   322 YIANLPPHFKETDLEAMLAKFGQVVSTRILRDQQMNSKGVGFARMESREKCEQIIQMFNG 381

Query:   201 STLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADS-QLAYEHPMTP 259
             +T+ G+K+PLLVKFAD G KK+       N+++ P    R W   SA+   +AY+  M  
Sbjct:   382 NTITGAKDPLLVKFADGGPKKK-------NLFKTPDPNARAWRDVSAEGIPVAYDPTMQQ 434

Query:   260 --------IPATIQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHMSQVE 302
                      P  + Y RF A   G G+  AG + W+P  Y+M  P ++QV+
Sbjct:   435 NGVSVNVGTPIGVPYSRFGAPQVG-GYPVAG-SQWIPG-YMMTQP-ITQVD 481

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0009629 "response to gravity" evidence=ISS

UNIPROTKB|B3M3R5 shep "Protein alan shepard" [Drosophila ananassae (taxid:7217)]

 Score = 676 (243.0 bits), Expect = 1.7e-66, P = 1.7e-66
 Identities = 154/288 (53%), Positives = 192/288 (66%)

Query:    37 TTNNVQHNGSPGTPT--GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDK 94
             T  N+  NG+       G EQLSKTNLYIRGL Q TTDKDL+NMC+QYG IISTKAILDK
Sbjct:   212 TNTNMGPNGTAQNQNQQGGEQLSKTNLYIRGLQQGTTDKDLVNMCAQYGTIISTKAILDK 271

Query:    95 TTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR-----------QQEQDPTNLYIA 143
             TTNKC  YGFVDFE   +A  AVK LQ KG+ AQMA+           QQEQDPTNLYIA
Sbjct:   272 TTNKC--YGFVDFEQPAFAECAVKGLQGKGVQAQMAKVGIWVLHRPAIQQEQDPTNLYIA 329

Query:   144 NLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTL 203
             NLP ++KE DLE++L+KY  VVSTRILRD    SKGVGFAR+ES++KC+Q+IQ+FNG+T+
Sbjct:   330 NLPPHYKETDLEAMLSKYGQVVSTRILRDQQMNSKGVGFARMESREKCEQIIQMFNGNTI 389

Query:   204 PGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGRDSADS-QLAYEHPMTP--- 259
             PG K+PLLVKFAD G KK+       N+++ P    R W   SA+   +AY+  +     
Sbjct:   390 PGGKDPLLVKFADGGPKKK-------NLFKTPDPNARAWRDVSAEGIPVAYDPTLQQNGV 442

Query:   260 -----IPATIQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHMSQVE 302
                   P  + Y RF+A   G G+  AG + W+P  Y+M  P ++QV+
Sbjct:   443 SVNVGTPIGVPYSRFSAPQVG-GYPVAG-SQWIPG-YMMTQP-ITQVD 486

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0009629 "response to gravity" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5PQP1	RBMS1_RAT	No assigned EC number	0.58	0.6131	0.4640	yes	N/A
Q3ZBP3	RBMS1_BOVIN	No assigned EC number	0.5656	0.6655	0.5037	yes	N/A
Q8MSV2	SHEP_DROME	No assigned EC number	0.5942	0.7278	0.3840	yes	N/A
P29558	RBMS1_HUMAN	No assigned EC number	0.59	0.6131	0.4605	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	305
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	6e-42
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	7e-35
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	6e-34
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	3e-29
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-28
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	2e-27
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	5e-25
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	6e-25
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	7e-24
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	3e-22
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-20
smart00360	73	smart00360, RRM, RNA recognition motif	1e-18
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-16
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-14
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	7e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-13
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	4e-13
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	8e-13
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	1e-12
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-12
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-12
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	4e-12
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-12
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	6e-12
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	6e-12
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-12
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	8e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-11
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-11
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-11
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	4e-11
smart00360	73	smart00360, RRM, RNA recognition motif	5e-11
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	6e-11
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	8e-11
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	1e-10
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	3e-10
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-10
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	4e-10
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	5e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	5e-10
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	9e-10
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-09
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-09
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-09
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	3e-09
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	4e-09
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	8e-09
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	8e-09
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	1e-08
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-08
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-08
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	2e-08
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-08
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	2e-08
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-08
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-08
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-08
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-08
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-08
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	2e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-08
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	3e-08
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	3e-08
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	4e-08
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	5e-08
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-08
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	5e-08
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	6e-08
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	6e-08
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	6e-08
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	9e-08
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	9e-08
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-07
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-07
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-07
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	2e-07
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	2e-07
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	3e-07
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	3e-07
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	3e-07
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	3e-07
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	4e-07
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	4e-07
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	4e-07
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	5e-07
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	5e-07
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	5e-07
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	5e-07
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	5e-07
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	6e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	7e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	7e-07
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	7e-07
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	7e-07
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	7e-07
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	9e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-06
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-06
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	1e-06
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	1e-06
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	1e-06
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-06
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	2e-06
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	2e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-06
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	2e-06
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	3e-06
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	4e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-06
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	4e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	4e-06
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	4e-06
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	5e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	6e-06
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	7e-06
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	8e-06
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	9e-06
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	9e-06
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-05
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-05
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-05
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	2e-05
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	2e-05
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	3e-05
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	3e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	3e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-05
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	4e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	5e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	5e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-05
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	5e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	6e-05
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	6e-05
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	6e-05
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	7e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	7e-05
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	8e-05
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	8e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	8e-05
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	8e-05
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	9e-05
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	9e-05
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-04
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	1e-04
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-04
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	1e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-04
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	1e-04
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	1e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	1e-04
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	1e-04
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-04
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-04
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-04
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	2e-04
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	2e-04
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-04
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	2e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-04
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	3e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	3e-04
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-04
cd12686	81	cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif	3e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	3e-04
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	4e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	4e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	4e-04
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	4e-04
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	5e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	5e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	5e-04
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	5e-04
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	5e-04
cd12420	79	cd12420, RRM_RBPMS_like, RNA recognition motif in	5e-04
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	6e-04
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	6e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	6e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	6e-04
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	6e-04
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	7e-04
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	7e-04
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	9e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	0.001
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	0.001
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.001
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	0.001
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.001
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	0.001
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	0.001
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	0.001
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	0.002
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	0.002
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	0.002
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	0.002
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	0.002
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	0.002
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	0.002
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.003
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	0.003
cd12359	76	cd12359, RRM2_VICKZ, RNA recognition motif 2 in th	0.003
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	0.003
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	0.003
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	0.003
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.003
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	0.003
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	0.003
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	0.003
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	0.003
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	0.004
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	0.004
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.004
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	0.004
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	0.004
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	0.004
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	0.004
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	0.004

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

 Score =  139 bits (352), Expect = 6e-42
 Identities = 49/79 (62%), Positives = 61/79 (77%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
           TNLYI+NLPL+  E DLE++L  Y  V+STRILRD+   S+GVGFAR+ES++KC+ +I  
Sbjct: 1   TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISK 60

Query: 198 FNGSTLPGSKEPLLVKFAD 216
           FNG  L G  EPLLVKFAD
Sbjct: 61  FNGKYLKGEGEPLLVKFAD 79

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

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

 Score =  120 bits (304), Expect = 7e-35
 Identities = 43/71 (60%), Positives = 54/71 (76%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           TN+YIRGL  +TTD+DL  +C  +G IISTKAILDK TNKC+GYGFVDF+S   AL A++
Sbjct: 1   TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

Query: 119 ALQDKGIHAQM 129
            L  +G+ AQ 
Sbjct: 61  GLNGRGVQAQF 71

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

 Score =  119 bits (298), Expect = 6e-34
 Identities = 59/86 (68%), Positives = 70/86 (81%)

Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           G +QLSKTNLYIRGL  +TTD+DL+ +C  YG I+STKAILDKTTNKC+GYGFVDF+S  
Sbjct: 1   GWDQLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPA 60

Query: 112 YALAAVKALQDKGIHAQMARQQEQDP 137
            A  AV AL+  G+ AQMA+QQEQDP
Sbjct: 61  AAQKAVSALKASGVQAQMAKQQEQDP 86

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score =  106 bits (265), Expect = 3e-29
 Identities = 53/80 (66%), Positives = 63/80 (78%)

Query: 55  QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYAL 114
           QLSKTNLYIRGL   TTD+DLI +C  YG I+STKAILDK TN+C+GYGFVDF+S   A 
Sbjct: 1   QLSKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQ 60

Query: 115 AAVKALQDKGIHAQMARQQE 134
            AV +L+  G+ AQMA+QQE
Sbjct: 61  KAVASLKANGVQAQMAKQQE 80

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

 Score =  111 bits (278), Expect = 3e-28
 Identities = 71/245 (28%), Positives = 110/245 (44%), Gaps = 16/245 (6%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           SKTNL +  L Q  T +++ ++ +  G I S K + DK T +  GYGFV++     A  A
Sbjct: 2   SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61

Query: 117 VKA-----LQDKGIHAQMARQQEQD--PTNLYIANLPLNFKECDLESLLAKYVTVVSTRI 169
           V +     LQ+K I    AR         NLY++ LP    + +LES+ + +  ++++RI
Sbjct: 62  VNSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRI 121

Query: 170 LRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS-------GLKK 221
           L DN    SKGVGF R + +D+ D+ I+  NG+T  G  EP+ VKFA++       GL  
Sbjct: 122 LSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLS 181

Query: 222 RGAGAGGPNIYRGPGAEVRLWGRDS-ADSQLAYEHPMTPIPATIQYQRFTAGPGGTGHIP 280
           +      P   R P + +             A   P       +   +         H  
Sbjct: 182 QLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAA 241

Query: 281 AGYTP 285
              +P
Sbjct: 242 QRASP 246

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

 Score =  101 bits (252), Expect = 2e-27
 Identities = 50/75 (66%), Positives = 59/75 (78%)

Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           KTNLYIRGL   TTD+DL+ +C  YG I+STKAILDKTTNKC+GYGFVDF+S   A  AV
Sbjct: 1   KTNLYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60

Query: 118 KALQDKGIHAQMARQ 132
            AL+  G+ AQMA+Q
Sbjct: 61  TALKASGVQAQMAKQ 75

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

 Score = 95.9 bits (238), Expect = 5e-25
 Identities = 49/88 (55%), Positives = 62/88 (70%), Gaps = 6/88 (6%)

Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
           PTNLYI+NLP++  E +LE++L  +  V+STRILRD N  S+GVGFAR+ES +KC+ +IQ
Sbjct: 1   PTNLYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGFARMESTEKCEVVIQ 60

Query: 197 LFNGSTL------PGSKEPLLVKFADSG 218
            FNG  L      P   EPLL KFAD G
Sbjct: 61  HFNGKYLKTPPGVPAPTEPLLCKFADGG 88

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|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 95.5 bits (237), Expect = 6e-25
 Identities = 47/85 (55%), Positives = 60/85 (70%), Gaps = 6/85 (7%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
           TNLYI+NLPL+  E +LES+L  +  V+STRILRD + TS+GVGFAR+ES +KC+ +I  
Sbjct: 1   TNLYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGFARMESTEKCEAIITH 60

Query: 198 FNGSTL------PGSKEPLLVKFAD 216
           FNG  +      P   EPLL KFAD
Sbjct: 61  FNGKYIKTPPGVPAPTEPLLCKFAD 85

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

 Score = 92.5 bits (229), Expect = 7e-24
 Identities = 48/85 (56%), Positives = 62/85 (72%), Gaps = 6/85 (7%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
           TNLYI+NLPL+  E +LE++L  +  V+STRILRD++ TS+GVGFAR+ES +KC+ +I  
Sbjct: 1   TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVISH 60

Query: 198 FNG---STLPG---SKEPLLVKFAD 216
           FNG    T PG     EPLL KFAD
Sbjct: 61  FNGKFIKTPPGVSAPAEPLLCKFAD 85

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

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

 Score = 94.7 bits (235), Expect = 3e-22
 Identities = 66/213 (30%), Positives = 101/213 (47%), Gaps = 10/213 (4%)

Query: 21  SSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCS 80
           SS+   GS     +  +TN++   GS G+       S TNL +  L QD TD++L  +  
Sbjct: 70  SSACGLGSMGNMANMASTNSLNSLGSGGSDDNDTNNSGTNLIVNYLPQDMTDRELYALFR 129

Query: 81  QYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL-----QDKGIHAQMAR---Q 132
             GPI + + + D  T    GY FVDF S   +  A+K L     ++K +    AR   +
Sbjct: 130 TIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGE 189

Query: 133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKC 191
             +D TNLY+ NLP    +  L+++  KY  +V   ILRD    T +GV F R   +++ 
Sbjct: 190 SIKD-TNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEA 248

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGA 224
            + I   N     G  +PL V+ A+   K +  
Sbjct: 249 QEAISALNNVIPEGGSQPLTVRLAEEHGKAKAH 281

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

 Score = 83.9 bits (208), Expect = 1e-20
 Identities = 31/78 (39%), Positives = 51/78 (65%), Gaps = 1/78 (1%)

Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT-SKGVGFARLESKDKCDQMIQL 197
           NLY++ LP    + +LE+L + Y  ++++RIL DN    S+GVGF R + + + ++ I+ 
Sbjct: 2   NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 198 FNGSTLPGSKEPLLVKFA 215
            NG+  PG+ EP+ VKFA
Sbjct: 62  LNGTIPPGATEPITVKFA 79

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|214636 smart00360, RRM, RNA recognition motif

 Score = 78.0 bits (193), Expect = 1e-18
 Identities = 24/67 (35%), Positives = 41/67 (61%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
            L++  L  DTT+++L  + S++G + S + + DK T K +G+ FV+FES   A  A++A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 120 LQDKGIH 126
           L  K + 
Sbjct: 61  LNGKELD 67

Length = 73

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

 Score = 79.9 bits (197), Expect = 1e-16
 Identities = 46/164 (28%), Positives = 77/164 (46%), Gaps = 13/164 (7%)

Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
             N++++ L +   +K L +  S++G I+S K   D+   K RGYGFV FE    A AA+
Sbjct: 88  VGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDEN-GKSRGYGFVHFEKEESAKAAI 146

Query: 118 K-----ALQDKGI-------HAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVV 165
           +      L DK +         +      +  TNLY+ NL  +  E  L  L AK+  + 
Sbjct: 147 QKVNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEIT 206

Query: 166 STRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEP 209
           S  +++D +  S+G  F   E  +   + ++  NG  +  +KE 
Sbjct: 207 SAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEG 250

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

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

 Score = 78.3 bits (193), Expect = 3e-16
 Identities = 44/186 (23%), Positives = 79/186 (42%), Gaps = 32/186 (17%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           TNLY++ L     +  L  + +++G I S   + D +  + RG+ FV+FE    A  AV+
Sbjct: 179 TNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGS-GRSRGFAFVNFEKHEDAAKAVE 237

Query: 119 ALQDKGI--------------------HAQMARQQEQDP---------TNLYIANLPLNF 149
            +  K I                     A++ R+ E+            NLY+ NL    
Sbjct: 238 EMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTV 297

Query: 150 KECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEP 209
            +  L  L ++   + S +++ D    S+G GF    + ++ ++ +   +G  L G  +P
Sbjct: 298 TDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGG--KP 355

Query: 210 LLVKFA 215
           L V  A
Sbjct: 356 LYVALA 361

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

 Score = 66.9 bits (164), Expect = 1e-14
 Identities = 24/66 (36%), Positives = 39/66 (59%), Gaps = 1/66 (1%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++  L  DTT++DL  + S++G I S + I+     K +G+ FV+FES   A  A++AL
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVR-IVRDKDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 121 QDKGIH 126
             K + 
Sbjct: 60  NGKELD 65

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

 Score = 65.3 bits (160), Expect = 7e-14
 Identities = 27/78 (34%), Positives = 43/78 (55%), Gaps = 4/78 (5%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           TN+Y++ L +D  D+ L  +  +YG I S K + D    K +G+GFV+FE+   A  AV+
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVE 60

Query: 119 ALQDKGIHAQM---ARQQ 133
            L  K ++ +     R Q
Sbjct: 61  ELNGKEVNGKKLYVGRAQ 78

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 64.2 bits (157), Expect = 2e-13
 Identities = 24/65 (36%), Positives = 41/65 (63%), Gaps = 1/65 (1%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++  L  DTT++DL ++ S++GPI S + I+   T + +G+ FV+FE    A  A++AL
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIR-IVRDETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 121 QDKGI 125
             K +
Sbjct: 60  NGKEL 64

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

 Score = 63.4 bits (154), Expect = 4e-13
 Identities = 30/79 (37%), Positives = 49/79 (62%), Gaps = 1/79 (1%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQ 196
            NLY++ LP    + +LE L ++Y  ++++RILRD     S+GVGF R + + + ++ I+
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 197 LFNGSTLPGSKEPLLVKFA 215
             NG    G+ EP+ VKFA
Sbjct: 61  GLNGQKPEGASEPITVKFA 79

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

 Score = 62.9 bits (152), Expect = 8e-13
 Identities = 31/84 (36%), Positives = 53/84 (63%), Gaps = 1/84 (1%)

Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQL 197
           NLY++ LP    + +LE L ++Y  ++++RIL D     S+GVGF R + + + ++ I+ 
Sbjct: 7   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 66

Query: 198 FNGSTLPGSKEPLLVKFADSGLKK 221
            NG   PG+ EP+ VKFA++  +K
Sbjct: 67  LNGQKPPGATEPITVKFANNPSQK 90

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

 Score = 62.0 bits (150), Expect = 1e-12
 Identities = 29/80 (36%), Positives = 49/80 (61%), Gaps = 1/80 (1%)

Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQL 197
           NLYI+ LP    + D+E + +++  ++++R+L D     S+GV F R + + + ++ I  
Sbjct: 2   NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 198 FNGSTLPGSKEPLLVKFADS 217
           FNG   PGS EP+ VKFA +
Sbjct: 62  FNGHKPPGSSEPITVKFAAN 81

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

 Score = 67.1 bits (164), Expect = 2e-12
 Identities = 42/157 (26%), Positives = 75/157 (47%), Gaps = 10/157 (6%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           LY+  L  D T+  L ++   +GP++S +   D  T +  GYG+V+F++   A  A++ +
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 121 QDKGIHAQMAR--QQEQDP-------TNLYIANLPLNFKECDLESLLAKYVTVVSTRILR 171
             K +  +  R    ++DP        N+++ NL  +     L    +K+  ++S ++  
Sbjct: 63  NFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVAT 122

Query: 172 DNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKE 208
           D N  S+G GF   E ++     IQ  NG  L   KE
Sbjct: 123 DENGKSRGYGFVHFEKEESAKAAIQKVNG-MLLNDKE 158

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

 Score = 65.4 bits (158), Expect = 3e-12
 Identities = 36/165 (21%), Positives = 61/165 (36%), Gaps = 32/165 (19%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
               L++  L  D T++DL  +  ++GP+   + + D+ T K RG+ FV+FES   A  A
Sbjct: 114 ENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKA 173

Query: 117 VKALQDKGIH-------------------------------AQMARQQEQDPTNLYIANL 145
           ++ L  K +                                ++      +   NLY+ NL
Sbjct: 174 IEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNL 233

Query: 146 PLNFKECDLESLLAKYVTVVSTRI-LRDNNNTSKGVGFARLESKD 189
           PL   E +L  L      +V   +    +    K   F   E+  
Sbjct: 234 PLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASK 278

Length = 306

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

 Score = 60.7 bits (148), Expect = 4e-12
 Identities = 25/64 (39%), Positives = 34/64 (53%), Gaps = 3/64 (4%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           T +++ GL   TTD  L    SQ+G I     I D+ T K RGYGFV F+      +A +
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKD---KESAER 57

Query: 119 ALQD 122
           A +D
Sbjct: 58  ACKD 61

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

 Score = 60.4 bits (147), Expect = 5e-12
 Identities = 24/62 (38%), Positives = 34/62 (54%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           TNL +  L QD T ++L ++    GPI S K + D+ T +  GYGFVD+     A  A+ 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 119 AL 120
            L
Sbjct: 61  TL 62

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

 Score = 60.4 bits (146), Expect = 6e-12
 Identities = 28/79 (35%), Positives = 49/79 (62%), Gaps = 1/79 (1%)

Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQL 197
           NLY++ LP    + ++E L ++Y  ++++RIL D     S+GVGF R + + + ++ I+ 
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKG 62

Query: 198 FNGSTLPGSKEPLLVKFAD 216
            NG    G+ EP+ VKFA+
Sbjct: 63  LNGQKPLGAAEPITVKFAN 81

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

 Score = 60.1 bits (145), Expect = 6e-12
 Identities = 29/78 (37%), Positives = 48/78 (61%), Gaps = 1/78 (1%)

Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQL 197
           NLY++ LP    + +LE L ++Y  ++++RIL D     S+GVGF R + + + ++ I+ 
Sbjct: 4   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63

Query: 198 FNGSTLPGSKEPLLVKFA 215
            NG    G+ EP+ VKFA
Sbjct: 64  LNGQKPSGAAEPITVKFA 81

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|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 = 59.9 bits (146), Expect = 7e-12
 Identities = 24/68 (35%), Positives = 39/68 (57%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
             L++ GL+  TT+K+L  + S++G +     + D  T + RG+GFV FES   A AA++
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 119 ALQDKGIH 126
            L  K + 
Sbjct: 62  DLNGKELE 69

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|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 = 59.6 bits (145), Expect = 8e-12
 Identities = 22/60 (36%), Positives = 38/60 (63%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L+I  L  + TD+DL  + + +G +IS K  +DK T + + +GFV +++   A AA+KA+
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

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

 Score = 58.9 bits (143), Expect = 1e-11
 Identities = 25/68 (36%), Positives = 38/68 (55%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           L++ NLP +  E DL  L +K+  + S RI+RD +  SKG  F   ES +  ++ ++  N
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 200 GSTLPGSK 207
           G  L G K
Sbjct: 61  GKELDGRK 68

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

 Score = 59.5 bits (145), Expect = 1e-11
 Identities = 23/64 (35%), Positives = 39/64 (60%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           NLY+  L  + T++DL ++  Q+G + S + I D+ T + RG+GFV+ E+   A AA++ 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 120 LQDK 123
           L   
Sbjct: 61  LNGT 64

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|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 = 58.0 bits (141), Expect = 3e-11
 Identities = 20/55 (36%), Positives = 34/55 (61%)

Query: 69  DTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDK 123
           D T++ LI + S+ GP++S + + D+ T K +GYGF +FE    A +A++ L   
Sbjct: 9   DATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGY 63

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

 Score = 58.0 bits (140), Expect = 4e-11
 Identities = 28/79 (35%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQ 196
           TNLY+ NLP    E +L  +   Y  +V   +LRD      +GV F R + +++    I 
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 197 LFNGSTLPGSKEPLLVKFA 215
             NG+  PGS  PL V++A
Sbjct: 61  SLNGTIPPGSTMPLSVRYA 79

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|214636 smart00360, RRM, RNA recognition motif

 Score = 57.2 bits (139), Expect = 5e-11
 Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQL 197
            L++ NLP +  E +L  L +K+  V S R++RD     SKG  F   ES++  ++ ++ 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 198 FNGSTLPGSK 207
            NG  L G  
Sbjct: 61  LNGKELDGRP 70

Length = 73

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

 Score = 57.6 bits (139), Expect = 6e-11
 Identities = 30/84 (35%), Positives = 47/84 (55%), Gaps = 5/84 (5%)

Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           GPE     NL+I  L Q+  D +L+ M   +G +IS K  +D+ TN+ + +GFV F++  
Sbjct: 1   GPE---GCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPA 57

Query: 112 YALAAVKALQDKGIHAQMARQQEQ 135
            A AA++A+   G    M R + Q
Sbjct: 58  SAQAAIQAMN--GFQIGMKRLKVQ 79

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

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

 Score = 56.9 bits (138), Expect = 8e-11
 Identities = 21/48 (43%), Positives = 31/48 (64%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           L++ GL +D T++DL    SQYG + S + + DK T K RG+ FV F+
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFD 49

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

 Score = 56.3 bits (136), Expect = 1e-10
 Identities = 20/49 (40%), Positives = 32/49 (65%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           +++ GL+ +TT+ D+    SQ+G +     + DK TN+ RG+GFV FES
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFES 50

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

 Score = 55.6 bits (134), Expect = 3e-10
 Identities = 24/71 (33%), Positives = 36/71 (50%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++R L    T +DL +  S   PI     + D  T + RGYGFV F     A  A+  L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 121 QDKGIHAQMAR 131
           ++K +H ++ R
Sbjct: 62  KNKKLHGRILR 72

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|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 = 54.9 bits (132), Expect = 4e-10
 Identities = 25/71 (35%), Positives = 40/71 (56%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L+I GL+ DT ++ L  + S+YG I     + D+ T + RG+GFV FE+   A  A+ A+
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 121 QDKGIHAQMAR 131
             K +  +  R
Sbjct: 63  NGKSVDGRQIR 73

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

 Score = 55.0 bits (133), Expect = 4e-10
 Identities = 21/62 (33%), Positives = 34/62 (54%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
             +++  L  D  +  L  + S +G + + K I D TTNKC+GYGFV   +   A +A+ 
Sbjct: 2   WCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIA 61

Query: 119 AL 120
           +L
Sbjct: 62  SL 63

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

 Score = 54.6 bits (132), Expect = 5e-10
 Identities = 24/61 (39%), Positives = 36/61 (59%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           NLY+ GL +  T ++L  + S YG II+++ + D  T   RG GF+ F+    A  A+KA
Sbjct: 2   NLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA 61

Query: 120 L 120
           L
Sbjct: 62  L 62

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 54.5 bits (132), Expect = 5e-10
 Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 2/63 (3%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           LY+R L    T++DL    S YG +   + + +K  ++ RG+ FV+F S   A AA+K L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58

Query: 121 QDK 123
              
Sbjct: 59  NGL 61

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

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

 Score = 53.8 bits (130), Expect = 9e-10
 Identities = 25/62 (40%), Positives = 36/62 (58%)

Query: 65  GLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG 124
           GL+  TT++DL  + S+YGPI   + + D+ T + RG+GFV FES   A  A + L    
Sbjct: 6   GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGME 65

Query: 125 IH 126
           I 
Sbjct: 66  ID 67

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

 Score = 53.8 bits (129), Expect = 1e-09
 Identities = 23/57 (40%), Positives = 32/57 (56%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           L++ GL  D  + DL    SQ+GP+   + I DK T K RG+GFV F++   A  A 
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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 54.2 bits (131), Expect = 1e-09
 Identities = 27/69 (39%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           KT L++  L  DTT+  L     +YGPI   + + DK T K RGY F++FE      AA 
Sbjct: 2   KT-LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAY 60

Query: 118 KALQDKGIH 126
           K    K I 
Sbjct: 61  KYADGKKID 69

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

 Score = 53.4 bits (128), Expect = 2e-09
 Identities = 25/62 (40%), Positives = 37/62 (59%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
            NLY+ GL +  T K+L  + SQYG II+++ + D+ T   RG GF+ F+    A  A+K
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 119 AL 120
            L
Sbjct: 61  GL 62

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

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 3/78 (3%)

Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQL 197
           NLY+ NLP N  E DL+ L  ++  V S R++ D     S+G GF  +E+ ++ +  I+ 
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 198 FNGSTLPGSKEPLLVKFA 215
            NG+   G    L V  A
Sbjct: 61  LNGTDFGG--RTLTVNEA 76

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|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 = 52.7 bits (127), Expect = 2e-09
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 1/65 (1%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++R L   TT+++L  +   +G I      LDK T + +G+ FV F    +A+ A   L
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 121 QDKGI 125
            D  I
Sbjct: 62  -DGSI 65

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

 Score = 52.9 bits (128), Expect = 3e-09
 Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYG--PIISTKAILDKTTNKCRGYGFVDFESGGYAL 114
           + T L +RGL   TT++D++   S     PI   + I DK T   RG+ FV+F S   A 
Sbjct: 2   TNT-LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60

Query: 115 AAVKALQ 121
             + AL 
Sbjct: 61  QWMDALN 67

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

 Score = 52.4 bits (126), Expect = 4e-09
 Identities = 20/72 (27%), Positives = 38/72 (52%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
            L++  L+    D+ L     ++G ++  + I D+ T + RG+G+VDFES   A  A++A
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 120 LQDKGIHAQMAR 131
           +  K +  +   
Sbjct: 61  MDGKELDGRPIN 72

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 51.1 bits (123), Expect = 8e-09
 Identities = 23/68 (33%), Positives = 38/68 (55%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           L++ NLP +  E DL+ L +K+  + S RI+RD    SKG  F   E ++  ++ ++  N
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 200 GSTLPGSK 207
           G  L G +
Sbjct: 61  GKELGGRE 68

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

 Score = 51.5 bits (123), Expect = 8e-09
 Identities = 27/69 (39%), Positives = 40/69 (57%), Gaps = 3/69 (4%)

Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           GPE     NL+I  L Q+ TD DL      +G +IS K  +DK TN  + +GFV +++  
Sbjct: 1   GPE---GCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPD 57

Query: 112 YALAAVKAL 120
            A AA++A+
Sbjct: 58  SAQAAIQAM 66

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

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

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 21/51 (41%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           TNLYI  L     ++DL  M   YG +IST+ + D      RG GF   ES
Sbjct: 1   TNLYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQS-RGVGFARMES 50

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

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

 Score = 51.0 bits (123), Expect = 1e-08
 Identities = 20/59 (33%), Positives = 31/59 (52%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           L+I GL+ DTT++ L    S+YG ++    + D  T + RG+GFV F         + A
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 59

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

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 20/64 (31%), Positives = 36/64 (56%), Gaps = 4/64 (6%)

Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           +T ++IR L  D T+++L  + SQ+G +   + + DK T   +G  FV F++     +A 
Sbjct: 1   RT-VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKT---KESAQ 56

Query: 118 KALQ 121
           K L+
Sbjct: 57  KCLE 60

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

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

 Score = 50.5 bits (120), Expect = 2e-08
 Identities = 25/61 (40%), Positives = 38/61 (62%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           NLY+ GL +  T K+L  + SQYG II+++ ++D+ T   RG GF+ F+    A  A+K 
Sbjct: 4   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 63

Query: 120 L 120
           L
Sbjct: 64  L 64

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

 Score = 50.4 bits (121), Expect = 2e-08
 Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 4/75 (5%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +++ GL  D T+++     SQ+G ++  + + D  T + RG+GFV F+S     +AV+ +
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSE----SAVERV 57

Query: 121 QDKGIHAQMARQQEQ 135
              G+     +Q E 
Sbjct: 58  FSAGMLELGGKQVEV 72

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

>gnl|CDD|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 50.6 bits (121), Expect = 2e-08
 Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           L++  L     E D+  + A + ++    +LRD N  S+G  F    S+      I+  +
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMH 63

Query: 200 GS-TLPGSKEPLLVKFAD 216
            S T+ G   PL+VKFAD
Sbjct: 64  HSQTMEGCSSPLVVKFAD 81

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

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

 Score = 50.8 bits (121), Expect = 2e-08
 Identities = 29/88 (32%), Positives = 48/88 (54%), Gaps = 3/88 (3%)

Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           GPE     NL+I  L Q+  D+DL+ M   +G ++S K  +DK TN  + +GFV +++  
Sbjct: 4   GPE---GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 60

Query: 112 YALAAVKALQDKGIHAQMARQQEQDPTN 139
            A AA++A+    I  +  + Q +   N
Sbjct: 61  SAQAAIQAMNGFQIGMKRLKVQLKRSKN 88

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

>gnl|CDD|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 = 50.2 bits (120), Expect = 2e-08
 Identities = 18/63 (28%), Positives = 39/63 (61%)

Query: 69  DTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ 128
           + T++ L ++ S+ GP++S + + D+ T K +GYGF +++    AL+A++ L    ++ +
Sbjct: 9   EATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYELNGR 68

Query: 129 MAR 131
             R
Sbjct: 69  QLR 71

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

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 28/81 (34%), Positives = 41/81 (50%), Gaps = 5/81 (6%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           TNL I  L Q  TD++  ++    GP+ + K + DK T    G+GFVD++S   A  A++
Sbjct: 1   TNLIINYLPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIR 60

Query: 119 AL-----QDKGIHAQMARQQE 134
            L     Q+K I    AR   
Sbjct: 61  TLNGLQLQNKRIKVAYARPGG 81

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

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 50.4 bits (121), Expect = 2e-08
 Identities = 25/59 (42%), Positives = 33/59 (55%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           L+I GL+ +TTD  L N  SQ+G I     + D  T + RG+GFV F S     AA+ A
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

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

 Score = 50.2 bits (121), Expect = 2e-08
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 2/76 (2%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLF 198
           L++  LP    E D+ +L  +Y  +    I+RD +   SKG  F +  S+++  + I+  
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 199 NGS-TLPGSKEPLLVK 213
           +G  T+PG+  PL VK
Sbjct: 62  HGKVTMPGASRPLQVK 77

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

 Score = 52.0 bits (124), Expect = 2e-08
 Identities = 28/88 (31%), Positives = 47/88 (53%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           N    +  G  +L  T L+I GL+  T D  L +  + +G ++  K I+D+ T + RG+G
Sbjct: 20  NVPVTSMLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFG 79

Query: 104 FVDFESGGYALAAVKALQDKGIHAQMAR 131
           FV+F   G A AA+  +  K ++ +  R
Sbjct: 80  FVNFNDEGAATAAISEMDGKELNGRHIR 107

Length = 144

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

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 5/77 (6%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK-- 118
           L++R L  DTTD+ L    S+ GPI     + DK + KCRG+G+V F     A  A++  
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 119 ---ALQDKGIHAQMARQ 132
                  + IH + A++
Sbjct: 62  KKTKFGGRKIHVEFAKK 78

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

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

 Score = 50.0 bits (119), Expect = 3e-08
 Identities = 22/61 (36%), Positives = 37/61 (60%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           NLYI GL +  T KD+ +M S++G II+++ ++D+ T   RG  F+ F+    A  A+ +
Sbjct: 2   NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

Query: 120 L 120
            
Sbjct: 62  F 62

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

 Score = 50.0 bits (119), Expect = 3e-08
 Identities = 23/62 (37%), Positives = 38/62 (61%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           NLY+ GL +  + K++  + SQYG II+++ ++D+ T   RG GF+ F+    A  A+K 
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKG 62

Query: 120 LQ 121
           L 
Sbjct: 63  LN 64

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

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF 198
           NLY+ NL  +  +  L    + + T+ S +++ D    SKG GF    S ++  + +   
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 199 NGSTLPGSKEPLLVKFA 215
           NG  + G K PL V  A
Sbjct: 63  NGRII-GGK-PLYVALA 77

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

 Score = 49.1 bits (118), Expect = 5e-08
 Identities = 20/68 (29%), Positives = 37/68 (54%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
           TN+Y+ NL  +  +  L+ L  KY  + S ++++D+   SKG GF   E+ +   + ++ 
Sbjct: 2   TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEE 61

Query: 198 FNGSTLPG 205
            NG  + G
Sbjct: 62  LNGKEVNG 69

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|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 = 49.1 bits (118), Expect = 5e-08
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMI 195
              L+++ L     E +LE+L +K+  V    +++D     S+G GF   ES +  D  I
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 196 QLFNGSTLPG 205
           +  NG  L G
Sbjct: 61  RDLNGKELEG 70

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

 Score = 49.1 bits (118), Expect = 5e-08
 Identities = 16/49 (32%), Positives = 27/49 (55%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           LY+  L  D T+  L  + S  GP++S +   D  T +  GY +V+F++
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQN 50

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

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

 Score = 49.4 bits (117), Expect = 6e-08
 Identities = 25/65 (38%), Positives = 39/65 (60%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           +   NLY+ GL +  T K+L  + SQYG II+++ ++D+ T   RG GF+ F+    A  
Sbjct: 3   IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEE 62

Query: 116 AVKAL 120
           A+K L
Sbjct: 63  AIKGL 67

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

 Score = 48.9 bits (117), Expect = 6e-08
 Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           L+++N+P  F++ DL  +  ++  ++   I+  N   SKG GF    +    D+  +  +
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIF-NERGSKGFGFVTFANSADADRAREKLH 61

Query: 200 GSTLPGSK 207
           G+ + G K
Sbjct: 62  GTVVEGRK 69

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

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

 Score = 48.9 bits (117), Expect = 6e-08
 Identities = 19/72 (26%), Positives = 35/72 (48%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           NL++ GL+  T   DL  + S+YG ++  K + +  +   R +GFV   S   A   ++ 
Sbjct: 1   NLWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQH 60

Query: 120 LQDKGIHAQMAR 131
           L    +H ++  
Sbjct: 61  LHRTELHGRVIS 72

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

 Score = 48.5 bits (115), Expect = 9e-08
 Identities = 20/49 (40%), Positives = 32/49 (65%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           +++ GL+ +TT +D+     Q+G +     + DKTTN+ RG+GFV FES
Sbjct: 2   IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES 50

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

 Score = 48.6 bits (116), Expect = 9e-08
 Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           KTNL +  L Q+ T  ++ ++ S  G I S K I DK T +  GYGFV++     A  A+
Sbjct: 1   KTNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

Query: 118 KA-----LQDKGI 125
                  LQ+K I
Sbjct: 61  NTLNGLRLQNKTI 73

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

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L +R L    T+ DL  + S +G +     I  K   K +G+ FV F S   A  A+K +
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVT-IPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 121 QDKGIH 126
             K I 
Sbjct: 61  NGKKIK 66

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

 Score = 47.6 bits (114), Expect = 1e-07
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 3/61 (4%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           LY+  L  + T+ DL  +   +G I   +   D  T + +GYGF+ F     A  A KAL
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFAD---AEDAKKAL 57

Query: 121 Q 121
           +
Sbjct: 58  E 58

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

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTR-ILRDNNNTSKGVGFARLES 187
           TN+YI  LP N  + DLE L   +  ++ST+ IL    N  KG GF   +S
Sbjct: 1   TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDS 51

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

 Score = 47.6 bits (113), Expect = 2e-07
 Identities = 21/62 (33%), Positives = 33/62 (53%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           TNLY+  L +  T+ +L  +   YG I+    + DK+T   RG  FV ++    A AA+ 
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 119 AL 120
           +L
Sbjct: 61  SL 62

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

 Score = 47.1 bits (112), Expect = 2e-07
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++  L+ +TT+ +L     + G I   + +  + + KC+G+ FVDFE       A  AL
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIE---FATNAL 57

Query: 121 QDKGIHAQMARQQ 133
           + K ++ +  R +
Sbjct: 58  KGKHLNGRALRVE 70

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

 Score = 47.1 bits (113), Expect = 2e-07
 Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 12/80 (15%)

Query: 61  LYIRGLTQDTTDKDLIN----MCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           LYI  L +     +L      + SQ+GP++    I+   T K RG  FV F+    A  A
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLD---IVASKTLKMRGQAFVVFKDVESATNA 58

Query: 117 VKALQ-----DKGIHAQMAR 131
           ++ALQ     DK +  Q A+
Sbjct: 59  LRALQGFPFYDKPMRIQYAK 78

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

>gnl|CDD|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 = 46.9 bits (112), Expect = 3e-07
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 4/71 (5%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAIL---DKTTNKCRGYGFVDFESGGYALAAV 117
           LY+  LT  TTD+DL    ++ G ++  K+I     K   K +G+ +V+F S   A A  
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAG-VVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVK 59

Query: 118 KALQDKGIHAQ 128
           + L+ +  + +
Sbjct: 60  EKLEGREFNGK 70

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

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

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 20/76 (26%), Positives = 35/76 (46%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L +  L  + TD+    + S +G +     +  ++T + +GYGFV++ S   AL A   L
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 121 QDKGIHAQMARQQEQD 136
             K I  +  +    D
Sbjct: 62  DGKQIGGRKLQVDWAD 77

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

 Score = 46.8 bits (111), Expect = 3e-07
 Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 4/66 (6%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +++ GL+ DTT KDL    S++G ++     +D  T + RG+GFV F+      A+V+ +
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDA----ASVEKV 56

Query: 121 QDKGIH 126
            D+  H
Sbjct: 57  LDQKEH 62

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

 Score = 47.6 bits (113), Expect = 3e-07
 Identities = 18/60 (30%), Positives = 32/60 (53%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
             L++R L  D T++ L    S++G +     ++DK+T + +G GFV F+      A +K
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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 46.8 bits (111), Expect = 4e-07
 Identities = 16/48 (33%), Positives = 26/48 (54%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           ++I GL  +TTD  L     Q+G +     + D  T + RG+GF+ F+
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFK 48

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

 Score = 46.8 bits (111), Expect = 4e-07
 Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           L++  L     E ++E + + Y  V    ++RD    S+G  F +  SK+     I+  N
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALN 61

Query: 200 GS-TLPGSKEPLLVKFAD 216
           G  T+ G  +PL+V+FAD
Sbjct: 62  GVYTMRGCDQPLIVRFAD 79

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|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 46.6 bits (110), Expect = 4e-07
 Identities = 18/48 (37%), Positives = 30/48 (62%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           +++ GL+ +T  +D+     Q+G +     + DKTTN+ RG+GFV FE
Sbjct: 6   IFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFE 53

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which 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. Musashi-2 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 = 79

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

 Score = 49.9 bits (118), Expect = 5e-07
 Identities = 28/98 (28%), Positives = 48/98 (48%), Gaps = 3/98 (3%)

Query: 126 HAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN-TSKGVGFAR 184
             +  ++ +++   L++ NLP +  E DL  L  K+  V   R++RD     S+G  F  
Sbjct: 104 SPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVE 163

Query: 185 LESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKR 222
            ES++  ++ I+  NG  L G   PL V+ A    + R
Sbjct: 164 FESEESAEKAIEELNGKELEGR--PLRVQKAQPASQPR 199

Length = 306

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

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           NLY++ L     D+ L    S +G I S K + D    + +G+GFV F S   A  AV  
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAVTE 61

Query: 120 LQDKGIHA 127
           +  + I  
Sbjct: 62  MNGRIIGG 69

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

 Score = 46.4 bits (111), Expect = 5e-07
 Identities = 16/64 (25%), Positives = 34/64 (53%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           T +++  + +  +D  +  +  + G ++S K + D +T K + +GF +FE    AL A++
Sbjct: 1   TTVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALR 60

Query: 119 ALQD 122
            L  
Sbjct: 61  LLNG 64

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 46.3 bits (110), Expect = 5e-07
 Identities = 19/59 (32%), Positives = 32/59 (54%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           L++ GL   T+D  L    ++YG +     ++D  T + RG+GF+ F S   A  A++A
Sbjct: 5   LFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEA 63

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

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

 Score = 46.2 bits (110), Expect = 5e-07
 Identities = 16/49 (32%), Positives = 32/49 (65%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           +++ GL+ +TT++ +     ++G I+  +  +DK TNK RG+ F+ F+S
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDS 50

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

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

 Score = 46.1 bits (109), Expect = 6e-07
 Identities = 23/65 (35%), Positives = 40/65 (61%), Gaps = 3/65 (4%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L+++GL++DTT++ L      +   I+ + + D+ T   +G+GFVDF S   A AA +A+
Sbjct: 3   LFVKGLSEDTTEETLKE---SFDGSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 121 QDKGI 125
           +D  I
Sbjct: 60  EDGEI 64

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

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

 Score = 49.6 bits (118), Expect = 7e-07
 Identities = 33/128 (25%), Positives = 56/128 (43%), Gaps = 6/128 (4%)

Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
           + +   NLY+ GL +  T  +L ++ S +G II+++ + D  T   +G GF+ F+    A
Sbjct: 85  DSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEA 144

Query: 114 LAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN 173
             A+K L               +P  +  AN P +     L S L       +TR+    
Sbjct: 145 DRAIKTLNGT------TPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLST 198

Query: 174 NNTSKGVG 181
             T+ G+G
Sbjct: 199 ILTAAGIG 206

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 45.6 bits (109), Expect = 7e-07
 Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 1/68 (1%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           LY+ NLP +  E DL    + Y  V   R++R+ +   +G  F    S +  +  ++  N
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDR-PRGFAFVEFASPEDAEAALKKLN 59

Query: 200 GSTLPGSK 207
           G  L G  
Sbjct: 60  GLVLDGRT 67

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

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

 Score = 46.1 bits (110), Expect = 7e-07
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 5/71 (7%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++  L   TTD+DL  + S++G I S + I DK T     Y F++FE+      A   +
Sbjct: 6   LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKM 65

Query: 121 Q-----DKGIH 126
                 D+ IH
Sbjct: 66  DNVLIDDRRIH 76

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

 Score = 45.6 bits (109), Expect = 7e-07
 Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 4/62 (6%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           N++I+ L +   +K L +  S +G I+S K   D+     +GYGFV FE+     AAV+A
Sbjct: 4   NIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDEN-GGSKGYGFVHFET---EEAAVRA 59

Query: 120 LQ 121
           ++
Sbjct: 60  IE 61

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

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

 Score = 45.7 bits (109), Expect = 7e-07
 Identities = 17/48 (35%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 62  YIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           ++ G+  DTT+++L +  S++G +   K I D+     +GYGFV FE+
Sbjct: 6   FVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFET 52

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

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

 Score = 45.3 bits (108), Expect = 9e-07
 Identities = 21/57 (36%), Positives = 30/57 (52%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           LY+ GL ++  +K L      +G I   +  LD  T K RG+ FV+FE    A AA+
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57

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

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

 Score = 49.2 bits (117), Expect = 1e-06
 Identities = 22/90 (24%), Positives = 38/90 (42%), Gaps = 5/90 (5%)

Query: 31  GGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKA 90
             T   T           +       +   +++  L+ DT +  L  +   +G + + K 
Sbjct: 247 PATDGQTAGLAAGAQIAASDG-----AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKI 301

Query: 91  ILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           I D TTN+C+GYGFV   +   A  A+ +L
Sbjct: 302 IRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

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

 Score = 45.6 bits (108), Expect = 1e-06
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++  L +  T+K++  + S YG +     + D+   + RG  FV + S   A AA+KAL
Sbjct: 2   LFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEM-KQSRGCAFVKYSSKEMAQAAIKAL 60

Query: 121 QD 122
             
Sbjct: 61  NG 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|241079 cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           L++  L     E D+  L   + T+    ILR  +  SKG  F +  S  +    I   +
Sbjct: 4   LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAINALH 63

Query: 200 GS-TLPGSKEPLLVKFAD 216
           GS T+PG+   L+VKFAD
Sbjct: 64  GSQTMPGASSSLVVKFAD 81

This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 81

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

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 19/56 (33%), Positives = 31/56 (55%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           L++  L+  TT++ L  + S+YG I   + + D  T   +GY FV++E    AL A
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRA 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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 45.7 bits (109), Expect = 1e-06
 Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 15/77 (19%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQY---------GPIISTKAILDK------TTNKCRGYG 103
           T L IR L +   +K L  +  +            I   K + D          K +GYG
Sbjct: 1   TRLSIRNLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYG 60

Query: 104 FVDFESGGYALAAVKAL 120
           FV+F +  +AL A++AL
Sbjct: 61  FVEFTNHEHALKALRAL 77

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

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

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           L + NLP    E DL+ L + +  V    I R  +   KG  F +  SK   ++ I+  N
Sbjct: 2   LIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVN 61

Query: 200 GSTLPGSKEPLLVKFA 215
           G  + G   P+ V +A
Sbjct: 62  GKKIKG--RPVAVDWA 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|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 44.8 bits (106), Expect = 2e-06
 Identities = 21/47 (44%), Positives = 31/47 (65%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
           L++ GL+ +TT + L    SQYG ++    + DKTTN+ RG+GFV F
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKF 48

This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 82

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 44.6 bits (105), Expect = 2e-06
 Identities = 20/48 (41%), Positives = 31/48 (64%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           ++I GL+ DTT KDL +  S++G ++     LD  T + RG+GFV F+
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFK 48

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 66  LTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG- 124
           L++D  + DL  +   +GPI       DK T + RG+ FV F +   A  A++ L   G 
Sbjct: 7   LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGFGY 66

Query: 125 ----IHAQMAR 131
               +  + A+
Sbjct: 67  DNLILSVEWAK 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|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 8/63 (12%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           LY+R L   TT++ L  + S+YG +   K I D        Y FV FE    A+ A++ +
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 121 QDK 123
             K
Sbjct: 56  NGK 58

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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 18/48 (37%), Positives = 30/48 (62%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           +YI GL  + T+ D++ + SQYG I+    + DK T K +G+ F+ +E
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYE 59

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

 Score = 43.4 bits (103), Expect = 4e-06
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 7/68 (10%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           L++ NLP      +L +L  KY TV    ++++        GF  +E ++  +  I+  N
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN-------YGFVHMEEEEDAEDAIKALN 54

Query: 200 GSTLPGSK 207
           G    G +
Sbjct: 55  GYEFMGKR 62

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

 Score = 47.6 bits (113), Expect = 4e-06
 Identities = 44/202 (21%), Positives = 80/202 (39%), Gaps = 24/202 (11%)

Query: 28  SQNGGTHPITTNNVQ-----HNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQY 82
           S N    P    + +        +   P    +     +++  L     ++DL    S+ 
Sbjct: 54  SPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKV 113

Query: 83  GPIISTKAILDKTTNKCRGYGFVDF---ESGGYALAA-----------VKALQ-DKGIHA 127
           G +   + I D+ + + +G  +V+F   ES   ALA            V++ Q +K   A
Sbjct: 114 GKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAA 173

Query: 128 QMARQQEQD---PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT-SKGVGFA 183
           + A  Q  D      LY+ NL  N  E +L  +   +  +   ++ RD     SKG GF 
Sbjct: 174 KAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFI 233

Query: 184 RLESKDKCDQMIQLFNGSTLPG 205
           +    ++  + +++ NG  L G
Sbjct: 234 QFHDAEEAKEALEVMNGFELAG 255

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 21/63 (33%), Positives = 31/63 (49%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +++  L  + TD+ L    S+Y      K + DK T K +GYGFV F      L A+K +
Sbjct: 9   IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEM 68

Query: 121 QDK 123
             K
Sbjct: 69  NGK 71

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

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

 Score = 43.7 bits (104), Expect = 4e-06
 Identities = 19/61 (31%), Positives = 33/61 (54%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +Y+  L +  T++ L  +  Q GP+++     D+ T   +GYGFV+F S   A  A+K +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 121 Q 121
            
Sbjct: 61  N 61

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|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 43.6 bits (102), Expect = 4e-06
 Identities = 21/70 (30%), Positives = 35/70 (50%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           NL++ GL+  T   DL N+ S+YG ++  K + +  +   R YGFV   +   A   +  
Sbjct: 3   NLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINH 62

Query: 120 LQDKGIHAQM 129
           L    +H +M
Sbjct: 63  LHRTELHGRM 72

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. 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. Length = 76

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

 Score = 43.9 bits (103), Expect = 5e-06
 Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 5/68 (7%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV---DFESGGYALAAV 117
           ++I  L QD  +  L  M   +G + + K I D  TNKC+G+GFV   ++E    A+A++
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 118 KA--LQDK 123
               L DK
Sbjct: 64  NGYRLGDK 71

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

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 16/60 (26%), Positives = 33/60 (55%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +Y+  +  D ++ D+ ++   +G I S     D  T K +GYGF+++E+   A  A+ ++
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

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

 Score = 43.2 bits (102), Expect = 7e-06
 Identities = 21/69 (30%), Positives = 35/69 (50%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L+IR L    T++DL  + S+YGP+      +DK T K +G+ FV +    +A+ A   L
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 121 QDKGIHAQM 129
                  ++
Sbjct: 65  DGTVFQGRL 73

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

 Score = 43.0 bits (101), Expect = 8e-06
 Identities = 18/44 (40%), Positives = 28/44 (63%)

Query: 65  GLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           GL+  TT++DL  + S+YGP+     + D+ T + RG+ FV FE
Sbjct: 6   GLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFE 49

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

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

 Score = 42.8 bits (101), Expect = 9e-06
 Identities = 18/63 (28%), Positives = 31/63 (49%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++R L     + DL  + S++G +      +DK + K +G+ +V F     A+ A K L
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 121 QDK 123
             K
Sbjct: 65  DGK 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|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 42.7 bits (100), Expect = 9e-06
 Identities = 18/48 (37%), Positives = 29/48 (60%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           ++I GL+ DT+ KDL    S++G ++      D  T + RG+GFV F+
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFK 49

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

 Score = 42.5 bits (101), Expect = 1e-05
 Identities = 13/58 (22%), Positives = 28/58 (48%), Gaps = 3/58 (5%)

Query: 69  DTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
           D  +++L       G + + + + D+ T   +G+G+V F++     +   AL+  GI 
Sbjct: 10  DIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKT---KDSVALALKLNGIK 64

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

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 19/50 (38%), Positives = 28/50 (56%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           T+LY+R +   T   DL  +  +YGPI+     LD  T + RG+ +V FE
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFE 50

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|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 = 42.1 bits (100), Expect = 2e-05
 Identities = 20/60 (33%), Positives = 32/60 (53%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++  L +  T++D+  +  +YG I     I DK T + +G  FV F S   A  A++AL
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 22/67 (32%), Positives = 32/67 (47%), Gaps = 3/67 (4%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKC---RGYGFVDFESGGYALAA 116
            L+I  L    T+  L+ + S+YG I     +  K+       RGY FV FE+   A  A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 117 VKALQDK 123
           +K+L  K
Sbjct: 61  LKSLNGK 67

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 7/69 (10%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNK------CRGYGFVDFESGGY 112
           T L+++ L   TT++ L     + G + S   I  K   K        GYGFV+F+S   
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVT-IAKKKDPKGPGKLLSMGYGFVEFKSKEA 59

Query: 113 ALAAVKALQ 121
           A  A+K LQ
Sbjct: 60  AQKALKRLQ 68

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 15/63 (23%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           K  L++ GL    T ++L  +  ++G + S + + ++ + K +G  +V++E+   A  AV
Sbjct: 2   KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAV 60

Query: 118 KAL 120
             +
Sbjct: 61  LKM 63

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

 Score = 45.7 bits (108), Expect = 2e-05
 Identities = 22/114 (19%), Positives = 41/114 (35%), Gaps = 8/114 (7%)

Query: 31  GGTHPITTNNVQHNGSP-GTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTK 89
             +     +N ++      + T  +  SK  +YI  L     +  +  +   +G + +  
Sbjct: 269 EVSQKNPDDNAKNVEKLVNSTTVLD--SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFN 326

Query: 90  AILDKTTNKCRGYGFVDFESGGYALAAVKALQ-----DKGIHAQMARQQEQDPT 138
            I D  T   +GY F +++       A+ AL      D  +H Q A       T
Sbjct: 327 LIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQAT 380

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

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           ++L++R +  DT  +DL     +YGPI+     LD  T + RG+ +V FE    A  A+ 
Sbjct: 1   SSLFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALH 60

Query: 119 ALQDK-----GIHAQMARQQEQDP 137
            L  K      I  Q A+   + P
Sbjct: 61  NLDRKWICGRQIEIQFAQGDRKTP 84

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

 Score = 41.2 bits (97), Expect = 3e-05
 Identities = 15/70 (21%), Positives = 35/70 (50%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
           +   L+++ LP +  + +LE L  K+  V S R++ + +   KG+ +   E++    Q +
Sbjct: 1   EKHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAV 60

Query: 196 QLFNGSTLPG 205
              +G+ +  
Sbjct: 61  LKMDGTEIKE 70

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

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 29/80 (36%), Positives = 40/80 (50%), Gaps = 5/80 (6%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           SKTNL +  L Q+ T ++L ++    G I S K + DK T +  GYGFV++     A  A
Sbjct: 3   SKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 62

Query: 117 VKA-----LQDKGIHAQMAR 131
           +       LQ K I    AR
Sbjct: 63  INTLNGLRLQTKTIKVSYAR 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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 19/49 (38%), Positives = 31/49 (63%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           L + GL+  TT++DL  + S+YGPI     + D+ + + RG+ FV FE+
Sbjct: 12  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

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|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 = 41.1 bits (97), Expect = 3e-05
 Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 6/73 (8%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           T +Y+  L    T+++L    S +G I   +   DK      GY FV F++   A  A+ 
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIV 54

Query: 119 ALQDKGIHAQMAR 131
           A+    I+ Q  +
Sbjct: 55  AVNGTSINGQTVK 67

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

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN-TSKGVGFARLESKDKCDQMIQLF 198
           +Y++NLP +    DL  + +KY  VV   I++D     SKGV F     ++   + ++  
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 199 NGSTLPGSK 207
           N   L G  
Sbjct: 64  NNKELFGRT 72

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|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 41.2 bits (96), Expect = 4e-05
 Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 2/65 (3%)

Query: 55  QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYAL 114
           QL K  L+I GL+ +TTD+ L +   Q+G +     + D  T + RG+GFV + S     
Sbjct: 1   QLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVD 58

Query: 115 AAVKA 119
           AA+ A
Sbjct: 59  AAMNA 63

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

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

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           L++ NLP +  E + + L +KY  V    +     N  KG GF RL+++   ++     +
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFL-----NKEKGFGFIRLDTRTNAEKAKAELD 58

Query: 200 GSTLPGSKEPLLVKF 214
           G    G    L V+F
Sbjct: 59  GIMRKG--RQLRVRF 71

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

 Score = 40.8 bits (96), Expect = 4e-05
 Identities = 15/66 (22%), Positives = 33/66 (50%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           ++++  L+ +   + L    + +G I   + + D  T K +GYGFV F     A  A+++
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 120 LQDKGI 125
           +  + +
Sbjct: 61  MNGQWL 66

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|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 = 40.3 bits (95), Expect = 5e-05
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLF 198
           L+I +LP  F + DL  L A +  V+S ++  D N   SK  GF   ++ +     I+  
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 199 NGSTLPGSK 207
           NG  + G +
Sbjct: 61  NGFQVGGKR 69

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

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 5/72 (6%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAIL----DKTTNKCRGYGFVDFESGGYAL 114
           TNLY+  L    T++ L     ++GP+ S K I+    ++   + R  GFV F +   A 
Sbjct: 2   TNLYVGNLNPKVTEEVLCQEFGRFGPLASVK-IMWPRTEEERRRNRNCGFVAFMNRADAE 60

Query: 115 AAVKALQDKGIH 126
            A+  L  K + 
Sbjct: 61  RALDELDGKDVM 72

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

 Score = 40.8 bits (96), Expect = 5e-05
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 7/76 (9%)

Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           K ++++  L+ D T ++L    S++G I+    I  K  N    + F+ FE    A  AV
Sbjct: 3   KYSIFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAV 60

Query: 118 KA-----LQDKGIHAQ 128
           ++     L++K +H Q
Sbjct: 61  ESENHSMLKNKTMHVQ 76

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

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAIL-DKTTNKCRGYGFVDFESGGYALAAVK 118
           NL+I  L  +  +K L +  S +G I+ T  I+ D  T   +G+ F+ ++S   + AA++
Sbjct: 3   NLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIE 62

Query: 119 AL 120
           A+
Sbjct: 63  AM 64

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|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 = 40.3 bits (95), Expect = 6e-05
 Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
           T +Y+ NLP    E +L+   + +  +   R+ +D     KG  F R ++ +     I  
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVA 55

Query: 198 FNGSTLPGS 206
            NG+++ G 
Sbjct: 56  VNGTSINGQ 64

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

 Score = 40.4 bits (95), Expect = 6e-05
 Identities = 22/66 (33%), Positives = 34/66 (51%)

Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           K+ +Y+  L    T+ DL  + S+YG ++    + DK T K +G  F+ F     A   V
Sbjct: 1   KSTVYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCV 60

Query: 118 KALQDK 123
           KAL +K
Sbjct: 61  KALNNK 66

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

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           +++ NLP +    DL+ L  +   V+   +  DN+  SKG G    ES +   + I++FN
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 200 GSTLPGSKEPLLVK 213
           G  L G    L V+
Sbjct: 61  GYDLEG--RELEVR 72

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

 Score = 43.7 bits (103), Expect = 7e-05
 Identities = 23/85 (27%), Positives = 35/85 (41%), Gaps = 3/85 (3%)

Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMI 195
              +YI NLPL   E  ++ LL  +  + +  +++D     SKG  F   +     D  I
Sbjct: 295 KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAI 354

Query: 196 QLFNGSTLPGSKEPLLVKFADSGLK 220
              NG     +K  L V+ A  G  
Sbjct: 355 AALNGKDTGDNK--LHVQRACVGAN 377

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

 Score = 40.5 bits (94), Expect = 7e-05
 Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 5/79 (6%)

Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           +TNL +  L Q+ T  +L ++ S  G + S K I DK      GYGFV++ +   A  A+
Sbjct: 1   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAI 60

Query: 118 KA-----LQDKGIHAQMAR 131
                  LQ K I    AR
Sbjct: 61  NTLNGLRLQSKTIKVSYAR 79

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

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

 Score = 40.2 bits (95), Expect = 8e-05
 Identities = 19/72 (26%), Positives = 33/72 (45%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
              N++I NL  +     L    + +  ++S ++  D N  SKG GF   E+++   + I
Sbjct: 1   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAI 60

Query: 196 QLFNGSTLPGSK 207
           +  NG  L   K
Sbjct: 61  EKVNGMLLNDKK 72

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

 Score = 40.5 bits (94), Expect = 8e-05
 Identities = 28/80 (35%), Positives = 39/80 (48%), Gaps = 5/80 (6%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           SKTNL +  L Q+ T ++  ++    G I S K + DK T +  GYGFV++     A  A
Sbjct: 2   SKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKA 61

Query: 117 VKA-----LQDKGIHAQMAR 131
           +       LQ K I    AR
Sbjct: 62  INTLNGLKLQTKTIKVSYAR 81

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

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 40.0 bits (93), Expect = 8e-05
 Identities = 15/51 (29%), Positives = 30/51 (58%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           +++ GL+ DT+ KDL +  +++G +      +D  T + RG+GF+ F+   
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDAS 52

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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 40.1 bits (93), Expect = 8e-05
 Identities = 28/80 (35%), Positives = 39/80 (48%), Gaps = 5/80 (6%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           SKTNL +  L Q+ T ++  ++    G I S K + DK T +  GYGFV++     A  A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 117 VKA-----LQDKGIHAQMAR 131
           +       LQ K I    AR
Sbjct: 61  INTLNGLRLQTKTIKVSYAR 80

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

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

 Score = 39.9 bits (93), Expect = 9e-05
 Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 2/79 (2%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQ-L 197
           L++ ++P    E ++  +  ++  V+   I++D      +G  F +  ++D+ D+ I+ L
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 198 FNGSTLPGSKEPLLVKFAD 216
            N  TLPG   P+ V++AD
Sbjct: 62  HNQRTLPGGASPVQVRYAD 80

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

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 40.1 bits (93), Expect = 9e-05
 Identities = 20/59 (33%), Positives = 32/59 (54%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           L+I GL+ +TT++ L N   Q+G +     + D  + + RG+GFV F       AA+ A
Sbjct: 5   LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILR-DNNNTSKGVGFARLESKD 189
           L + NLPL F +     L++ +  V    ++  ++   SKG GF    SK 
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKA 52

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 18/68 (26%), Positives = 33/68 (48%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +Y+  L ++ T + L  + S+YG ++       K T   +G+ F++FE+   A  A K L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 121 QDKGIHAQ 128
            +    A 
Sbjct: 62  NNPPETAT 69

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

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 19/60 (31%), Positives = 31/60 (51%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +++  L  D  +  L  M   +G + + K I D  TNKC+G+GFV   +   A  A+ +L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

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

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 2/65 (3%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           LY+  L++D T+  ++ + SQ GP  S K I+D   N    Y FV+F    +A A++ A+
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGND--PYCFVEFFEHRHAAASLAAM 59

Query: 121 QDKGI 125
             + I
Sbjct: 60  NGRKI 64

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

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 16/69 (23%), Positives = 39/69 (56%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +++ G+ ++  ++D+ +  +++G I +    LD+ T   +GY  +++E+   A AA++ L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 121 QDKGIHAQM 129
             K +  Q 
Sbjct: 69  NGKELLGQT 77

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|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 6/49 (12%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           L++R L  D T+ DLI + S +G +  T  +L +  N+      V+ +S
Sbjct: 2   LHLRNLPPDVTESDLIALVSPFGKV--TNVLLLRGKNQ----ALVEMDS 44

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|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

 Score = 39.3 bits (91), Expect = 1e-04
 Identities = 19/70 (27%), Positives = 33/70 (47%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           NL++ GL+ +T   DL N+  +YG ++S K + +  +   + YG V   S       +  
Sbjct: 1   NLWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISH 60

Query: 120 LQDKGIHAQM 129
           L    +H Q 
Sbjct: 61  LHRTELHGQQ 70

This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains 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. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. . Length = 74

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

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 18/60 (30%), Positives = 33/60 (55%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +++  L+ +  +  L  +   +G + + K I D TTNKC+G+GFV   +   A  A+ +L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

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|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 17/48 (35%), Positives = 30/48 (62%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           L++ G+ +DT +  L +   +YG I + + I D+ + K RG+GFV F+
Sbjct: 3   LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFD 50

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 3/54 (5%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVG---FARLESKDK 190
           L++ NL  + ++ DLE    +   VV  RI +D++  SKG G   FA  E   K
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQK 55

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQ 196
           TNL +  LP +  + +L SL      + S +I+RD     S G GF     ++   + I 
Sbjct: 1   TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 197 LFNGSTLPGSKEPLLVKFA 215
             NG  +   +  L V +A
Sbjct: 61  TLNGFEIRNKR--LKVSYA 77

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

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQL 197
            L++ NL  +  +  L++   K+ TVV  R++ D     S+G G+   ES +   + I+ 
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 198 FNGSTLPG 205
            +G  L G
Sbjct: 61  MDGKELDG 68

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

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 2/68 (2%)

Query: 141 YIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFN 199
           ++ NLP + +E +L         V + RI+RD      KG G+   ++KD     ++L N
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL-N 61

Query: 200 GSTLPGSK 207
           G  L G K
Sbjct: 62  GIKLKGRK 69

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

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

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 18/49 (36%), Positives = 24/49 (48%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           L++  L      K+L    SQ+G + S     DK T   +GYGFV F S
Sbjct: 2   LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSS 50

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|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 26/81 (32%), Positives = 38/81 (46%), Gaps = 4/81 (4%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRD---NNNTSKGVGFARLES-KDKCDQMI 195
           +++  +P ++ E DL  L  +Y  V    +LRD   N   SKG  F    + K   +   
Sbjct: 4   MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 63

Query: 196 QLFNGSTLPGSKEPLLVKFAD 216
            L N  TLPG   P+ +K AD
Sbjct: 64  ALHNMKTLPGMHHPIQMKPAD 84

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ-LF 198
           L+I  +     E D+  + + +  +   RILR  +  S+G  F    ++      I+ + 
Sbjct: 4   LFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 63

Query: 199 NGSTLPGSKEPLLVKFAD 216
              T+ G   P++VKFAD
Sbjct: 64  QAQTMEGCSSPIVVKFAD 81

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 19/71 (26%), Positives = 35/71 (49%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++  L+ D  +  +     +YG I S +   D  + + +G+G+V+F S   A AA+ AL
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 121 QDKGIHAQMAR 131
               +  +  R
Sbjct: 61  GGTDLLGRPVR 71

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|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 = 2e-04
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 3/68 (4%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           LY+  L +  T+  L  + SQ GPI S K I +   +    Y FV++     A AA++ +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGNDP---YAFVEYYDHRSAAAALQTM 57

Query: 121 QDKGIHAQ 128
             + I  Q
Sbjct: 58  NGRLILGQ 65

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|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 = 38.9 bits (91), Expect = 2e-04
 Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCD 192
           + D   L++  +P N +E DL  L  ++  +    +L+D      KG  F    +++   
Sbjct: 2   DDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESAL 61

Query: 193 QMIQLFNGS-TLPGSKEPLLVKFADS 217
           +     +   TLPG   P+ VK ADS
Sbjct: 62  KAQSALHEQKTLPGMNRPIQVKPADS 87

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

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 8/62 (12%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTT-NKCRGYGFVDFESGGYALAAVKA 119
           L++ GL   T+  +L     ++G I        +   +  R Y ++++ES   A AA +A
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAI-------RRIDYDPGRNYAYIEYESIEAAQAAKEA 53

Query: 120 LQ 121
           L+
Sbjct: 54  LR 55

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

 Score = 38.3 bits (90), Expect = 3e-04
 Identities = 19/60 (31%), Positives = 31/60 (51%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++  LT++     L  + S YG +      +D+  N  RGY +V+FES   A  A+K +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

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

 Score = 38.9 bits (90), Expect = 3e-04
 Identities = 18/60 (30%), Positives = 33/60 (55%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +++  L+ D+ +  L  +   +G + + K I D  TNKC+G+GFV   +   A  A+ +L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

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

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 14/58 (24%), Positives = 26/58 (44%)

Query: 68  QDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGI 125
           +  T+ DL    + +G I     + DK T + +G  +V F     A  A++ +  K +
Sbjct: 12  KSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGKCL 69

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

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 18/64 (28%), Positives = 30/64 (46%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           N+++  L+ + TD  L    S +      + + D  + + RGYGFV F S   A  A+  
Sbjct: 1   NIFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINE 60

Query: 120 LQDK 123
           +  K
Sbjct: 61  MNGK 64

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|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2)

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 4/57 (7%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           L++R L  + T+++LI +C  +G I++TK  +    N+     FV+F     A+A V
Sbjct: 5   LHLRNLPWECTEEELIELCKPFGKIVNTKCNVGANRNQ----AFVEFADLNQAIAMV 57

This subfamily corresponds to the RRM1 of PTBPH1 and PTBPH2. Although their biological roles remain unclear, PTBPH1 and PTBPH2 show 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. Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 81

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

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 7/74 (9%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
            S T L+I  L++  T++DL N+  +YG I S   I        RG  +V  E+   A  
Sbjct: 1   CSTT-LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPP------RGCAYVCMETRQDAHR 53

Query: 116 AVKALQDKGIHAQM 129
           A++ L++  +  + 
Sbjct: 54  ALQKLRNVKLAGKK 67

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

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMI 195
              +++ NLP +  E  L  L + +  V + +++RD   N  KG GF  + + ++    I
Sbjct: 1   GWCIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAI 60

Query: 196 QLFNGSTLPGSKEPLLVKF 214
              NG  L G    L V F
Sbjct: 61  ASLNGYRLGG--RVLQVSF 77

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

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 14/63 (22%), Positives = 34/63 (53%)

Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
           P  +++  +P +  E +L    +++ +V   +I+ D    SKG GF   E+++  ++++ 
Sbjct: 2   PNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEKILA 61

Query: 197 LFN 199
           + N
Sbjct: 62  MGN 64

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

>gnl|CDD|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 = 38.0 bits (89), Expect = 4e-04
 Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 1/64 (1%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           T L +R +  + T K+L  + S +G + S + +  K     RG+ FV+F +   A  A++
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVR-LPKKFDGSHRGFAFVEFVTKQEAQNAME 59

Query: 119 ALQD 122
           AL+ 
Sbjct: 60  ALKS 63

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

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

 Score = 38.0 bits (88), Expect = 4e-04
 Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           ++I  L +D  + +LI +C + G I   + ++D   N  RGY FV F +   A  A+K L
Sbjct: 4   IFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFNGNN-RGYAFVTFSNKQEAKNAIKQL 62

Query: 121 QDKGI 125
            +  I
Sbjct: 63  NNYEI 67

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

 Score = 37.7 bits (87), Expect = 5e-04
 Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQ 196
            NL+I +LP  F + DL      +  V+S ++  D   N SK  GF   ++ D     IQ
Sbjct: 5   CNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQ 64

Query: 197 LFNG 200
             NG
Sbjct: 65  AMNG 68

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

>gnl|CDD|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 = 38.2 bits (89), Expect = 5e-04
 Identities = 19/71 (26%), Positives = 34/71 (47%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++  + ++  +KDL  +  Q+G I     + DK T   +G  F+ + +   AL A  AL
Sbjct: 8   LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSAL 67

Query: 121 QDKGIHAQMAR 131
            ++     M R
Sbjct: 68  HEQKTLPGMNR 78

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

 Score = 38.1 bits (88), Expect = 5e-04
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 5/84 (5%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           T+L++R +   T  +DL     +YGPI+     LD  T + RG+ ++ FE    A  A+ 
Sbjct: 1   TSLFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALY 60

Query: 119 ALQDK-----GIHAQMARQQEQDP 137
            L  K      I  Q A+   + P
Sbjct: 61  NLNRKWVCGRQIEIQFAQGDRKTP 84

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

 Score = 37.9 bits (88), Expect = 5e-04
 Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           T + ++ L  + T KD+  + S YG + S + +  K     RG+ FV+F +   AL A+ 
Sbjct: 1   TKILVKNLPFEATKKDVRTLFSSYGQLKSVR-VPKKFDQSARGFAFVEFSTAKEALNAMN 59

Query: 119 ALQDKGIH 126
           AL  K  H
Sbjct: 60  AL--KDTH 65

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

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

 Score = 37.8 bits (88), Expect = 5e-04
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           +L + GL   TT++DL +  S +G ++  +   D  T + +G+GFV F         VK 
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFAD---YEDQVKV 57

Query: 120 L 120
           L
Sbjct: 58  L 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|240866 cd12420, RRM_RBPMS_like, RNA recognition motif in RNA-binding protein with multiple splicing (RBP-MS)-like proteins

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 7/66 (10%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRG----YGFVDFESGGYALAA 116
           L++ GL  D  +++L ++   + P    +A       K  G     GFVDF S   A AA
Sbjct: 3   LFVSGLPSDVKERELAHL---FRPFPGYEASRLVFKEKKGGEKQPVGFVDFSSAQCAAAA 59

Query: 117 VKALQD 122
           + ALQ 
Sbjct: 60  MDALQG 65

This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. Length = 79

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

 Score = 37.8 bits (87), Expect = 6e-04
 Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           TNLYI  L     +++L NM   +G +IST+ IL  ++   RG GF   ES
Sbjct: 1   TNLYISNLPLSMDEQELENMLKPFGQVISTR-ILRDSSGTSRGVGFARMES 50

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

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

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPI-ISTKAILDKTTNKCRGYGFVDFES 109
            + +RGL    T++D+ N    +G      + +  KTT   RG+ FV+F S
Sbjct: 4   TIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMS 54

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|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 = 37.6 bits (88), Expect = 6e-04
 Identities = 18/79 (22%), Positives = 42/79 (53%), Gaps = 3/79 (3%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVS-TRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
           + L + NLP +  E +L+   +K+   ++  ++LR  +  S+ + F   +++++  +   
Sbjct: 1   SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAKD 60

Query: 197 LFNGSTLPGSKEPLLVKFA 215
            FN + +  SK  + V+FA
Sbjct: 61  YFNNTYINTSK--ISVEFA 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|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 = 6e-04
 Identities = 13/60 (21%), Positives = 29/60 (48%), Gaps = 4/60 (6%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +++  L     + +L  + S+ G I   + + +    K +GY +V+FE+     +  +AL
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFEN---EESVQEAL 57

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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 4/74 (5%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +++ GL  + T+ DL    SQ+G +     + D    + RG+GF+ FES      +V  +
Sbjct: 5   IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESE----DSVDQV 60

Query: 121 QDKGIHAQMARQQE 134
            ++  H    ++ E
Sbjct: 61  VNEHFHDINGKKVE 74

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

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

 Score = 37.5 bits (87), Expect = 7e-04
 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLF 198
           L+I  L  +  E  LE + +KY  +    +++D     S+G GF   E+ D     +   
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 199 NGSTLPG 205
           NG ++ G
Sbjct: 63  NGKSVDG 69

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

 Score = 37.8 bits (87), Expect = 7e-04
 Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 2/65 (3%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           LY+  L++D T+  ++ + SQ GP  S K I + T+N    Y FV+F     A AA+ A+
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSND--PYCFVEFYEHRDAAAALAAM 59

Query: 121 QDKGI 125
             + I
Sbjct: 60  NGRKI 64

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

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

 Score = 37.4 bits (87), Expect = 9e-04
 Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 8/80 (10%)

Query: 140 LYIANLPLNFKECDLESLLAKY----VTVVSTRILRDNNNTSK--GVGFARLESKDKCDQ 193
           +YI+NL  +  E DLE  L  +    V + S  +    +   +  G+ +A   S ++ ++
Sbjct: 2   VYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEK 61

Query: 194 MIQLFNGSTLPGSKEPLLVK 213
           +++  NG      K  L VK
Sbjct: 62  VVKDLNGKVFKNRK--LFVK 79

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 9/76 (11%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           LY+ NLPL+  E  L  L ++Y  V   + ++D         F   E +D   + ++  N
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD-------YAFVHFEERDDAVKAMEEMN 56

Query: 200 GSTLPGSKEPLLVKFA 215
           G  L GS  P+ V  A
Sbjct: 57  GKELEGS--PIEVSLA 70

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|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 36.8 bits (85), Expect = 0.001
 Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           L++ NLP +  E D + L  KY       I RD     +G GF RLES+   +      +
Sbjct: 4   LFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELD 58

Query: 200 GSTLPGSKEPLLVKF 214
           G+ L     PL ++F
Sbjct: 59  GTIL--KNRPLRIRF 71

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 3/43 (6%)

Query: 80  SQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQD 122
           ++ G + S K I +K T K  GYGFV+F +  +  AA +ALQ 
Sbjct: 21  AECGEVTSVKIIRNKQTGKSAGYGFVEFAT--HE-AAEQALQS 60

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

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

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 15/48 (31%), Positives = 28/48 (58%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           +++ G+ +DT +  L +   QYG I   + + D+ + K RG+ FV F+
Sbjct: 3   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 50

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
           + + + NLP    E  L         V   +++R  +  S+  GF   +S++   Q ++ 
Sbjct: 1   SRIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKY 60

Query: 198 FNGSTLPGSKEPLLVKFA 215
           FN + +  SK  + V+ A
Sbjct: 61  FNKTFIDTSK--ISVELA 76

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

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

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 3/61 (4%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++  L  DTT +DL+      G   S + + DK T K +G  FV+F++   A A  KAL
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDT---AEAMTKAL 59

Query: 121 Q 121
           +
Sbjct: 60  K 60

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

>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT--SKGVGFARLESKDKCDQM 194
           P   Y+ NLP +  E D++    + + V S R+ R+  +    +G G+A  E +D   Q 
Sbjct: 1   PYTAYLGNLPYDVTEEDIKEFF-RGLNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQA 59

Query: 195 IQL 197
           + L
Sbjct: 60  LSL 62

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 10/43 (23%), Positives = 22/43 (51%)

Query: 66  LTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           L+    ++DL    S+ G +   + I D+ + + +G  +V+F 
Sbjct: 7   LSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFY 49

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

 Score = 36.0 bits (83), Expect = 0.002
 Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQM 194
           +  NL+I +LP  F + +L  +   +  V+S ++  D   N SK  GF   ++       
Sbjct: 3   EGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAA 62

Query: 195 IQLFNG 200
           IQ  NG
Sbjct: 63  IQAMNG 68

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

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQ 196
           ++I NLP +  E +L+ L +++  V   RI++D     SKG  F + ++K+   + ++
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN-TSKGVGFARLESKDKCDQMIQ 196
           TNL +  LP N  + ++ SL +    + S +++RD     S G GF      +  ++ I 
Sbjct: 2   TNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAIN 61

Query: 197 LFNGSTL 203
             NG  L
Sbjct: 62  TLNGLRL 68

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN-TSKGVGFARLESKDK 190
            Q +D   +YI  LP    E D+  + ++Y  +V   ++RD     SKG  F   E +  
Sbjct: 4   DQYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRS 63

Query: 191 CDQMIQLFNGSTLPG 205
               +   NG  L G
Sbjct: 64  TILAVDNLNGIKLLG 78

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 5/68 (7%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPI---ISTKAI--LDKTTNKCRGYGFVDFESGGYALA 115
           +YI  L+  ++++DL      + P+   I ++ +        +  G  + +F S   A  
Sbjct: 2   VYISNLSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEK 61

Query: 116 AVKALQDK 123
            VK L  K
Sbjct: 62  VVKDLNGK 69

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 14/50 (28%), Positives = 25/50 (50%)

Query: 68  QDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           +  T++DL     ++G I     + DK T + +G+G+V F     A  A+
Sbjct: 10  KSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 6/64 (9%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIIST---KAILDKTTNKCRGYGFVDFESGGYALAAV 117
           +Y+R L     + DL  + S++G + S    K   +K      G+ FV F+    A +A 
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKD---ASSAE 59

Query: 118 KALQ 121
            ALQ
Sbjct: 60  NALQ 63

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|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 35.6 bits (81), Expect = 0.003
 Identities = 23/51 (45%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTR-ILRDNNNTSKGVGFARLES 187
           TNLYI  LP    + DL  L   Y  +VST+ IL  N N  KG GF   +S
Sbjct: 5   TNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDS 55

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|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 24/79 (30%), Positives = 34/79 (43%), Gaps = 1/79 (1%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           TNLYI  L     +++L +M   +G +IST+ IL   +   RG GF   ES     A + 
Sbjct: 1   TNLYISNLPLSMDEQELESMLKPFGQVISTR-ILRDASGTSRGVGFARMESTEKCEAIIT 59

Query: 119 ALQDKGIHAQMARQQEQDP 137
               K I          +P
Sbjct: 60  HFNGKYIKTPPGVPAPTEP 78

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|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family proteins

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 2/66 (3%)

Query: 142 IANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGS 201
           I+N+P + +  DL+SLL+ Y TV +   +   + T+        ES ++  Q +   NG 
Sbjct: 5   ISNIPPHVRWEDLDSLLSTYGTVKNCEQVPTKSETA--TVNVTYESPEQAQQAVNKLNGH 62

Query: 202 TLPGSK 207
              GSK
Sbjct: 63  EYEGSK 68

This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. . Length = 76

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

 Score = 35.6 bits (83), Expect = 0.003
 Identities = 13/49 (26%), Positives = 25/49 (51%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           L++ GL+   T+ DL    S++G +   + I  K     RG+ ++D  +
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRT 50

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 12/68 (17%), Positives = 29/68 (42%), Gaps = 4/68 (5%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL-- 197
           +Y+   P +    D++    K+  V + R+ RD +   KG  F   ++++   + ++   
Sbjct: 2   VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEKEK 61

Query: 198 --FNGSTL 203
             +    L
Sbjct: 62  LKYKEKEL 69

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 55  QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
           QL K  L+I GL+ +TTD  L     ++G +     + D  T + RG+GFV +
Sbjct: 1   QLRK--LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTY 51

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           LY+  L    T+  L  +    GP+ + K I DK  NK   YGFV++     A  A++ L
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKN-NKGVNYGFVEYHQSHDAEIALQTL 59

Query: 121 QDKGIHAQMAR 131
             + I     R
Sbjct: 60  NGRQIENNEIR 70

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

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 35.4 bits (81), Expect = 0.003
 Identities = 17/47 (36%), Positives = 27/47 (57%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
           ++I GL+  T+   L +  S++G I     + D TT + RG+GFV F
Sbjct: 2   MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTF 48

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which 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. Musashi-2 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 = 76

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 5/51 (9%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESK 188
           + L++ NLP +  E ++  L  KY       I +D     KG GF RLE++
Sbjct: 2   SRLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD-----KGFGFIRLETR 47

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 140 LYIANLPLNFKE-CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF 198
           L I NLP + K+   L+ +  +Y  V    I R       G  F  ++ +   +  ++  
Sbjct: 3   LIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALENT 62

Query: 199 NGSTLPGSKEPLLVKFA 215
           NG  + G   P+ V +A
Sbjct: 63  NGLEIDG--RPVAVDWA 77

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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           +++ G+   T + DL    SQYG +   K + D+     +GYGFV FE+
Sbjct: 5   IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFET 52

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

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

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 72  DKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGI 125
           D DL  M  Q+GPI+  + I ++  +K  G+GFV F +   A  A + L    +
Sbjct: 14  DPDLRQMFGQFGPILDVEIIFNERGSK--GFGFVTFANSADADRAREKLHGTVV 65

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

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

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 6/71 (8%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++  L  D T+++   + S+YG +           NK +G+GF+  ++   A  A   L
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFL------NKEKGFGFIRLDTRTNAEKAKAEL 57

Query: 121 QDKGIHAQMAR 131
                  +  R
Sbjct: 58  DGIMRKGRQLR 68

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

 Score = 35.2 bits (82), Expect = 0.004
 Identities = 17/49 (34%), Positives = 25/49 (51%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           +YI  L     + +L    SQ+G +   +    K T K +GY FV+FES
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFES 50

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

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

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 4/53 (7%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCD 192
           +Y+ NLP + +E D+E L  KY  + +  +     N  +G  FA +E +D  D
Sbjct: 2   IYVGNLPGDIRERDIEDLFYKYGPIKAIDL----KNRRRGPPFAFVEFEDPRD 50

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|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 16/47 (34%), Positives = 25/47 (53%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
           ++I GL+  TT + L     Q+G +     + D  T + RG+GFV F
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49

This subgroup corresponds to the RRM1 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). Musashi-1 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, 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 = 77

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

 Score = 35.2 bits (82), Expect = 0.004
 Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 10/83 (12%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRI--LRDNNNTSKGVGFARLE--SKDKCDQ 193
           + L++ N P +F + D+  L  +Y  ++S R   LR N        F  ++  S +    
Sbjct: 1   STLWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLRFNKTRR----FCYVQFTSPESAAA 56

Query: 194 MIQLFNGSTLPGSKEPLLVKFAD 216
            + L NG    G K  L+VK +D
Sbjct: 57  AVALLNGKLGEGYK--LVVKISD 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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 35.2 bits (81), Expect = 0.004
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT--SKGVGFARLESKDKCDQMIQL 197
           +YI +LP  F E +L+   +++ TV + R+ R +  T  SK  GF +  + +      + 
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVAR-SKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 198 FNGSTLPGSK 207
            N   L G  
Sbjct: 61  MNNYLLMGKV 70

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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 18/47 (38%), Positives = 27/47 (57%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
           ++I GL+  TT + L    S++G I     + D TT + RG+GFV F
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTF 47

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	305
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
KOG0148|consensus	321		100.0
KOG0144|consensus	510		100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
KOG0117|consensus	506		100.0
KOG0145|consensus	360		100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.98
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.98
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.97
KOG0131|consensus	203		99.96
KOG0145|consensus	360		99.95
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.95
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.95
KOG0109|consensus	346		99.95
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.94
KOG0127|consensus	678		99.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.94
KOG0146|consensus	371		99.94
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.92
KOG0124|consensus	544		99.92
KOG4205|consensus	311		99.92
KOG0127|consensus	678		99.92
KOG0144|consensus	510		99.91
KOG0123|consensus	369		99.91
KOG0148|consensus	321		99.9
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.87
KOG0110|consensus	725		99.87
KOG0147|consensus	549		99.87
KOG0123|consensus	369		99.86
KOG0105|consensus	241		99.85
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.83
KOG0147|consensus	549		99.81
KOG4212|consensus	608		99.8
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.75
KOG4206|consensus	221		99.75
KOG1548|consensus	382		99.74
KOG4211|consensus	510		99.71
KOG0110|consensus	725		99.71
KOG1457|consensus	284		99.7
KOG0149|consensus	247		99.7
KOG0124|consensus	544		99.68
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.67
KOG0149|consensus	247		99.67
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.66
KOG0106|consensus	216		99.65
KOG0121|consensus	153		99.65
KOG4212|consensus	608		99.64
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.64
KOG0122|consensus	270		99.63
KOG1190|consensus	492		99.63
KOG0122|consensus	270		99.62
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.61
KOG0107|consensus	195		99.61
KOG0125|consensus	376		99.6
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.59
KOG0125|consensus	376		99.59
KOG0121|consensus	153		99.58
KOG0120|consensus	500		99.58
KOG4207|consensus	256		99.57
PLN03120	260	nucleic acid binding protein; Provisional	99.57
KOG0113|consensus	335		99.56
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.56
KOG0105|consensus	241		99.54
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.54
KOG0126|consensus	219		99.54
KOG0107|consensus	195		99.54
KOG0117|consensus	506		99.53
KOG0129|consensus	520		99.51
KOG0113|consensus	335		99.51
PLN03120	260	nucleic acid binding protein; Provisional	99.51
KOG1365|consensus	508		99.49
KOG0126|consensus	219		99.47
KOG4207|consensus	256		99.47
KOG0114|consensus	124		99.46
smart00362	72	RRM_2 RNA recognition motif.	99.46
KOG4454|consensus	267		99.45
KOG1190|consensus	492		99.45
KOG0146|consensus	371		99.45
PLN03121	243	nucleic acid binding protein; Provisional	99.44
smart00362	72	RRM_2 RNA recognition motif.	99.44
KOG0111|consensus	298		99.44
PLN03213	759	repressor of silencing 3; Provisional	99.44
PLN03213	759	repressor of silencing 3; Provisional	99.43
PLN03121	243	nucleic acid binding protein; Provisional	99.43
KOG0108|consensus	435		99.42
KOG0108|consensus	435		99.41
smart00360	71	RRM RNA recognition motif.	99.4
KOG0132|consensus	894		99.4
smart00360	71	RRM RNA recognition motif.	99.39
KOG0130|consensus	170		99.39
KOG0131|consensus	203		99.38
KOG1456|consensus	494		99.38
KOG0114|consensus	124		99.38
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.37
KOG1456|consensus	494		99.35
KOG0226|consensus	290		99.34
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.34
KOG0132|consensus	894		99.34
KOG0111|consensus	298		99.32
KOG0109|consensus	346		99.31
KOG0120|consensus	500		99.31
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.3
KOG4211|consensus	510		99.3
KOG0130|consensus	170		99.29
KOG4210|consensus	285		99.29
KOG0128|consensus	881		99.28
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.28
smart00361	70	RRM_1 RNA recognition motif.	99.27
smart00361	70	RRM_1 RNA recognition motif.	99.27
KOG0112|consensus	975		99.26
KOG0415|consensus	479		99.14
KOG4206|consensus	221		99.11
KOG4208|consensus	214		99.06
KOG4661|consensus	940		99.04
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.04
KOG0116|consensus	419		99.04
KOG4208|consensus	214		99.03
KOG0153|consensus	377		99.03
KOG4660|consensus	549		98.96
KOG4849|consensus	498		98.94
KOG0415|consensus	479		98.94
KOG4205|consensus	311		98.94
KOG0533|consensus	243		98.94
KOG4307|consensus	944		98.92
KOG0533|consensus	243		98.89
KOG0153|consensus	377		98.86
KOG1457|consensus	284		98.85
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.84
KOG0226|consensus	290		98.81
KOG2193|consensus	584		98.8
KOG4454|consensus	267		98.78
KOG0106|consensus	216		98.77
KOG4661|consensus	940		98.7
KOG4209|consensus	231		98.7
KOG1365|consensus	508		98.69
KOG4209|consensus	231		98.63
KOG4307|consensus	944		98.61
KOG0116|consensus	419		98.6
KOG4660|consensus	549		98.57
KOG1548|consensus	382		98.56
KOG0151|consensus	877		98.5
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.47
KOG4676|consensus	479		98.44
KOG0151|consensus	877		98.42
KOG4849|consensus	498		98.28
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.24
KOG1995|consensus	351		98.15
KOG1995|consensus	351		98.0
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.95
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.86
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.84
KOG0115|consensus	275		97.81
KOG2314|consensus	698		97.81
KOG0128|consensus	881		97.8
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.79
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.77
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.56
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.54
KOG0129|consensus	520		97.5
KOG1855|consensus	484		97.49
KOG2314|consensus	698		97.49
KOG4210|consensus	285		97.42
KOG2202|consensus	260		97.35
KOG1996|consensus	378		97.32
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.32
KOG3152|consensus	278		97.32
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.12
KOG3152|consensus	278		97.08
KOG0115|consensus	275		97.07
KOG1855|consensus	484		97.05
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.98
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.95
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.9
KOG2202|consensus	260		96.79
KOG2416|consensus	718		96.62
KOG2591|consensus	684		96.55
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.53
KOG2193|consensus	584		96.47
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.98
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.73
KOG0112|consensus	975		95.62
KOG2068|consensus	327		95.62
KOG1996|consensus	378		95.62
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.55
KOG2135|consensus	526		95.16
KOG4574|consensus	1007		95.0
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	95.0
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.77
KOG4676|consensus	479		94.76
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.67
KOG2591|consensus	684		94.54
KOG2416|consensus	718		94.48
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	94.48
KOG2068|consensus	327		94.27
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.2
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.05
KOG2318|consensus	650		94.04
KOG2253|consensus	668		94.01
KOG4285|consensus	350		93.88
KOG0804|consensus	493		93.45
KOG4285|consensus	350		93.0
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	92.81
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	92.44
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	92.05
KOG0804|consensus	493		91.38
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	91.03
KOG2253|consensus	668		90.76
KOG2135|consensus	526		89.75
KOG4574|consensus	1007		87.56
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	86.57
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	85.98
KOG2295|consensus	648		82.39
KOG4410|consensus	396		81.54

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=7.4e-39  Score=287.00  Aligned_cols=171  Identities=31%  Similarity=0.510  Sum_probs=155.6

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          52 GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        52 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..+....++|||+|||+++||++|+++|+.||+|++|+|++|+.+++++|||||+|.++++|++||+.||+..|..+.++
T Consensus       101 ~~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~  180 (346)
T TIGR01659       101 NDTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLK  180 (346)
T ss_pred             cCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceee
Confidence            34566788999999999999999999999999999999999999999999999999999999999999999888777665


Q ss_pred             cc-------cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCC
Q psy4086         132 QQ-------EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTL  203 (305)
Q Consensus       132 ~~-------~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~  203 (305)
                      ..       ....++|||+|||.++||++|+++|++||.|+.|+|++++ ++++++||||+|.+.++|++||+.||+..+
T Consensus       181 V~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~  260 (346)
T TIGR01659       181 VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIP  260 (346)
T ss_pred             eecccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCcc
Confidence            32       2345789999999999999999999999999999999998 899999999999999999999999999999


Q ss_pred             CCCCccEEEEeccCCCcCC
Q psy4086         204 PGSKEPLLVKFADSGLKKR  222 (305)
Q Consensus       204 ~g~~~~l~v~~a~~~~~~~  222 (305)
                      .+..++|+|++++.....+
T Consensus       261 ~g~~~~l~V~~a~~~~~~~  279 (346)
T TIGR01659       261 EGGSQPLTVRLAEEHGKAK  279 (346)
T ss_pred             CCCceeEEEEECCcccccc
Confidence            8877889999999765544

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).

>KOG0148|consensus

Probab=100.00  E-value=3.2e-35  Score=242.82  Aligned_cols=154  Identities=22%  Similarity=0.460  Sum_probs=143.0

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc------
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR------  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~------  131 (305)
                      ...|||+.|..+++.++|++.|.+||+|.+++|++|..|+++|||+||.|.+.++|++||..|||+.|..|.++      
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            45699999999999999999999999999999999999999999999999999999999999999999888777      


Q ss_pred             -----------------cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHH
Q psy4086         132 -----------------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQM  194 (305)
Q Consensus       132 -----------------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~A  194 (305)
                                       ....+.++|||||++..+||++|++.|+.||.|.+|+|+.+     +|||||+|++.|+|.+|
T Consensus       142 Kp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-----qGYaFVrF~tkEaAahA  216 (321)
T KOG0148|consen  142 KPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-----QGYAFVRFETKEAAAHA  216 (321)
T ss_pred             CccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-----cceEEEEecchhhHHHH
Confidence                             23345688999999999999999999999999999999966     88999999999999999


Q ss_pred             HHHhCCCCCCCCCccEEEEeccCC
Q psy4086         195 IQLFNGSTLPGSKEPLLVKFADSG  218 (305)
Q Consensus       195 i~~l~g~~~~g~~~~l~v~~a~~~  218 (305)
                      |..+|+++|.|  ..+++.|.+..
T Consensus       217 Iv~mNntei~G--~~VkCsWGKe~  238 (321)
T KOG0148|consen  217 IVQMNNTEIGG--QLVRCSWGKEG  238 (321)
T ss_pred             HHHhcCceeCc--eEEEEeccccC
Confidence            99999999999  77888886653

>KOG0144|consensus

Probab=100.00  E-value=2.5e-35  Score=257.32  Aligned_cols=167  Identities=26%  Similarity=0.497  Sum_probs=153.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCc--------ccc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG--------IHA  127 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~--------i~~  127 (305)
                      .+..+||||-||..++|+||+++|++||.|.+|.|++|+.|+.++|||||.|.+.++|.+|+.+|+++.        |.+
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            455679999999999999999999999999999999999999999999999999999999999998763        445


Q ss_pred             eecccccC---CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCC-CC
Q psy4086         128 QMARQQEQ---DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGS-TL  203 (305)
Q Consensus       128 ~~~~~~~~---~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~  203 (305)
                      +++..+..   +.++||||-|+..+||.+++++|++||.|++|.|++|.++.+||||||.|++.|.|..||+.|||. .+
T Consensus       112 k~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tm  191 (510)
T KOG0144|consen  112 KYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTM  191 (510)
T ss_pred             cccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceee
Confidence            55553333   378999999999999999999999999999999999999999999999999999999999999986 78


Q ss_pred             CCCCccEEEEeccCCCcCC
Q psy4086         204 PGSKEPLLVKFADSGLKKR  222 (305)
Q Consensus       204 ~g~~~~l~v~~a~~~~~~~  222 (305)
                      +|+..+|.|+||+.++.|.
T Consensus       192 eGcs~PLVVkFADtqkdk~  210 (510)
T KOG0144|consen  192 EGCSQPLVVKFADTQKDKD  210 (510)
T ss_pred             ccCCCceEEEecccCCCch
Confidence            9999999999999988775

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

Probab=100.00  E-value=5.1e-33  Score=261.81  Aligned_cols=163  Identities=19%  Similarity=0.324  Sum_probs=148.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccccc--
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQE--  134 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~--  134 (305)
                      ..++|||+||++++++++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|++|++.|||+.|.++.++...  
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            457899999999999999999999999999999999999999999999999999999999999999888877665211  


Q ss_pred             ----------------CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHH
Q psy4086         135 ----------------QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQL  197 (305)
Q Consensus       135 ----------------~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~  197 (305)
                                      ...++|||+||+.++++++|+++|+.||.|++|+|.+++ +++++|||||+|.+.++|.+||+.
T Consensus       186 ~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~a  265 (612)
T TIGR01645       186 NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIAS  265 (612)
T ss_pred             cccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHH
Confidence                            123689999999999999999999999999999999998 788999999999999999999999


Q ss_pred             hCCCCCCCCCccEEEEeccCCCcC
Q psy4086         198 FNGSTLPGSKEPLLVKFADSGLKK  221 (305)
Q Consensus       198 l~g~~~~g~~~~l~v~~a~~~~~~  221 (305)
                      ||+..|+|  +.|+|.++..+...
T Consensus       266 mNg~elgG--r~LrV~kAi~pP~~  287 (612)
T TIGR01645       266 MNLFDLGG--QYLRVGKCVTPPDA  287 (612)
T ss_pred             hCCCeeCC--eEEEEEecCCCccc
Confidence            99999999  67999998875443

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=7.1e-33  Score=252.44  Aligned_cols=164  Identities=35%  Similarity=0.580  Sum_probs=150.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc---
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ---  133 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~---  133 (305)
                      .+++|||+|||++++|++|+++|++||+|.+|+|++|+.+|+++|||||+|.+.++|++||+.|||+.|.++.++..   
T Consensus         2 ~~~~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~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            35789999999999999999999999999999999999999999999999999999999999999988887766532   


Q ss_pred             ----cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCc
Q psy4086         134 ----EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKE  208 (305)
Q Consensus       134 ----~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~  208 (305)
                          ....++|||+|||.++++++|+++|+.||.|..++++.+. ++.++|||||+|.+.++|++||+.|||..+.+..+
T Consensus        82 ~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~  161 (352)
T TIGR01661        82 PSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTE  161 (352)
T ss_pred             ccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCce
Confidence                2245789999999999999999999999999999999987 78899999999999999999999999999998777


Q ss_pred             cEEEEeccCCCc
Q psy4086         209 PLLVKFADSGLK  220 (305)
Q Consensus       209 ~l~v~~a~~~~~  220 (305)
                      +|.|++++....
T Consensus       162 ~i~v~~a~~~~~  173 (352)
T TIGR01661       162 PITVKFANNPSS  173 (352)
T ss_pred             eEEEEECCCCCc
Confidence            899999987653

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

>KOG0117|consensus

Probab=100.00  E-value=1.5e-32  Score=240.99  Aligned_cols=172  Identities=24%  Similarity=0.416  Sum_probs=149.3

Q ss_pred             cCCCCCCCCCCCCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhc
Q psy4086          42 QHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ  121 (305)
Q Consensus        42 ~~~~~~~~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~  121 (305)
                      .-.+++..+........|.||||.||.++.|+||..||++.|+|.+++|++|+.+|.+||||||.|.+.++|++||+.||
T Consensus        67 k~ggPpP~weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~ln  146 (506)
T KOG0117|consen   67 KYGGPPPGWEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELN  146 (506)
T ss_pred             ccCCCCCcccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhh
Confidence            33456666777777888999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCcccc-eecc---------------------------------------------------------------------
Q psy4086         122 DKGIHA-QMAR---------------------------------------------------------------------  131 (305)
Q Consensus       122 g~~i~~-~~~~---------------------------------------------------------------------  131 (305)
                      +++|.. +.+.                                                                     
T Consensus       147 n~Eir~GK~igvc~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRr  226 (506)
T KOG0117|consen  147 NYEIRPGKLLGVCVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARR  226 (506)
T ss_pred             CccccCCCEeEEEEeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHh
Confidence            886642 1111                                                                     


Q ss_pred             ---------------------cccCC------CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEE
Q psy4086         132 ---------------------QQEQD------PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFAR  184 (305)
Q Consensus       132 ---------------------~~~~~------~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~  184 (305)
                                           ..+.+      -+.|||.||+.++||+.|+++|++||.|+.|+.++|       ||||.
T Consensus       227 Kl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVH  299 (506)
T KOG0117|consen  227 KLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVH  299 (506)
T ss_pred             hccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEe
Confidence                                 01111      145999999999999999999999999999998866       99999


Q ss_pred             ecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCCCcCC
Q psy4086         185 LESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKR  222 (305)
Q Consensus       185 f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~~~~~  222 (305)
                      |.+.++|.+|++.+||++|+|  ..|.|.+|++...++
T Consensus       300 f~eR~davkAm~~~ngkeldG--~~iEvtLAKP~~k~k  335 (506)
T KOG0117|consen  300 FAEREDAVKAMKETNGKELDG--SPIEVTLAKPVDKKK  335 (506)
T ss_pred             ecchHHHHHHHHHhcCceecC--ceEEEEecCChhhhc
Confidence            999999999999999999999  669999999866554

>KOG0145|consensus

Probab=100.00  E-value=9.1e-33  Score=227.08  Aligned_cols=168  Identities=31%  Similarity=0.525  Sum_probs=155.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc---
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR---  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~---  131 (305)
                      +..++.|.|.-||.++|+|||+.+|...|+|++|++++|+.+|.+.||+||.|.+++||++|+..|||-+++.+.++   
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            45678899999999999999999999999999999999999999999999999999999999999998777665554   


Q ss_pred             --c--ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCC
Q psy4086         132 --Q--QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGS  206 (305)
Q Consensus       132 --~--~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  206 (305)
                        +  ......+|||.+||..+|..+|+++|++||.|...+|+.|. +|.+||.+||+|.-.++|++||..|||..-.|+
T Consensus       118 ARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~  197 (360)
T KOG0145|consen  118 ARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGC  197 (360)
T ss_pred             ccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCC
Confidence              2  33456789999999999999999999999999999999999 999999999999999999999999999999998


Q ss_pred             CccEEEEeccCCCcCC
Q psy4086         207 KEPLLVKFADSGLKKR  222 (305)
Q Consensus       207 ~~~l~v~~a~~~~~~~  222 (305)
                      ..+|.|+||+.+..+.
T Consensus       198 tepItVKFannPsq~t  213 (360)
T KOG0145|consen  198 TEPITVKFANNPSQKT  213 (360)
T ss_pred             CCCeEEEecCCccccc
Confidence            8999999999886664

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

Probab=100.00  E-value=2e-31  Score=256.83  Aligned_cols=163  Identities=25%  Similarity=0.470  Sum_probs=147.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccc----ceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH----AQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~----~~~~~  131 (305)
                      ...++|||+||++++|+++|+++|+.||+|.+++++++. +++++|||||+|.+.++|.+|++.|||+.|.    ++.+.
T Consensus       176 ~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~  254 (562)
T TIGR01628       176 KKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLY  254 (562)
T ss_pred             cCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeE
Confidence            445779999999999999999999999999999999986 6899999999999999999999999999887    44332


Q ss_pred             c-------------------------ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEec
Q psy4086         132 Q-------------------------QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLE  186 (305)
Q Consensus       132 ~-------------------------~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~  186 (305)
                      .                         ......+|||+||+.++++++|+++|++||.|++|+|+.+.+|.++|||||+|.
T Consensus       255 v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~  334 (562)
T TIGR01628       255 VGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFS  334 (562)
T ss_pred             eecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeC
Confidence            1                         022346799999999999999999999999999999999988999999999999


Q ss_pred             CHHHHHHHHHHhCCCCCCCCCccEEEEeccCCCcC
Q psy4086         187 SKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKK  221 (305)
Q Consensus       187 ~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~~~~  221 (305)
                      +.++|.+|+..|||..|.|  ++|.|.+|..+..+
T Consensus       335 ~~~~A~~A~~~~~g~~~~g--k~l~V~~a~~k~~~  367 (562)
T TIGR01628       335 NPEEANRAVTEMHGRMLGG--KPLYVALAQRKEQR  367 (562)
T ss_pred             CHHHHHHHHHHhcCCeeCC--ceeEEEeccCcHHH
Confidence            9999999999999999999  77999999986544

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

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

Probab=99.98  E-value=7.3e-31  Score=246.91  Aligned_cols=165  Identities=22%  Similarity=0.362  Sum_probs=139.8

Q ss_pred             CCCCCCCCCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcc
Q psy4086          46 SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGI  125 (305)
Q Consensus        46 ~~~~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i  125 (305)
                      ++..+........|+|||+|||++++|++|+++|++||.|.+|+|++| .+|+++|||||+|.+.++|++||+.||+..|
T Consensus        46 Pp~~~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i  124 (578)
T TIGR01648        46 PPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEI  124 (578)
T ss_pred             CCCcccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCee
Confidence            444444444556789999999999999999999999999999999999 6899999999999999999999999987655


Q ss_pred             c-ceecc-------------------------------------------------------------------------
Q psy4086         126 H-AQMAR-------------------------------------------------------------------------  131 (305)
Q Consensus       126 ~-~~~~~-------------------------------------------------------------------------  131 (305)
                      . .+.+.                                                                         
T Consensus       125 ~~Gr~l~V~~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~  204 (578)
T TIGR01648       125 RPGRLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMP  204 (578)
T ss_pred             cCCccccccccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhc
Confidence            3 11100                                                                         


Q ss_pred             ----------------cc-------cCCCCceEEecCCCCCCHHHHHHHHhhC--CCeEEEEEeeCCCCCcccEEEEEec
Q psy4086         132 ----------------QQ-------EQDPTNLYIANLPLNFKECDLESLLAKY--VTVVSTRILRDNNNTSKGVGFARLE  186 (305)
Q Consensus       132 ----------------~~-------~~~~~~l~V~nlp~~~te~~l~~~F~~~--g~v~~v~i~~~~~g~~~g~afV~f~  186 (305)
                                      ..       ....++|||+||++++++++|+++|++|  |.|++|+++       ++||||+|+
T Consensus       205 gki~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~-------rgfAFVeF~  277 (578)
T TIGR01648       205 GRIQLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI-------RDYAFVHFE  277 (578)
T ss_pred             cceEecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee-------cCeEEEEeC
Confidence                            00       0112569999999999999999999999  999999876       459999999


Q ss_pred             CHHHHHHHHHHhCCCCCCCCCccEEEEeccCCCc
Q psy4086         187 SKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLK  220 (305)
Q Consensus       187 ~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~~~  220 (305)
                      +.++|++|++.||+..|.+  +.|+|.|+++...
T Consensus       278 s~e~A~kAi~~lnG~~i~G--r~I~V~~Akp~~~  309 (578)
T TIGR01648       278 DREDAVKAMDELNGKELEG--SEIEVTLAKPVDK  309 (578)
T ss_pred             CHHHHHHHHHHhCCCEECC--EEEEEEEccCCCc
Confidence            9999999999999999999  7799999987544

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.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.98  E-value=3.8e-31  Score=241.05  Aligned_cols=162  Identities=28%  Similarity=0.434  Sum_probs=144.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccce-------e
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ-------M  129 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~-------~  129 (305)
                      ..++|||+|||+++++++|+++|+.||.|..++++.+..++.++|||||+|.+.++|+.|++.|||..+.+.       +
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~  167 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKF  167 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            456799999999999999999999999999999999988899999999999999999999999998866432       1


Q ss_pred             cccc----------------------------------------------------------------------------
Q psy4086         130 ARQQ----------------------------------------------------------------------------  133 (305)
Q Consensus       130 ~~~~----------------------------------------------------------------------------  133 (305)
                      ....                                                                            
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            1000                                                                            


Q ss_pred             ------------------cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHH
Q psy4086         134 ------------------EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQM  194 (305)
Q Consensus       134 ------------------~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A  194 (305)
                                        .....+|||+|||+++++++|+++|++||.|++|+|++|. ++.++|||||+|.+.++|.+|
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~A  327 (352)
T TIGR01661       248 ATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMA  327 (352)
T ss_pred             cccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHH
Confidence                              0011259999999999999999999999999999999998 999999999999999999999


Q ss_pred             HHHhCCCCCCCCCccEEEEeccCCCc
Q psy4086         195 IQLFNGSTLPGSKEPLLVKFADSGLK  220 (305)
Q Consensus       195 i~~l~g~~~~g~~~~l~v~~a~~~~~  220 (305)
                      |+.|||..|.|  +.|+|.|+..+..
T Consensus       328 i~~lnG~~~~g--r~i~V~~~~~~~~  351 (352)
T TIGR01661       328 ILSLNGYTLGN--RVLQVSFKTNKAY  351 (352)
T ss_pred             HHHhCCCEECC--eEEEEEEccCCCC
Confidence            99999999999  7799999987654

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

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

Probab=99.97  E-value=2.3e-30  Score=243.81  Aligned_cols=161  Identities=21%  Similarity=0.445  Sum_probs=145.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccccc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQE  134 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~  134 (305)
                      +...++|||+|||.++++++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|++||. |+|..+.++.+....
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            4456789999999999999999999999999999999999999999999999999999999997 888877766544111


Q ss_pred             -------------------CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHH
Q psy4086         135 -------------------QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQM  194 (305)
Q Consensus       135 -------------------~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A  194 (305)
                                         ...++|||+|||..+++++|+++|+.||.|..|.|+.+. +|.++|||||+|.+.++|.+|
T Consensus       165 ~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A  244 (457)
T TIGR01622       165 SQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEA  244 (457)
T ss_pred             cchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHH
Confidence                               124789999999999999999999999999999999998 679999999999999999999


Q ss_pred             HHHhCCCCCCCCCccEEEEeccCC
Q psy4086         195 IQLFNGSTLPGSKEPLLVKFADSG  218 (305)
Q Consensus       195 i~~l~g~~~~g~~~~l~v~~a~~~  218 (305)
                      ++.|||..|.|  ++|+|.|+...
T Consensus       245 ~~~l~g~~i~g--~~i~v~~a~~~  266 (457)
T TIGR01622       245 LEVMNGFELAG--RPIKVGYAQDS  266 (457)
T ss_pred             HHhcCCcEECC--EEEEEEEccCC
Confidence            99999999999  77999998753

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

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

Probab=99.97  E-value=4.1e-30  Score=247.73  Aligned_cols=156  Identities=25%  Similarity=0.445  Sum_probs=141.7

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc------
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ------  133 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~------  133 (305)
                      +|||+|||+++||++|+++|++||.|.+|+|++|..+++++|||||+|.+.++|++|++.||+..|.++.++..      
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            59999999999999999999999999999999999999999999999999999999999998887776655521      


Q ss_pred             ---cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         134 ---EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       134 ---~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                         .....+|||+||+.++++++|+++|++||.|.+|+|..+.+|+++|||||+|.+.++|.+|++.|||..+.+  +.|
T Consensus        82 ~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~--~~i  159 (562)
T TIGR01628        82 SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLND--KEV  159 (562)
T ss_pred             cccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEecC--ceE
Confidence               122457999999999999999999999999999999999988999999999999999999999999999999  568


Q ss_pred             EEEeccC
Q psy4086         211 LVKFADS  217 (305)
Q Consensus       211 ~v~~a~~  217 (305)
                      .|.....
T Consensus       160 ~v~~~~~  166 (562)
T TIGR01628       160 YVGRFIK  166 (562)
T ss_pred             EEecccc
Confidence            8865443

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

>KOG0131|consensus

Probab=99.96  E-value=2e-28  Score=191.72  Aligned_cols=163  Identities=27%  Similarity=0.410  Sum_probs=144.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc---
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ---  133 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~---  133 (305)
                      ...|||||||+..++++-|.++|-+.|+|..+++.+|+.+...+|||||+|.++++|+-|++-||..++.++.++..   
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            34679999999999999999999999999999999999999999999999999999999999988666666655522   


Q ss_pred             -----cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEE-EEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCC
Q psy4086         134 -----EQDPTNLYIANLPLNFKECDLESLLAKYVTVVS-TRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGS  206 (305)
Q Consensus       134 -----~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~-v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  206 (305)
                           .....+|||+||.++++|..|.+.|+.||.+.+ -+|+++. +|.+++|+||.|.+.+.+.+|+..+||..+.. 
T Consensus        88 ~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~n-  166 (203)
T KOG0131|consen   88 AHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCN-  166 (203)
T ss_pred             cccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcC-
Confidence                 223478999999999999999999999999766 4888888 78999999999999999999999999999998 


Q ss_pred             CccEEEEeccCCCcC
Q psy4086         207 KEPLLVKFADSGLKK  221 (305)
Q Consensus       207 ~~~l~v~~a~~~~~~  221 (305)
                       ++++|.++..+..+
T Consensus       167 -r~itv~ya~k~~~k  180 (203)
T KOG0131|consen  167 -RPITVSYAFKKDTK  180 (203)
T ss_pred             -CceEEEEEEecCCC
Confidence             77999998775444

>KOG0145|consensus

Probab=99.95  E-value=3.9e-27  Score=193.94  Aligned_cols=164  Identities=28%  Similarity=0.470  Sum_probs=145.5

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCc-------c
Q psy4086          53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG-------I  125 (305)
Q Consensus        53 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~-------i  125 (305)
                      .+..+...|||.+||+.+|..||+++|++||.|..-+|+.|..||.+||.+||.|...++|+.||+.|||..       |
T Consensus       122 s~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepI  201 (360)
T KOG0145|consen  122 SDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPI  201 (360)
T ss_pred             hhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCe
Confidence            345567789999999999999999999999999999999999999999999999999999999999999873       2


Q ss_pred             cceecc-----------------------------------------------------------------cccCCCCce
Q psy4086         126 HAQMAR-----------------------------------------------------------------QQEQDPTNL  140 (305)
Q Consensus       126 ~~~~~~-----------------------------------------------------------------~~~~~~~~l  140 (305)
                      .++++.                                                                 .......+|
T Consensus       202 tVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ci  281 (360)
T KOG0145|consen  202 TVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCI  281 (360)
T ss_pred             EEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEE
Confidence            333322                                                                 111123579


Q ss_pred             EEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCC
Q psy4086         141 YIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSG  218 (305)
Q Consensus       141 ~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~  218 (305)
                      ||=||..+.+|..|.++|..||.|..|+|++|- ++++|||+||.+.+.++|..||..|||+.+.+  +.|.|.|...+
T Consensus       282 FvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~--rvLQVsFKtnk  358 (360)
T KOG0145|consen  282 FVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGD--RVLQVSFKTNK  358 (360)
T ss_pred             EEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccc--eEEEEEEecCC
Confidence            999999999999999999999999999999998 68999999999999999999999999999999  78999997654

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

Probab=99.95  E-value=1.6e-26  Score=218.10  Aligned_cols=156  Identities=22%  Similarity=0.303  Sum_probs=132.8

Q ss_pred             CCCCeEEEcCCCC-CCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc-
Q psy4086          56 LSKTNLYIRGLTQ-DTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ-  133 (305)
Q Consensus        56 ~~~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~-  133 (305)
                      ...++|||+||++ .+|+++|+++|+.||.|.+|+|++++     +|||||+|.+.++|++|++.|||..|.++.++.. 
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            3567899999998 69999999999999999999999874     5899999999999999999999887766554410 


Q ss_pred             ----------c---------------------------------CCCCceEEecCCCCCCHHHHHHHHhhCCC--eEEEE
Q psy4086         134 ----------E---------------------------------QDPTNLYIANLPLNFKECDLESLLAKYVT--VVSTR  168 (305)
Q Consensus       134 ----------~---------------------------------~~~~~l~V~nlp~~~te~~l~~~F~~~g~--v~~v~  168 (305)
                                .                                 ....+|||+|||.++++++|+++|+.||.  |+.++
T Consensus       348 s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik  427 (481)
T TIGR01649       348 SKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFK  427 (481)
T ss_pred             cccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEE
Confidence                      0                                 11357999999999999999999999998  88888


Q ss_pred             EeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCC----ccEEEEeccC
Q psy4086         169 ILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSK----EPLLVKFADS  217 (305)
Q Consensus       169 i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~----~~l~v~~a~~  217 (305)
                      +..++++ .+++|||+|++.++|.+||..||++.|.++.    ..|+|.|++.
T Consensus       428 ~~~~~~~-~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~  479 (481)
T TIGR01649       428 FFPKDNE-RSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTS  479 (481)
T ss_pred             EecCCCC-cceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccC
Confidence            8765543 5789999999999999999999999998842    1489999865

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

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

Probab=99.95  E-value=2.3e-26  Score=217.05  Aligned_cols=152  Identities=18%  Similarity=0.222  Sum_probs=127.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHh--ccCccc-----ceec
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL--QDKGIH-----AQMA  130 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l--~g~~i~-----~~~~  130 (305)
                      +++|||+|||++++|++|+++|++||.|.+|+|+++      ||||||+|.+.++|++|++.+  ++..|.     +.+.
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            367999999999999999999999999999999864      469999999999999999864  444444     4433


Q ss_pred             cccc----C----------CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH
Q psy4086         131 RQQE----Q----------DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ  196 (305)
Q Consensus       131 ~~~~----~----------~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~  196 (305)
                      ....    .          ...+|||+||++.+|+++|+++|+.||.|++|.|++++   .+++|||+|.+.++|.+|++
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~---~~~~afVef~~~~~A~~A~~  152 (481)
T TIGR01649        76 TSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN---NVFQALVEFESVNSAQHAKA  152 (481)
T ss_pred             CCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC---CceEEEEEECCHHHHHHHHH
Confidence            2111    0          11268999999999999999999999999999998763   34689999999999999999


Q ss_pred             HhCCCCCCCCCccEEEEeccCC
Q psy4086         197 LFNGSTLPGSKEPLLVKFADSG  218 (305)
Q Consensus       197 ~l~g~~~~g~~~~l~v~~a~~~  218 (305)
                      .|||..|.+....|+|.|++..
T Consensus       153 ~Lng~~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       153 ALNGADIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             HhcCCcccCCceEEEEEEecCC
Confidence            9999999775467999998753

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).

>KOG0109|consensus

Probab=99.95  E-value=1.8e-27  Score=198.77  Aligned_cols=145  Identities=22%  Similarity=0.475  Sum_probs=131.0

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccc-----ceeccccc
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH-----AQMARQQE  134 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~-----~~~~~~~~  134 (305)
                      +|||||||.++++.+|+.+|++||+|.+|.|+++        ||||..+++..|+.||+.|||..|+     ++.++.+.
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            5999999999999999999999999999999986        9999999999999999987766555     44555666


Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ....+|+||||.+.++.++|+..|++||.|.+|+|.+|       |+||.|.-.++|..||+.||+++|.|  ++++|..
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd-------y~fvh~d~~eda~~air~l~~~~~~g--k~m~vq~  146 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD-------YAFVHFDRAEDAVEAIRGLDNTEFQG--KRMHVQL  146 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc-------eeEEEEeeccchHHHHhccccccccc--ceeeeee
Confidence            67789999999999999999999999999999999955       99999999999999999999999999  7799999


Q ss_pred             ccCCCcC
Q psy4086         215 ADSGLKK  221 (305)
Q Consensus       215 a~~~~~~  221 (305)
                      ...+-+.
T Consensus       147 stsrlrt  153 (346)
T KOG0109|consen  147 STSRLRT  153 (346)
T ss_pred             ecccccc
Confidence            8775443

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

Probab=99.94  E-value=3.7e-26  Score=218.06  Aligned_cols=155  Identities=21%  Similarity=0.351  Sum_probs=130.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhcc------------CCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhcc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQY------------GPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQD  122 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~------------G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g  122 (305)
                      ....++|||||||+++|+++|+++|..|            +.|..+.+      ++.+|||||+|.+.++|..||+ |||
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~-l~g  244 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMA-LDS  244 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhc-CCC
Confidence            3456789999999999999999999975            23333333      4467899999999999999995 888


Q ss_pred             Ccccceecccc------------------------------------cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEE
Q psy4086         123 KGIHAQMARQQ------------------------------------EQDPTNLYIANLPLNFKECDLESLLAKYVTVVS  166 (305)
Q Consensus       123 ~~i~~~~~~~~------------------------------------~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~  166 (305)
                      ..+.+..++..                                    ....++|||+|||..+++++|+++|+.||.|..
T Consensus       245 ~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~  324 (509)
T TIGR01642       245 IIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKA  324 (509)
T ss_pred             eEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeE
Confidence            77665544311                                    112368999999999999999999999999999


Q ss_pred             EEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCC
Q psy4086         167 TRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSG  218 (305)
Q Consensus       167 v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~  218 (305)
                      +.|+.+. +|.++|||||+|.+.++|..||+.|||..|.+  +.|.|.++...
T Consensus       325 ~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~--~~l~v~~a~~~  375 (509)
T TIGR01642       325 FNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGD--NKLHVQRACVG  375 (509)
T ss_pred             EEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECC--eEEEEEECccC
Confidence            9999987 88999999999999999999999999999999  66999998754

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

>KOG0127|consensus

Probab=99.94  E-value=2.1e-26  Score=206.83  Aligned_cols=160  Identities=24%  Similarity=0.439  Sum_probs=143.6

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc-------
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR-------  131 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~-------  131 (305)
                      .||||++||+.++.++|.++|+.+|+|..|.++.++.++.+|||+||.|.-.+|++.|++.+++..+.++.++       
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            6799999999999999999999999999999999999999999999999999999999999776665555444       


Q ss_pred             ------------------c------c--cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEe
Q psy4086         132 ------------------Q------Q--EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARL  185 (305)
Q Consensus       132 ------------------~------~--~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f  185 (305)
                                        .      .  .....+|.|.|||+.+.+.+|+.+|+.||.|.+|.|++..+|+-+|||||+|
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~f  165 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQF  165 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEE
Confidence                              0      0  0113579999999999999999999999999999999888888889999999


Q ss_pred             cCHHHHHHHHHHhCCCCCCCCCccEEEEeccCCCc
Q psy4086         186 ESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLK  220 (305)
Q Consensus       186 ~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~~~  220 (305)
                      ....+|..|++.+|+..|+|  |+|.|.||-.+..
T Consensus       166 k~~~dA~~Al~~~N~~~i~g--R~VAVDWAV~Kd~  198 (678)
T KOG0127|consen  166 KEKKDAEKALEFFNGNKIDG--RPVAVDWAVDKDT  198 (678)
T ss_pred             eeHHHHHHHHHhccCceecC--ceeEEeeeccccc
Confidence            99999999999999999999  8899999887543

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

Probab=99.94  E-value=7e-26  Score=216.16  Aligned_cols=159  Identities=19%  Similarity=0.303  Sum_probs=136.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc---
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ---  133 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~---  133 (305)
                      ..++|||+|||..+|+++|+++|+.||.|..+.|+++..+|.++|||||+|.+.++|..|++.|||..|.++.+...   
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            45679999999999999999999999999999999999999999999999999999999999999888776544310   


Q ss_pred             --------------------------------cCCCCceEEecCCCC--C--------CHHHHHHHHhhCCCeEEEEEee
Q psy4086         134 --------------------------------EQDPTNLYIANLPLN--F--------KECDLESLLAKYVTVVSTRILR  171 (305)
Q Consensus       134 --------------------------------~~~~~~l~V~nlp~~--~--------te~~l~~~F~~~g~v~~v~i~~  171 (305)
                                                      .....+|+|.||...  +        ..++|+++|++||.|+.|.|++
T Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~  453 (509)
T TIGR01642       374 VGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPR  453 (509)
T ss_pred             cCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeec
Confidence                                            112356888888532  1        1367999999999999999987


Q ss_pred             CC----CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         172 DN----NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       172 ~~----~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      +.    ++..+|++||+|.+.++|++||..|||..|.|  +.|.|.|...
T Consensus       454 ~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~g--r~v~~~~~~~  501 (509)
T TIGR01642       454 PNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFND--RVVVAAFYGE  501 (509)
T ss_pred             cCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECC--eEEEEEEeCH
Confidence            63    34567999999999999999999999999999  7799999764

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

>KOG0146|consensus

Probab=99.94  E-value=4.2e-26  Score=188.53  Aligned_cols=163  Identities=23%  Similarity=0.412  Sum_probs=145.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcc--------cce
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGI--------HAQ  128 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i--------~~~  128 (305)
                      +.++||||-|.+.-.|||++.+|..||.|++|.+.+.. .|.+||||||+|.+..+|..||..|+|...        -++
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            45679999999999999999999999999999999988 699999999999999999999999998532        122


Q ss_pred             ecc-----------------------------------------------------------------------------
Q psy4086         129 MAR-----------------------------------------------------------------------------  131 (305)
Q Consensus       129 ~~~-----------------------------------------------------------------------------  131 (305)
                      ++.                                                                             
T Consensus        97 ~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~A  176 (371)
T KOG0146|consen   97 FADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLAA  176 (371)
T ss_pred             eccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhccccc
Confidence            221                                                                             


Q ss_pred             --------------------------------------------------------------------------------
Q psy4086         132 --------------------------------------------------------------------------------  131 (305)
Q Consensus       132 --------------------------------------------------------------------------------  131 (305)
                                                                                                      
T Consensus       177 ~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~Aa  256 (371)
T KOG0146|consen  177 APVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAAA  256 (371)
T ss_pred             CCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhhh
Confidence                                                                                            


Q ss_pred             -----------------------cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecC
Q psy4086         132 -----------------------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLES  187 (305)
Q Consensus       132 -----------------------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~  187 (305)
                                             ....+.|+|||=+||.++.+.+|...|-.||.|.+.+++.|+ ++.+|.|+||.|.+
T Consensus       257 ypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDN  336 (371)
T KOG0146|consen  257 YPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDN  336 (371)
T ss_pred             cchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCC
Confidence                                   344567999999999999999999999999999999999999 99999999999999


Q ss_pred             HHHHHHHHHHhCCCCCCCCCccEEEEeccCCCcCC
Q psy4086         188 KDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKR  222 (305)
Q Consensus       188 ~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~~~~~  222 (305)
                      ..+|+.||.+|||..|.-  +.|+|.+.+++...|
T Consensus       337 p~SaQaAIqAMNGFQIGM--KRLKVQLKRPkdanR  369 (371)
T KOG0146|consen  337 PASAQAAIQAMNGFQIGM--KRLKVQLKRPKDANR  369 (371)
T ss_pred             chhHHHHHHHhcchhhhh--hhhhhhhcCccccCC
Confidence            999999999999999999  669999988766544

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

Probab=99.92  E-value=2.9e-24  Score=202.40  Aligned_cols=155  Identities=21%  Similarity=0.294  Sum_probs=132.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc----
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ----  133 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~----  133 (305)
                      .++|||+|||..+|+++|+++|+.||.|..|.|+++..+|+++|||||+|.+.++|.+|++.|||..|.++.++..    
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~~  265 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            5789999999999999999999999999999999999999999999999999999999999999876655433300    


Q ss_pred             --------------------------------------------------------------------------------
Q psy4086         134 --------------------------------------------------------------------------------  133 (305)
Q Consensus       134 --------------------------------------------------------------------------------  133 (305)
                                                                                                      
T Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  345 (457)
T TIGR01622       266 STYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALA  345 (457)
T ss_pred             CCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccc
Confidence                                                                                            


Q ss_pred             -------------cCCCCceEEecCCCCCC----------HHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHH
Q psy4086         134 -------------EQDPTNLYIANLPLNFK----------ECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK  190 (305)
Q Consensus       134 -------------~~~~~~l~V~nlp~~~t----------e~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~  190 (305)
                                   .....+|+|.||....+          .+||++.|++||.|++|.|...   ...|++||+|.+.++
T Consensus       346 ~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~---~~~G~~fV~F~~~e~  422 (457)
T TIGR01622       346 IMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTK---NSAGKIYLKFSSVDA  422 (457)
T ss_pred             cccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCC---CCceeEEEEECCHHH
Confidence                         01234577888854433          2689999999999999998754   467999999999999


Q ss_pred             HHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         191 CDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       191 A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      |.+|++.|||..|+|  +.|.|.|...
T Consensus       423 A~~A~~~lnGr~f~g--r~i~~~~~~~  447 (457)
T TIGR01622       423 ALAAFQALNGRYFGG--KMITAAFVVN  447 (457)
T ss_pred             HHHHHHHhcCcccCC--eEEEEEEEcH
Confidence            999999999999999  7799999764

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.

>KOG0124|consensus

Probab=99.92  E-value=6.2e-25  Score=188.77  Aligned_cols=159  Identities=19%  Similarity=0.346  Sum_probs=145.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc-----
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ-----  132 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~-----  132 (305)
                      -|+||||.|.+++.||.|+..|..||+|++|.+-+|+.|+++||||||+|+-+|.|..|++.|||.-+.++.++.     
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  192 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCC
Confidence            467999999999999999999999999999999999999999999999999999999999999998888887762     


Q ss_pred             -------------ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHh
Q psy4086         133 -------------QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLF  198 (305)
Q Consensus       133 -------------~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l  198 (305)
                                   .....++|||..+..+++|+||+..|+.||+|.+|.+-++. .+..|||+||+|.+..+-.+||..|
T Consensus       193 mpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasM  272 (544)
T KOG0124|consen  193 MPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM  272 (544)
T ss_pred             CcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhc
Confidence                         22234789999999999999999999999999999999999 5678999999999999999999999


Q ss_pred             CCCCCCCCCccEEEEeccCC
Q psy4086         199 NGSTLPGSKEPLLVKFADSG  218 (305)
Q Consensus       199 ~g~~~~g~~~~l~v~~a~~~  218 (305)
                      |-..+.|  .-|+|-.+-..
T Consensus       273 NlFDLGG--QyLRVGk~vTP  290 (544)
T KOG0124|consen  273 NLFDLGG--QYLRVGKCVTP  290 (544)
T ss_pred             chhhccc--ceEecccccCC
Confidence            9999999  66888776543

>KOG4205|consensus

Probab=99.92  E-value=3.8e-24  Score=186.79  Aligned_cols=163  Identities=25%  Similarity=0.431  Sum_probs=145.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHH----hccCcccceeccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA----LQDKGIHAQMARQ  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~----l~g~~i~~~~~~~  132 (305)
                      +.++||||+|+++++++.|++.|.+||+|.+|.+++|+.+++++||+||+|.+.+...+++..    |+|+.|+.+.+..
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            568899999999999999999999999999999999999999999999999999999988865    7888888877664


Q ss_pred             ccC--------CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCC
Q psy4086         133 QEQ--------DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTL  203 (305)
Q Consensus       133 ~~~--------~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~  203 (305)
                      +..        ...+|||++|+.++++++|++.|++||.|..+.++.|. +.+.++|+||.|.+++++.+++. ..-+.|
T Consensus        85 r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~  163 (311)
T KOG4205|consen   85 REDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDF  163 (311)
T ss_pred             cccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeee
Confidence            332        23589999999999999999999999999999999998 78999999999999999999986 466888


Q ss_pred             CCCCccEEEEeccCCCcCC
Q psy4086         204 PGSKEPLLVKFADSGLKKR  222 (305)
Q Consensus       204 ~g~~~~l~v~~a~~~~~~~  222 (305)
                      .+  +.+.|+.|.++....
T Consensus       164 ~g--k~vevkrA~pk~~~~  180 (311)
T KOG4205|consen  164 NG--KKVEVKRAIPKEVMQ  180 (311)
T ss_pred             cC--ceeeEeeccchhhcc
Confidence            89  679999998876554

>KOG0127|consensus

Probab=99.92  E-value=3.9e-24  Score=192.33  Aligned_cols=158  Identities=25%  Similarity=0.404  Sum_probs=137.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc------
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR------  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~------  131 (305)
                      .-+|.|+|||+.+.+.+|+.+|+.||.|.+|.|.+...++.+ |||||.|.+..+|+.|++.+|+..|.++.+.      
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            566999999999999999999999999999999987754444 9999999999999999999998877766543      


Q ss_pred             --------------------------------------------------------------------------------
Q psy4086         132 --------------------------------------------------------------------------------  131 (305)
Q Consensus       132 --------------------------------------------------------------------------------  131 (305)
                                                                                                      
T Consensus       196 Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~  275 (678)
T KOG0127|consen  196 KDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKE  275 (678)
T ss_pred             cccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCc
Confidence                                                                                            


Q ss_pred             -----------cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHh-
Q psy4086         132 -----------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLF-  198 (305)
Q Consensus       132 -----------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l-  198 (305)
                                 .......+|||.|||+++||++|.++|++||.|..+.|+.++ ++.++|.|||.|.+..+|.+||+.- 
T Consensus       276 ~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~As  355 (678)
T KOG0127|consen  276 SDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAAS  355 (678)
T ss_pred             ccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcC
Confidence                       000012689999999999999999999999999999999999 8999999999999999999999876 


Q ss_pred             ----CC-CCCCCCCccEEEEeccCC
Q psy4086         199 ----NG-STLPGSKEPLLVKFADSG  218 (305)
Q Consensus       199 ----~g-~~~~g~~~~l~v~~a~~~  218 (305)
                          .| ..|+|  |.|.|..|-.+
T Consensus       356 pa~e~g~~ll~G--R~Lkv~~Av~R  378 (678)
T KOG0127|consen  356 PASEDGSVLLDG--RLLKVTLAVTR  378 (678)
T ss_pred             ccCCCceEEEec--cEEeeeeccch
Confidence                23 56778  77999987654

>KOG0144|consensus

Probab=99.91  E-value=1.3e-24  Score=190.41  Aligned_cols=160  Identities=26%  Similarity=0.429  Sum_probs=143.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccC--------cccce
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDK--------GIHAQ  128 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~--------~i~~~  128 (305)
                      +.++||||-|++.+||.|++++|.+||.|++|.|++|. .+.+||||||+|.+.+.|..||+.|||.        .+-++
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            35779999999999999999999999999999999998 5999999999999999999999999975        23333


Q ss_pred             ecc-----------------------------------------------------------------------------
Q psy4086         129 MAR-----------------------------------------------------------------------------  131 (305)
Q Consensus       129 ~~~-----------------------------------------------------------------------------  131 (305)
                      ++.                                                                             
T Consensus       202 FADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~~qq~~~~~  281 (510)
T KOG0144|consen  202 FADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQLQQAAALA  281 (510)
T ss_pred             ecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhHHHHHHHhh
Confidence            333                                                                             


Q ss_pred             --------------------------------------------------------------------------------
Q psy4086         132 --------------------------------------------------------------------------------  131 (305)
Q Consensus       132 --------------------------------------------------------------------------------  131 (305)
                                                                                                      
T Consensus       282 ~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~a~~~sp~a  361 (510)
T KOG0144|consen  282 AAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAGAGTTSPVA  361 (510)
T ss_pred             hhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccccccccccccCccc
Confidence                                                                                            


Q ss_pred             ---------------------------------------------------------cccCCCCceEEecCCCCCCHHHH
Q psy4086         132 ---------------------------------------------------------QQEQDPTNLYIANLPLNFKECDL  154 (305)
Q Consensus       132 ---------------------------------------------------------~~~~~~~~l~V~nlp~~~te~~l  154 (305)
                                                                               .+..+..+|||.+||.+.-+.+|
T Consensus       362 a~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlPqefgdq~l  441 (510)
T KOG0144|consen  362 ASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLPQEFGDQDL  441 (510)
T ss_pred             ccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCchhhhhHHH
Confidence                                                                     33445678999999999999999


Q ss_pred             HHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCCC
Q psy4086         155 ESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGL  219 (305)
Q Consensus       155 ~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~~  219 (305)
                      ...|..||.|++.++..|+ ++.++.|+||.|++..+|.+||..|||..|..  +.|+|....++.
T Consensus       442 ~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~--KrlkVQlk~~~~  505 (510)
T KOG0144|consen  442 IATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGS--KRLKVQLKRDRN  505 (510)
T ss_pred             HHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhcc--ccceEEeeeccC
Confidence            9999999999999999999 99999999999999999999999999999999  559998876643

>KOG0123|consensus

Probab=99.91  E-value=1.1e-23  Score=190.05  Aligned_cols=153  Identities=25%  Similarity=0.459  Sum_probs=138.1

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc--ccCCC
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ--QEQDP  137 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~--~~~~~  137 (305)
                      .||||   +++||..|.++|+.+|+|..++|++|. |  +.|||||.|.++++|++|++++|...+.++.++.  ...++
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            49999   899999999999999999999999999 6  9999999999999999999999887777776662  33444


Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      ..|||.||+.+++..+|.++|+.||.|++|++..+.+| ++|| ||+|++.++|.+||+.|||..+.+  +.|.|.....
T Consensus        77 ~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~--kki~vg~~~~  152 (369)
T KOG0123|consen   77 SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNG--KKIYVGLFER  152 (369)
T ss_pred             ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCC--CeeEEeeccc
Confidence            55999999999999999999999999999999999988 8999 999999999999999999999999  5698888776


Q ss_pred             CCcCC
Q psy4086         218 GLKKR  222 (305)
Q Consensus       218 ~~~~~  222 (305)
                      +..+.
T Consensus       153 ~~er~  157 (369)
T KOG0123|consen  153 KEERE  157 (369)
T ss_pred             hhhhc
Confidence            55543

>KOG0148|consensus

Probab=99.90  E-value=1e-23  Score=174.79  Aligned_cols=142  Identities=21%  Similarity=0.384  Sum_probs=116.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccccC
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQ  135 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~~  135 (305)
                      ...+|||||||+.++||+-|..||.+.|.|.+|+|+.|...        |..        |..       .....++...
T Consensus         4 ~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~~--------v~w--------a~~-------p~nQsk~t~~   60 (321)
T KOG0148|consen    4 DEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDELK--------VNW--------ATA-------PGNQSKPTSN   60 (321)
T ss_pred             CCCceEEeeccChhhHHHHHHHHHHhccccccceeehhhhc--------ccc--------ccC-------cccCCCCccc
Confidence            34578999999999999999999999999999999987310        000        000       0000111111


Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      .-..+||+.|...++-++|++.|.+||+|.+++|++|. ++++|||+||.|...++|++||..|||.+|..  |.|+..|
T Consensus        61 ~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~--R~IRTNW  138 (321)
T KOG0148|consen   61 QHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGR--RTIRTNW  138 (321)
T ss_pred             cceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeecc--ceeeccc
Confidence            12358999999999999999999999999999999999 99999999999999999999999999999999  7799999


Q ss_pred             ccCCCcCC
Q psy4086         215 ADSGLKKR  222 (305)
Q Consensus       215 a~~~~~~~  222 (305)
                      |..+..+.
T Consensus       139 ATRKp~e~  146 (321)
T KOG0148|consen  139 ATRKPSEM  146 (321)
T ss_pred             cccCcccc
Confidence            99877544

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

Probab=99.87  E-value=3.2e-21  Score=182.24  Aligned_cols=75  Identities=17%  Similarity=0.379  Sum_probs=69.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+||++++++++|+++|+.||.|.+|+|.+|+.++++||||||+|.+.++|.+|++.||+..|.++.++
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~Lr  277 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLR  277 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            346799999999999999999999999999999999999999999999999999999999999998877766555

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0110|consensus

Probab=99.87  E-value=1.1e-21  Score=181.81  Aligned_cols=161  Identities=24%  Similarity=0.423  Sum_probs=139.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCC---CccceEEEEecchhhHHHHHHHhccCcccceeccc-
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTN---KCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ-  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g---~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~-  132 (305)
                      ..++|||.||++++|.++|..+|...|.|..+.|.+.+...   .+.|||||+|.+.++|++|++.|+|..|++..+.. 
T Consensus       514 ~~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk  593 (725)
T KOG0110|consen  514 TETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELK  593 (725)
T ss_pred             cchhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEE
Confidence            44459999999999999999999999999999888766321   25599999999999999999999988777665441 


Q ss_pred             ---------------ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHH
Q psy4086         133 ---------------QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQ  196 (305)
Q Consensus       133 ---------------~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~  196 (305)
                                     .....++|+|.|||+..+-.+++++|..||.|.+|+|+... .+..+|||||+|-+..+|.+|+.
T Consensus       594 ~S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~  673 (725)
T KOG0110|consen  594 ISENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFD  673 (725)
T ss_pred             eccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHH
Confidence                           11123579999999999999999999999999999999884 56779999999999999999999


Q ss_pred             HhCCCCCCCCCccEEEEeccCCC
Q psy4086         197 LFNGSTLPGSKEPLLVKFADSGL  219 (305)
Q Consensus       197 ~l~g~~~~g~~~~l~v~~a~~~~  219 (305)
                      .|..+-+.|  |.|.+.||....
T Consensus       674 al~STHlyG--RrLVLEwA~~d~  694 (725)
T KOG0110|consen  674 ALGSTHLYG--RRLVLEWAKSDN  694 (725)
T ss_pred             hhcccceec--hhhheehhccch
Confidence            999999999  669999998754

>KOG0147|consensus

Probab=99.87  E-value=2.5e-22  Score=181.47  Aligned_cols=166  Identities=20%  Similarity=0.361  Sum_probs=145.6

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccce
Q psy4086          49 TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ  128 (305)
Q Consensus        49 ~~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~  128 (305)
                      .....++.+.++||+--|.-.++..+|.++|+.+|+|.+|.|+.|+.+++++|.|||+|.|.+.+..||. |.|+.+.+.
T Consensus       170 ~~l~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~  248 (549)
T KOG0147|consen  170 RILSPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGV  248 (549)
T ss_pred             ccCCchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCc
Confidence            3344556677889999999999999999999999999999999999999999999999999999999996 888876655


Q ss_pred             ecccc---------------------cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEec
Q psy4086         129 MARQQ---------------------EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLE  186 (305)
Q Consensus       129 ~~~~~---------------------~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~  186 (305)
                      .+..+                     ..+-..||||||.++++|++|+.+|+.||.|+.|.+..|. +|.++||+||+|.
T Consensus       249 pv~vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~  328 (549)
T KOG0147|consen  249 PVIVQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFV  328 (549)
T ss_pred             eeEecccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEe
Confidence            44310                     1112339999999999999999999999999999999998 9999999999999


Q ss_pred             CHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         187 SKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       187 ~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      +.++|.+|++.|||.+|-|  +.|+|.....
T Consensus       329 ~~~~ar~a~e~lngfelAG--r~ikV~~v~~  357 (549)
T KOG0147|consen  329 NKEDARKALEQLNGFELAG--RLIKVSVVTE  357 (549)
T ss_pred             cHHHHHHHHHHhccceecC--ceEEEEEeee
Confidence            9999999999999999999  7788877554

>KOG0123|consensus

Probab=99.86  E-value=3.1e-21  Score=174.28  Aligned_cols=155  Identities=27%  Similarity=0.475  Sum_probs=138.0

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc--------
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR--------  131 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~--------  131 (305)
                      .|||.||++.+|.++|.++|+.||+|.+|++..+.. | ++|| ||+|.+++.|.+|++.+||..+.++.+-        
T Consensus        78 ~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~  154 (369)
T KOG0123|consen   78 LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKE  154 (369)
T ss_pred             eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchh
Confidence            399999999999999999999999999999999984 5 9999 9999999999999999998766654433        


Q ss_pred             -------cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCC
Q psy4086         132 -------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLP  204 (305)
Q Consensus       132 -------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~  204 (305)
                             ........+||.|++.+++++.|.++|..+|.|.++.++.+..+.+++|+||.|.+.++|..|++.|++..++
T Consensus       155 er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~  234 (369)
T KOG0123|consen  155 EREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIFG  234 (369)
T ss_pred             hhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcCC
Confidence                   1112236789999999999999999999999999999999998889999999999999999999999999999


Q ss_pred             CCCccEEEEeccCCC
Q psy4086         205 GSKEPLLVKFADSGL  219 (305)
Q Consensus       205 g~~~~l~v~~a~~~~  219 (305)
                      +  ..+.|..+..+.
T Consensus       235 ~--~~~~V~~aqkk~  247 (369)
T KOG0123|consen  235 D--KELYVGRAQKKS  247 (369)
T ss_pred             c--cceeecccccch
Confidence            8  558888877743

>KOG0105|consensus

Probab=99.85  E-value=6.7e-20  Score=144.14  Aligned_cols=140  Identities=18%  Similarity=0.260  Sum_probs=117.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc-----
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR-----  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~-----  131 (305)
                      ..++|||||||.++.+.||.++|.+||.|.+|.|...+   ...+||||+|++..+|+.||..-||..+++..++     
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            45789999999999999999999999999999975433   3567999999999999999998776665554443     


Q ss_pred             ----------------------------cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEE
Q psy4086         132 ----------------------------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFA  183 (305)
Q Consensus       132 ----------------------------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV  183 (305)
                                                  +.......+.|.+||.+-+++||+++..+-|.|....+.+|      +++.|
T Consensus        82 ggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------g~GvV  155 (241)
T KOG0105|consen   82 GGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------GVGVV  155 (241)
T ss_pred             CCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------cceee
Confidence                                        12222356899999999999999999999999999998876      37899


Q ss_pred             EecCHHHHHHHHHHhCCCCCCC
Q psy4086         184 RLESKDKCDQMIQLFNGSTLPG  205 (305)
Q Consensus       184 ~f~~~~~A~~Ai~~l~g~~~~g  205 (305)
                      +|...|+.+-|+..|+...+.-
T Consensus       156 ~~~r~eDMkYAvr~ld~~~~~s  177 (241)
T KOG0105|consen  156 EYLRKEDMKYAVRKLDDQKFRS  177 (241)
T ss_pred             eeeehhhHHHHHHhhccccccC
Confidence            9999999999999999876643

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

Probab=99.83  E-value=9.7e-20  Score=143.95  Aligned_cols=87  Identities=22%  Similarity=0.393  Sum_probs=79.6

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....++|||+||+++++|++|+++|++||.|++|+|+.|+ ++++++||||+|++.++|++||+.||+..|++  +.|+|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~G--r~l~V  108 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNG--RHIRV  108 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECC--EEEEE
Confidence            3446789999999999999999999999999999999998 88999999999999999999999999999999  77999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      +++..+....
T Consensus       109 ~~a~~~~~~~  118 (144)
T PLN03134        109 NPANDRPSAP  118 (144)
T ss_pred             EeCCcCCCCC
Confidence            9998755443

>KOG0147|consensus

Probab=99.81  E-value=1.6e-19  Score=163.39  Aligned_cols=151  Identities=20%  Similarity=0.322  Sum_probs=125.8

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc---------
Q psy4086          61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR---------  131 (305)
Q Consensus        61 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~---------  131 (305)
                      ||||||.++++|++|+.+|+.||.|+.|.+.+|..||+++||+||+|.+.++|.+|++.|||..|.++.++         
T Consensus       281 l~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~  360 (549)
T KOG0147|consen  281 LYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVD  360 (549)
T ss_pred             hhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecc
Confidence            99999999999999999999999999999999999999999999999999999999999999888777666         


Q ss_pred             ------------------------------------------------------------------ccc-----------
Q psy4086         132 ------------------------------------------------------------------QQE-----------  134 (305)
Q Consensus       132 ------------------------------------------------------------------~~~-----------  134 (305)
                                                                                        ...           
T Consensus       361 ~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~  440 (549)
T KOG0147|consen  361 TKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAFD  440 (549)
T ss_pred             cccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccccC
Confidence                                                                              000           


Q ss_pred             CCCCceEEecC--CCCCCH--------HHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCC
Q psy4086         135 QDPTNLYIANL--PLNFKE--------CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLP  204 (305)
Q Consensus       135 ~~~~~l~V~nl--p~~~te--------~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~  204 (305)
                      ..+.++.+.|+  |...|+        +|+.+.+.+||.|..|.|-..    +.|+.||.|.+.+.|..|+.+|||.+|.
T Consensus       441 i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n----s~g~VYvrc~s~~~A~~a~~alhgrWF~  516 (549)
T KOG0147|consen  441 IPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN----SAGCVYVRCPSAEAAGTAVKALHGRWFA  516 (549)
T ss_pred             CccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC----CCceEEEecCcHHHHHHHHHHHhhhhhc
Confidence            11223445555  222222        577888899999998877654    3489999999999999999999999999


Q ss_pred             CCCccEEEEeccC
Q psy4086         205 GSKEPLLVKFADS  217 (305)
Q Consensus       205 g~~~~l~v~~a~~  217 (305)
                      |  +.|.++|-..
T Consensus       517 g--r~Ita~~~~~  527 (549)
T KOG0147|consen  517 G--RMITAKYLPL  527 (549)
T ss_pred             c--ceeEEEEeeh
Confidence            9  7799998543

>KOG4212|consensus

Probab=99.80  E-value=7.3e-18  Score=148.45  Aligned_cols=159  Identities=16%  Similarity=0.257  Sum_probs=136.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHh-ccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc----
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCS-QYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR----  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~-~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~----  131 (305)
                      ..+.+||.|||+++.+.+|++||. +.|+|+.|.++.|. +|++||||.|+|+++|.+++|++.||.+.+.++.+.    
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd  121 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKED  121 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEecc
Confidence            345599999999999999999996 78999999999998 699999999999999999999999886666655544    


Q ss_pred             --------------------------------------------------------------------------------
Q psy4086         132 --------------------------------------------------------------------------------  131 (305)
Q Consensus       132 --------------------------------------------------------------------------------  131 (305)
                                                                                                      
T Consensus       122 ~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~  201 (608)
T KOG4212|consen  122 HDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSA  201 (608)
T ss_pred             CchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchh
Confidence                                                                                            


Q ss_pred             --------cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCC
Q psy4086         132 --------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTL  203 (305)
Q Consensus       132 --------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~  203 (305)
                              .......++||+||.+.+..+.|++.|.-.|.|+.+.+-.|+.|.++|||.++|.++-+|..||..|++.-+
T Consensus       202 ~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g~  281 (608)
T KOG4212|consen  202 SFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQGL  281 (608)
T ss_pred             hhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCCC
Confidence                    011112579999999999999999999999999999999999889999999999999999999999997555


Q ss_pred             CCCCccEEEEeccCC
Q psy4086         204 PGSKEPLLVKFADSG  218 (305)
Q Consensus       204 ~g~~~~l~v~~a~~~  218 (305)
                      ..  ++..++...-.
T Consensus       282 ~~--~~~~~Rl~~~~  294 (608)
T KOG4212|consen  282 FD--RRMTVRLDRIP  294 (608)
T ss_pred             cc--ccceeeccccc
Confidence            55  66777775443

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

Probab=99.75  E-value=1.1e-17  Score=132.26  Aligned_cols=75  Identities=33%  Similarity=0.652  Sum_probs=70.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      ...++|||+|||+++||++|+++|++||.|.+|+|+.|+.+++++|||||+|.+.++|++|++.||+..|.++.+
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l  106 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHI  106 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            345779999999999999999999999999999999999999999999999999999999999999998877654

>KOG4206|consensus

Probab=99.75  E-value=6.5e-17  Score=132.02  Aligned_cols=150  Identities=26%  Similarity=0.405  Sum_probs=128.4

Q ss_pred             CeEEEcCCCCCCcHHHHHH----HHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc---
Q psy4086          59 TNLYIRGLTQDTTDKDLIN----MCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR---  131 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~----~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~---  131 (305)
                      .||||.||+..+..++|+.    +|++||+|.+|...+   +.+.||-|||.|.+.+.|..|++.|+|..+.++..+   
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            3799999999999999988    999999999998876   567899999999999999999999998766655444   


Q ss_pred             --------cc----------------------------------------------cCCCCceEEecCCCCCCHHHHHHH
Q psy4086         132 --------QQ----------------------------------------------EQDPTNLYIANLPLNFKECDLESL  157 (305)
Q Consensus       132 --------~~----------------------------------------------~~~~~~l~V~nlp~~~te~~l~~~  157 (305)
                              .+                                              ......||+.|||..++.+.|..+
T Consensus        87 A~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~l  166 (221)
T KOG4206|consen   87 AKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSDL  166 (221)
T ss_pred             ccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHHH
Confidence                    00                                              112245899999999999999999


Q ss_pred             HhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         158 LAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       158 F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      |++|....+++++..+    ++.|||+|.+...|..|...|++..|-. +..++|.+++
T Consensus       167 f~qf~g~keir~i~~~----~~iAfve~~~d~~a~~a~~~lq~~~it~-~~~m~i~~a~  220 (221)
T KOG4206|consen  167 FEQFPGFKEIRLIPPR----SGIAFVEFLSDRQASAAQQALQGFKITK-KNTMQITFAK  220 (221)
T ss_pred             HhhCcccceeEeccCC----CceeEEecchhhhhHHHhhhhccceecc-CceEEecccC
Confidence            9999999999998753    6699999999999999999999998875 3678888875

>KOG1548|consensus

Probab=99.74  E-value=2.1e-16  Score=135.76  Aligned_cols=163  Identities=21%  Similarity=0.288  Sum_probs=132.7

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeE--------EEEeeCCCCCCccceEEEEecchhhHHHHHHHhc
Q psy4086          50 PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIIS--------TKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ  121 (305)
Q Consensus        50 ~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~--------~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~  121 (305)
                      +...+...++.|||.|||.++|.+++.++|++||.|..        |+|.++.. |..+|=|+|.|-..++++.|+..||
T Consensus       126 ~~~~~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilD  204 (382)
T KOG1548|consen  126 WFNPEPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILD  204 (382)
T ss_pred             ccCcccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhC
Confidence            44455667788999999999999999999999998753        88888885 9999999999999999999999988


Q ss_pred             cCcccceecc---------------------------------------------cccCCCCceEEecCCC----CCC--
Q psy4086         122 DKGIHAQMAR---------------------------------------------QQEQDPTNLYIANLPL----NFK--  150 (305)
Q Consensus       122 g~~i~~~~~~---------------------------------------------~~~~~~~~l~V~nlp~----~~t--  150 (305)
                      +..+.+..++                                             .+....++|.+.|+--    ..+  
T Consensus       205 e~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~  284 (382)
T KOG1548|consen  205 EDELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPD  284 (382)
T ss_pred             cccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHH
Confidence            7666554444                                             1112246788888732    223  


Q ss_pred             -----HHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCC
Q psy4086         151 -----ECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSG  218 (305)
Q Consensus       151 -----e~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~  218 (305)
                           +++|++-+++||.|.+|.|.-.   .+.|.+-|.|.+.++|..||+.|+|.+|+|  |.|.....+..
T Consensus       285 l~~dlkedl~eec~K~G~v~~vvv~d~---hPdGvvtV~f~n~eeA~~ciq~m~GR~fdg--Rql~A~i~DG~  352 (382)
T KOG1548|consen  285 LLNDLKEDLTEECEKFGQVRKVVVYDR---HPDGVVTVSFRNNEEADQCIQTMDGRWFDG--RQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHHHHHHHHhCCcceEEEecc---CCCceeEEEeCChHHHHHHHHHhcCeeecc--eEEEEEEeCCc
Confidence                 3577888999999999988755   578899999999999999999999999999  66888776653

>KOG4211|consensus

Probab=99.71  E-value=3.5e-16  Score=140.22  Aligned_cols=153  Identities=19%  Similarity=0.266  Sum_probs=117.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHH----hccCcccceeccccc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA----LQDKGIHAQMARQQE  134 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~----l~g~~i~~~~~~~~~  134 (305)
                      -.|-+.+|||++|++||.++|+.|+ |+.+.+.+  .+|+..|-|||+|.+++++++|+++    |-.+-|.+-.+...+
T Consensus        11 ~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~e   87 (510)
T KOG4211|consen   11 FEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGAE   87 (510)
T ss_pred             eEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCcc
Confidence            4488999999999999999999995 77755544  4799999999999999999999985    334444433332111


Q ss_pred             -------------CCCCceEEecCCCCCCHHHHHHHHhhCCCeEE-EEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCC
Q psy4086         135 -------------QDPTNLYIANLPLNFKECDLESLLAKYVTVVS-TRILRDNNNTSKGVGFARLESKDKCDQMIQLFNG  200 (305)
Q Consensus       135 -------------~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~-v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g  200 (305)
                                   .....|-+.+||+.+|++||.++|+..-.|.. +.++.+..+++.|-|||+|++.+.|+.|+.. |-
T Consensus        88 ~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~r-hr  166 (510)
T KOG4211|consen   88 ADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGR-HR  166 (510)
T ss_pred             ccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHH-HH
Confidence                         12345888999999999999999998765555 4566666888999999999999999999975 33


Q ss_pred             CCCCCCCccEEEEeccC
Q psy4086         201 STLPGSKEPLLVKFADS  217 (305)
Q Consensus       201 ~~~~g~~~~l~v~~a~~  217 (305)
                      ..|.-  |-|.|-.+..
T Consensus       167 e~iGh--RYIEvF~Ss~  181 (510)
T KOG4211|consen  167 ENIGH--RYIEVFRSSR  181 (510)
T ss_pred             Hhhcc--ceEEeehhHH
Confidence            55555  5566655443

>KOG0110|consensus

Probab=99.71  E-value=1.3e-16  Score=148.39  Aligned_cols=155  Identities=23%  Similarity=0.326  Sum_probs=127.2

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc--
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR--  131 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~--  131 (305)
                      .+...+.|+|+|||..+..++|..+|..||+|..+.+.  + .|.   -++|+|.+..+|.+|.+.|....+....+.  
T Consensus       381 ~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp--~-~G~---~aiv~fl~p~eAr~Afrklaysr~k~~plyle  454 (725)
T KOG0110|consen  381 AERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP--P-GGT---GAIVEFLNPLEARKAFRKLAYSRFKSAPLYLE  454 (725)
T ss_pred             hhhhcceeeeccCccccccHHHHHHhhcccccceeecC--c-ccc---eeeeeecCccchHHHHHHhchhhhccCccccc
Confidence            44566789999999999999999999999999998544  2 121   489999999999999999875543321111  


Q ss_pred             -------------------------------------------------------cccCCCCceEEecCCCCCCHHHHHH
Q psy4086         132 -------------------------------------------------------QQEQDPTNLYIANLPLNFKECDLES  156 (305)
Q Consensus       132 -------------------------------------------------------~~~~~~~~l~V~nlp~~~te~~l~~  156 (305)
                                                                             ......++|||.||++++|.++|..
T Consensus       455 ~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~  534 (725)
T KOG0110|consen  455 WAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLED  534 (725)
T ss_pred             cChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHH
Confidence                                                                   0011124499999999999999999


Q ss_pred             HHhhCCCeEEEEEeeCCCCC----cccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         157 LLAKYVTVVSTRILRDNNNT----SKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       157 ~F~~~g~v~~v~i~~~~~g~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      +|...|.|.++.|...++..    +.|||||+|.+.++|++|++.|+|+.|+|  +.|.|+++.
T Consensus       535 ~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldG--H~l~lk~S~  596 (725)
T KOG0110|consen  535 LFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDG--HKLELKISE  596 (725)
T ss_pred             HHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecC--ceEEEEecc
Confidence            99999999999988877443    45999999999999999999999999999  779999988

>KOG1457|consensus

Probab=99.70  E-value=1.8e-16  Score=128.52  Aligned_cols=145  Identities=23%  Similarity=0.406  Sum_probs=114.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeC-CCCCCccceEEEEecchhhHHHHHHHhccCcccceec------
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILD-KTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA------  130 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~-~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~------  130 (305)
                      -+||||.+||.++...||..+|..|-..+.+.|... +.....+-+|||.|.+..+|.+|+..|||.+++.+..      
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            467999999999999999999999977776666543 3223466899999999999999999999987653221      


Q ss_pred             --c-----------------------------------------------------------------------------
Q psy4086         131 --R-----------------------------------------------------------------------------  131 (305)
Q Consensus       131 --~-----------------------------------------------------------------------------  131 (305)
                        +                                                                             
T Consensus       114 lAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~a  193 (284)
T KOG1457|consen  114 LAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPSA  193 (284)
T ss_pred             ehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCCcc
Confidence              1                                                                             


Q ss_pred             ----cc-------cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCC
Q psy4086         132 ----QQ-------EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNG  200 (305)
Q Consensus       132 ----~~-------~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g  200 (305)
                          .+       ...-.+|||.||..+++|++|+.+|+.|.....++|... .|  -..||++|++.+.|..|+..|+|
T Consensus       194 ~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~-~g--~~vaf~~~~~~~~at~am~~lqg  270 (284)
T KOG1457|consen  194 NAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR-GG--MPVAFADFEEIEQATDAMNHLQG  270 (284)
T ss_pred             cchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC-CC--cceEeecHHHHHHHHHHHHHhhc
Confidence                00       000147999999999999999999999988877776533 33  34799999999999999999998


Q ss_pred             CCCCC
Q psy4086         201 STLPG  205 (305)
Q Consensus       201 ~~~~g  205 (305)
                      ..|..
T Consensus       271 ~~~s~  275 (284)
T KOG1457|consen  271 NLLSS  275 (284)
T ss_pred             ceecc
Confidence            87754

>KOG0149|consensus

Probab=99.70  E-value=2.5e-17  Score=134.77  Aligned_cols=73  Identities=29%  Similarity=0.530  Sum_probs=65.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHH----hccCcccc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA----LQDKGIHA  127 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~----l~g~~i~~  127 (305)
                      |..-|+||||+|+|++..|+|+++|++||+|+++.|+.|+.+|++|||+||+|+|.+.|.+|++.    +||++-..
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNc   85 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANC   85 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCccccccccc
Confidence            44568899999999999999999999999999999999999999999999999999999999986    45554433

>KOG0124|consensus

Probab=99.68  E-value=7.6e-16  Score=133.08  Aligned_cols=156  Identities=16%  Similarity=0.314  Sum_probs=128.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc-----
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR-----  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~-----  131 (305)
                      .-.+|||..+.++.+|+||+..|+.||+|..|.+-++...+.+|||+|++|.+...-..||..||=.++.++.++     
T Consensus       209 ~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  209 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            445699999999999999999999999999999999998889999999999999999999999886666666555     


Q ss_pred             --------------------------------------------------------------------------------
Q psy4086         132 --------------------------------------------------------------------------------  131 (305)
Q Consensus       132 --------------------------------------------------------------------------------  131 (305)
                                                                                                      
T Consensus       289 TPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vSpA~~aa~p~~~l~qa~~a~~~pgvi~~v  368 (544)
T KOG0124|consen  289 TPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQPLGTLPQAVMAAQAPGVITGV  368 (544)
T ss_pred             CCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccCccccccCCCCCccccchhccCCceeccC
Confidence                                                                                            


Q ss_pred             ------------------------------------------------------------------------cccCCCCc
Q psy4086         132 ------------------------------------------------------------------------QQEQDPTN  139 (305)
Q Consensus       132 ------------------------------------------------------------------------~~~~~~~~  139 (305)
                                                                                              -+..+++.
T Consensus       369 tP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~G~sARhlvMqkLmR~~~S~V  448 (544)
T KOG0124|consen  369 TPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLSEQEHMSISGSSARHLVMQKLMRKQESTV  448 (544)
T ss_pred             CCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhhhhhCccccCccHHHHHHHHHhccccCcE
Confidence                                                                                    11223355


Q ss_pred             eEEecC--CCCCCH---HHHHHHHhhCCCeEEEEEeeCCCCCc-----ccEEEEEecCHHHHHHHHHHhCCCCCCCCCcc
Q psy4086         140 LYIANL--PLNFKE---CDLESLLAKYVTVVSTRILRDNNNTS-----KGVGFARLESKDKCDQMIQLFNGSTLPGSKEP  209 (305)
Q Consensus       140 l~V~nl--p~~~te---~~l~~~F~~~g~v~~v~i~~~~~g~~-----~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~  209 (305)
                      +.++|+  |.+++|   .+|.+.+.+||.|.+|.|...+.+..     ----||+|+...++.+|+++|+|..|.|+  .
T Consensus       449 ivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~e~edaeiiVKIFVefS~~~e~~rak~ALdGRfFgGr--~  526 (544)
T KOG0124|consen  449 IVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAEIIVKIFVEFSIASETHRAKQALDGRFFGGR--K  526 (544)
T ss_pred             EEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccccccchhhhheeeeeechhhHHHHHHHhhccceecCc--e
Confidence            677887  666654   58999999999999999888763321     12369999999999999999999999994  4


Q ss_pred             EEEEe
Q psy4086         210 LLVKF  214 (305)
Q Consensus       210 l~v~~  214 (305)
                      +..+.
T Consensus       527 VvAE~  531 (544)
T KOG0124|consen  527 VVAEV  531 (544)
T ss_pred             eehhh
Confidence            65544

>PF00076 RRM_1: RNA recognition motif

Probab=99.67  E-value=2.8e-16  Score=108.73  Aligned_cols=70  Identities=37%  Similarity=0.611  Sum_probs=66.0

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        61 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      |||+|||+++|+++|+++|++||.|..+.+..+ .++..+|||||+|.+.++|++|++.|||..+.++.++
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 5789999999999999999999999999999887653

(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 ....

>KOG0149|consensus

Probab=99.67  E-value=2.7e-16  Score=128.77  Aligned_cols=78  Identities=17%  Similarity=0.316  Sum_probs=71.2

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      -++||||+|+|.+..++|++.|++||+|+++.|+.|+ +|++|||+||+|.|.++|++|++.-| -.|+|  |...+++|
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdG--R~aNcnlA   88 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDG--RKANCNLA   88 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccc--cccccchh
Confidence            4689999999999999999999999999999999999 99999999999999999999998654 78999  55777777


Q ss_pred             cC
Q psy4086         216 DS  217 (305)
Q Consensus       216 ~~  217 (305)
                      .-
T Consensus        89 ~l   90 (247)
T KOG0149|consen   89 SL   90 (247)
T ss_pred             hh
Confidence            65

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.66  E-value=4.6e-16  Score=139.99  Aligned_cols=84  Identities=27%  Similarity=0.430  Sum_probs=77.7

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      .....++|||+|||+++||++|+++|+.||.|++|+|+.|. +++++|||||+|.++++|++||+.||+..|.+  ++|+
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~g--r~i~  180 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRN--KRLK  180 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCC--ceee
Confidence            34456899999999999999999999999999999999997 89999999999999999999999999999999  7799


Q ss_pred             EEeccCC
Q psy4086         212 VKFADSG  218 (305)
Q Consensus       212 v~~a~~~  218 (305)
                      |.+++..
T Consensus       181 V~~a~p~  187 (346)
T TIGR01659       181 VSYARPG  187 (346)
T ss_pred             eeccccc
Confidence            9998753

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).

>KOG0106|consensus

Probab=99.65  E-value=1.4e-16  Score=131.31  Aligned_cols=137  Identities=22%  Similarity=0.360  Sum_probs=116.9

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc--------
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR--------  131 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~--------  131 (305)
                      .||||+||+.+.+.+|.+||..||.|.++.+.        .||+||+|.+..+|+.|+..||++.+.+..+.        
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~   74 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKR   74 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecccccc
Confidence            59999999999999999999999999988875        24899999999999999999999988766411        


Q ss_pred             -------------------cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHH
Q psy4086         132 -------------------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCD  192 (305)
Q Consensus       132 -------------------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~  192 (305)
                                         ......+.|.|.++...+.+++|.+.|..+|.++...+       .++++||+|+..++|.
T Consensus        75 ~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~-------~~~~~~v~Fs~~~da~  147 (216)
T KOG0106|consen   75 RGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA-------RRNFAFVEFSEQEDAK  147 (216)
T ss_pred             cccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh-------hccccceeehhhhhhh
Confidence                               00112356889999999999999999999999966554       3568999999999999


Q ss_pred             HHHHHhCCCCCCCCCccEEEE
Q psy4086         193 QMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       193 ~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      +|++.|++..+.+  +.|.+.
T Consensus       148 ra~~~l~~~~~~~--~~l~~~  166 (216)
T KOG0106|consen  148 RALEKLDGKKLNG--RRISVE  166 (216)
T ss_pred             hcchhccchhhcC--ceeeec
Confidence            9999999999999  558773

>KOG0121|consensus

Probab=99.65  E-value=6.3e-16  Score=114.71  Aligned_cols=81  Identities=19%  Similarity=0.333  Sum_probs=75.9

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      .+++||||||...++|++|.++|+++|.|..|.+-.|+ +-.+.|||||+|.+.++|+.|++-++|+.++.  ++|+|.|
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLdd--r~ir~D~  112 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDD--RPIRIDW  112 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccc--cceeeec
Confidence            57899999999999999999999999999999999998 66789999999999999999999999999999  8899999


Q ss_pred             ccCC
Q psy4086         215 ADSG  218 (305)
Q Consensus       215 a~~~  218 (305)
                      ...-
T Consensus       113 D~GF  116 (153)
T KOG0121|consen  113 DAGF  116 (153)
T ss_pred             cccc
Confidence            6654

>KOG4212|consensus

Probab=99.64  E-value=4e-15  Score=131.36  Aligned_cols=73  Identities=29%  Similarity=0.440  Sum_probs=65.7

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .|+|||.|||.++||+.|++-|..||.|..+.|+.  .|+++|  .|+|.++++|++|+..|+|..++|  +.|.|.|.
T Consensus       536 a~qIiirNlP~dfTWqmlrDKfre~G~v~yadime--~GkskG--VVrF~s~edAEra~a~Mngs~l~G--r~I~V~y~  608 (608)
T KOG4212|consen  536 ACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME--NGKSKG--VVRFFSPEDAERACALMNGSRLDG--RNIKVTYF  608 (608)
T ss_pred             ccEEEEecCCccccHHHHHHHHHhccceehhhhhc--cCCccc--eEEecCHHHHHHHHHHhccCcccC--ceeeeeeC
Confidence            47899999999999999999999999999999843  456665  899999999999999999999999  55999873

>PF00076 RRM_1: RNA recognition motif

Probab=99.64  E-value=8.1e-16  Score=106.38  Aligned_cols=70  Identities=26%  Similarity=0.603  Sum_probs=66.0

Q ss_pred             eEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       140 l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      |||+|||.++++++|+++|++||.|..+.+..+.++..+++|||+|.+.++|++|++.|+|..+.+  +.|+
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 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKING--RKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETT--EEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECc--cCcC
Confidence            799999999999999999999999999999998778899999999999999999999999999999  5564

(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 ....

>KOG0122|consensus

Probab=99.63  E-value=3.3e-15  Score=122.89  Aligned_cols=76  Identities=26%  Similarity=0.437  Sum_probs=69.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      ..+.++|-|.||+.+++|++|++||..||.|..+.|.+|+.||.+||||||.|.+.++|.+||+.|||..+..-.+
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LIL  261 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLIL  261 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEE
Confidence            3366789999999999999999999999999999999999999999999999999999999999999987654433

>KOG1190|consensus

Probab=99.63  E-value=6.4e-15  Score=129.13  Aligned_cols=151  Identities=20%  Similarity=0.287  Sum_probs=127.7

Q ss_pred             CCeEEEcCCCCC-CcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc-----
Q psy4086          58 KTNLYIRGLTQD-TTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR-----  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~-~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~-----  131 (305)
                      ++.|.|.||..+ +|.+.|..+|..||+|.+|+|+.++.+     .|+|+|.|...|+.|++.|+|..+.++.++     
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd-----~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKD-----NALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCc-----ceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            677999999776 899999999999999999999998753     699999999999999999998888777666     


Q ss_pred             --------------------------c-----------ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCC
Q psy4086         132 --------------------------Q-----------QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN  174 (305)
Q Consensus       132 --------------------------~-----------~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~  174 (305)
                                                .           -.....+|...|+|.+++||+|+++|..-|...+......  
T Consensus       372 H~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~--  449 (492)
T KOG1190|consen  372 HTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ--  449 (492)
T ss_pred             CccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecC--
Confidence                                      0           0012357889999999999999999999887766554443  


Q ss_pred             CCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         175 NTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       175 g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                       +.+.+|++.+++.|+|..|+..++.+.+.++ ..|+|+|.+.
T Consensus       450 -kd~kmal~q~~sveeA~~ali~~hnh~lgen-~hlRvSFSks  490 (492)
T KOG1190|consen  450 -KDRKMALPQLESVEEAIQALIDLHNHYLGEN-HHLRVSFSKS  490 (492)
T ss_pred             -CCcceeecccCChhHhhhhccccccccCCCC-ceEEEEeecc
Confidence             4566999999999999999999999999775 5799999765

>KOG0122|consensus

Probab=99.62  E-value=1.8e-15  Score=124.34  Aligned_cols=82  Identities=27%  Similarity=0.432  Sum_probs=77.9

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      .+.++|-|.||+.+++|++|+++|.+||.|..|.|.+|+ +|.+||||||.|.+.++|.+||..|||+-++.  ..|+|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~--LILrvE  264 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDN--LILRVE  264 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccce--EEEEEE
Confidence            367889999999999999999999999999999999999 99999999999999999999999999999998  779999


Q ss_pred             eccCC
Q psy4086         214 FADSG  218 (305)
Q Consensus       214 ~a~~~  218 (305)
                      |+++.
T Consensus       265 wskP~  269 (270)
T KOG0122|consen  265 WSKPS  269 (270)
T ss_pred             ecCCC
Confidence            98874

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

Probab=99.61  E-value=4e-15  Score=140.85  Aligned_cols=104  Identities=17%  Similarity=0.261  Sum_probs=85.2

Q ss_pred             chhhHHHHHHHhccCcccceecc------------cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCC
Q psy4086         109 SGGYALAAVKALQDKGIHAQMAR------------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT  176 (305)
Q Consensus       109 ~~~~A~~a~~~l~g~~i~~~~~~------------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~  176 (305)
                      ..++|.+||.+++|..+......            ......++|||+|||++++|++|+++|++||.|.+|+|++|.+|+
T Consensus        18 ~~~~a~~a~~~~~gy~~~~~~g~r~~g~Pp~~~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~   97 (578)
T TIGR01648        18 PDEAALKALLERTGYTLVQENGQRKYGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQ   97 (578)
T ss_pred             ccHHHHHHHHHhhCccccccCCcccCCCCCCcccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCC
Confidence            36778888888877766544221            112235889999999999999999999999999999999999899


Q ss_pred             cccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         177 SKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       177 ~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ++|||||+|.+.++|++||+.||+..|... +.|.|.
T Consensus        98 sRGfaFV~F~~~e~A~~Ai~~lng~~i~~G-r~l~V~  133 (578)
T TIGR01648        98 NRGYAFVTFCGKEEAKEAVKLLNNYEIRPG-RLLGVC  133 (578)
T ss_pred             ccceEEEEeCCHHHHHHHHHHcCCCeecCC-cccccc
Confidence            999999999999999999999999888532 334444

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>KOG0107|consensus

Probab=99.61  E-value=5.7e-15  Score=115.63  Aligned_cols=80  Identities=20%  Similarity=0.408  Sum_probs=72.5

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ..++||||||+..+++.||+.+|..||.|.+|.|...    +.|||||+|++..+|+.|+..|+|+.|.|  ..|+|++.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn----PPGfAFVEFed~RDA~DAvr~LDG~~~cG--~r~rVE~S   82 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN----PPGFAFVEFEDPRDAEDAVRYLDGKDICG--SRIRVELS   82 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec----CCCceEEeccCcccHHHHHhhcCCccccC--ceEEEEee
Confidence            3688999999999999999999999999999998875    57899999999999999999999999999  55999998


Q ss_pred             cCCCcC
Q psy4086         216 DSGLKK  221 (305)
Q Consensus       216 ~~~~~~  221 (305)
                      ......
T Consensus        83 ~G~~r~   88 (195)
T KOG0107|consen   83 TGRPRG   88 (195)
T ss_pred             cCCccc
Confidence            875543

>KOG0125|consensus

Probab=99.60  E-value=1.9e-15  Score=129.03  Aligned_cols=84  Identities=25%  Similarity=0.523  Sum_probs=76.1

Q ss_pred             cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       132 ~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      +....+++|+|.|||+.+.|.||+.+|++||.|.+|+|+.+..| +|||+||+|++.++|++|.++|||+.|+|  |+|.
T Consensus        91 ~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRARa~LHgt~VEG--RkIE  167 (376)
T KOG0125|consen   91 SSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRARAELHGTVVEG--RKIE  167 (376)
T ss_pred             CCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHHHHHhhcceeec--eEEE
Confidence            33445688999999999999999999999999999999998754 79999999999999999999999999999  6699


Q ss_pred             EEeccCC
Q psy4086         212 VKFADSG  218 (305)
Q Consensus       212 v~~a~~~  218 (305)
                      |+.|..+
T Consensus       168 Vn~ATar  174 (376)
T KOG0125|consen  168 VNNATAR  174 (376)
T ss_pred             Eeccchh
Confidence            9998763

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.59  E-value=6e-15  Score=102.23  Aligned_cols=69  Identities=35%  Similarity=0.591  Sum_probs=63.5

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        61 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      |||+|||+++++++|+++|+.||.|..+.+..++. +..+|+|||+|.+.++|.+|++.+++..+.++.+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l   69 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKL   69 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEc
Confidence            79999999999999999999999999999999987 8999999999999999999999999888888765

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0125|consensus

Probab=99.59  E-value=9.7e-15  Score=124.74  Aligned_cols=71  Identities=21%  Similarity=0.387  Sum_probs=66.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .+|+|.|||+...|-||+.+|++||+|.+|.||.+.  .-+|||+||+|++.+||++|-++|||..|.+|.+.
T Consensus        97 kRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIE  167 (376)
T KOG0125|consen   97 KRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIE  167 (376)
T ss_pred             ceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEE
Confidence            349999999999999999999999999999999986  45999999999999999999999999988888776

>KOG0121|consensus

Probab=99.58  E-value=3.3e-15  Score=110.95  Aligned_cols=76  Identities=21%  Similarity=0.301  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||||||++.++|++|.+||+++|+|+.|.+=.|+.+..+-|||||+|.+.++|+.|++.++|..++.+.++
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir  109 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIR  109 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCccccccee
Confidence            4678899999999999999999999999999999999999999999999999999999999999999999888765

>KOG0120|consensus

Probab=99.58  E-value=8.3e-15  Score=134.51  Aligned_cols=158  Identities=16%  Similarity=0.349  Sum_probs=125.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccccc---
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQE---  134 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~---  134 (305)
                      ...|||++||..+++++++++++.||.+....++.|..+|.++||||.+|.+......|++.|||..+..+.+....   
T Consensus       289 ~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~  368 (500)
T KOG0120|consen  289 PNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIV  368 (500)
T ss_pred             cchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhc
Confidence            34599999999999999999999999999999999999999999999999999999999999999877655444100   


Q ss_pred             ---------C-------------------CCCceEEecC--CCCC-CH-------HHHHHHHhhCCCeEEEEEeeC-CC-
Q psy4086         135 ---------Q-------------------DPTNLYIANL--PLNF-KE-------CDLESLLAKYVTVVSTRILRD-NN-  174 (305)
Q Consensus       135 ---------~-------------------~~~~l~V~nl--p~~~-te-------~~l~~~F~~~g~v~~v~i~~~-~~-  174 (305)
                               .                   ....|.+-|+  +.++ .+       ++++.-+.+||.|..|.|.++ .+ 
T Consensus       369 g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~  448 (500)
T KOG0120|consen  369 GASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDE  448 (500)
T ss_pred             cchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCC
Confidence                     0                   0011111111  1111 11       456777889999999999998 32 


Q ss_pred             --CCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         175 --NTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       175 --g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                        ....|..||+|.+.+++++|.++|+|..|.+  +.+...|.+.
T Consensus       449 ~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~n--RtVvtsYyde  491 (500)
T KOG0120|consen  449 NPVPGTGKVFVEFADTEDSQRAMEELTGRKFAN--RTVVASYYDE  491 (500)
T ss_pred             CcCCCcccEEEEecChHHHHHHHHHccCceeCC--cEEEEEecCH
Confidence              3456789999999999999999999999999  7799988664

>KOG4207|consensus

Probab=99.57  E-value=7.9e-15  Score=117.69  Aligned_cols=83  Identities=29%  Similarity=0.439  Sum_probs=77.0

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...+|-|-||.+-++.++|+.+|++||.|-+|.|.+|+ +..++|||||.|.+..+|+.|+++|+|..|+|  +.|+|++
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldg--RelrVq~   89 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDG--RELRVQM   89 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeecc--ceeeehh
Confidence            34679999999999999999999999999999999999 89999999999999999999999999999999  6699999


Q ss_pred             ccCCCc
Q psy4086         215 ADSGLK  220 (305)
Q Consensus       215 a~~~~~  220 (305)
                      |.-...
T Consensus        90 arygr~   95 (256)
T KOG4207|consen   90 ARYGRP   95 (256)
T ss_pred             hhcCCC
Confidence            875433

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.57  E-value=1.6e-14  Score=122.21  Aligned_cols=77  Identities=10%  Similarity=0.247  Sum_probs=70.9

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      .++|||+||++.++|++|+++|+.||.|++|+|+.++  ..++||||+|++.++|+.||. |||..|.+  +.|+|.+++
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~--~~~GfAFVtF~d~eaAe~All-LnG~~l~g--r~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN--ERSQIAYVTFKDPQGAETALL-LSGATIVD--QSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC--CCCCEEEEEeCcHHHHHHHHH-hcCCeeCC--ceEEEEecc
Confidence            4789999999999999999999999999999999886  357899999999999999995 99999999  779999987


Q ss_pred             CC
Q psy4086         217 SG  218 (305)
Q Consensus       217 ~~  218 (305)
                      .-
T Consensus        79 ~~   80 (260)
T PLN03120         79 DY   80 (260)
T ss_pred             CC
Confidence            54

>KOG0113|consensus

Probab=99.56  E-value=1.4e-14  Score=122.38  Aligned_cols=82  Identities=26%  Similarity=0.385  Sum_probs=74.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccccC
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQ  135 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~~  135 (305)
                      ..-+||||+.|+++++|.+|+..|+.||+|+.|.|++|+.||+++|||||+|+++.+...|.+..+|..|+++.+.....
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999887764443


Q ss_pred             CC
Q psy4086         136 DP  137 (305)
Q Consensus       136 ~~  137 (305)
                      ..
T Consensus       179 Rg  180 (335)
T KOG0113|consen  179 RG  180 (335)
T ss_pred             cc
Confidence            33

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

Probab=99.56  E-value=3.9e-14  Score=123.72  Aligned_cols=138  Identities=28%  Similarity=0.478  Sum_probs=109.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccccc---
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQE---  134 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~---  134 (305)
                      .++|||+|||.++|+++|+++|.+||.|..+.+..++.+++++|||||+|.+.++|..|++.+++..+.++.+....   
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            58899999999999999999999999999999999998999999999999999999999999887766655444221   


Q ss_pred             ----------------------------CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCC-CcccEEEEEe
Q psy4086         135 ----------------------------QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN-TSKGVGFARL  185 (305)
Q Consensus       135 ----------------------------~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g-~~~g~afV~f  185 (305)
                                                  .....+++.+++..++..++...|..+|.+....+.....+ ......++.+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  274 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGN  274 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccch
Confidence                                        11256889999999999999999999999977777666532 2333334444


Q ss_pred             cCHHHHHHHH
Q psy4086         186 ESKDKCDQMI  195 (305)
Q Consensus       186 ~~~~~A~~Ai  195 (305)
                      .....+..+.
T Consensus       275 ~~~~~~~~~~  284 (306)
T COG0724         275 EASKDALESN  284 (306)
T ss_pred             hHHHhhhhhh
Confidence            4444444333

>KOG0105|consensus

Probab=99.54  E-value=4e-14  Score=111.73  Aligned_cols=81  Identities=22%  Similarity=0.388  Sum_probs=71.9

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...++|||+|||.++.|.+|+++|.+||.|.+|.+....  ....||||+|++..+|+.||..-+|+.+++  ..|+|+|
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~--g~ppfafVeFEd~RDAeDAiygRdGYdydg--~rLRVEf   79 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP--GPPPFAFVEFEDPRDAEDAIYGRDGYDYDG--CRLRVEF   79 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC--CCCCeeEEEecCccchhhhhhcccccccCc--ceEEEEe
Confidence            356889999999999999999999999999999887554  335699999999999999999999999999  5599999


Q ss_pred             ccCCC
Q psy4086         215 ADSGL  219 (305)
Q Consensus       215 a~~~~  219 (305)
                      +....
T Consensus        80 prggr   84 (241)
T KOG0105|consen   80 PRGGR   84 (241)
T ss_pred             ccCCC
Confidence            88754

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.54  E-value=2.4e-14  Score=99.17  Aligned_cols=70  Identities=27%  Similarity=0.612  Sum_probs=63.6

Q ss_pred             eEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       140 l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      |||+|||+++++++|+++|+.||.|..+++..++++..+++|||+|.+.++|.+|++.+++..+.|  +.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g--~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDG--RKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETT--EEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECC--EEcC
Confidence            799999999999999999999999999999999878899999999999999999999999999998  5453

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0126|consensus

Probab=99.54  E-value=5.7e-16  Score=121.82  Aligned_cols=77  Identities=31%  Similarity=0.512  Sum_probs=73.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      .++..|||||||++.||.||..+|++||+|++|.+++|+.||+++||||+.|++..+...|+..|||..|.++.++.
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirV  109 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRV  109 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEe
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999987763

>KOG0107|consensus

Probab=99.54  E-value=1.5e-14  Score=113.29  Aligned_cols=70  Identities=31%  Similarity=0.473  Sum_probs=63.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..|+||||||+..+++.||..+|..||+|..|.|-.+     +.|||||+|++..||+.|+..|||+.|.+..++
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~r   78 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIR   78 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEE
Confidence            3588999999999999999999999999999999764     478999999999999999999999998876554

>KOG0117|consensus

Probab=99.53  E-value=7.5e-14  Score=123.80  Aligned_cols=109  Identities=17%  Similarity=0.244  Sum_probs=89.2

Q ss_pred             cchhhHHHHHHHhccCcccceecc------------cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-C
Q psy4086         108 ESGGYALAAVKALQDKGIHAQMAR------------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-N  174 (305)
Q Consensus       108 ~~~~~A~~a~~~l~g~~i~~~~~~------------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~  174 (305)
                      .+.++|.++|.+-.|..|.+..-.            ......+.||||.||.++.|++|.-+|++.|+|-+++|+.|+ +
T Consensus        42 ~~~eaal~al~E~tgy~l~ve~gqrk~ggPpP~weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~s  121 (506)
T KOG0117|consen   42 QSEEAALKALLERTGYTLVVENGQRKYGGPPPGWEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFS  121 (506)
T ss_pred             ccHHHHHHHHHHhcCceEEEeccccccCCCCCcccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccC
Confidence            346777777776666666544332            223345889999999999999999999999999999999997 9


Q ss_pred             CCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         175 NTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       175 g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      |.+||||||+|.+.++|++||+.||+++|... +.|.|.....
T Consensus       122 G~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~G-K~igvc~Sva  163 (506)
T KOG0117|consen  122 GDNRGYAFVTFCTKEEAQEAIKELNNYEIRPG-KLLGVCVSVA  163 (506)
T ss_pred             CCCcceEEEEeecHHHHHHHHHHhhCccccCC-CEeEEEEeee
Confidence            99999999999999999999999999999533 6677776544

>KOG0129|consensus

Probab=99.51  E-value=6.9e-13  Score=120.03  Aligned_cols=144  Identities=17%  Similarity=0.243  Sum_probs=113.7

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCC-CCC--Cccc---eEEEEecchhhHHHHHHHhc-----
Q psy4086          53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDK-TTN--KCRG---YGFVDFESGGYALAAVKALQ-----  121 (305)
Q Consensus        53 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~-~~g--~~~G---~afV~f~~~~~A~~a~~~l~-----  121 (305)
                      ......++||||+||++++|++|...|..||.+. |...... ..+  .++|   |+|+.|+++..+...+.+..     
T Consensus       254 ~~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~  332 (520)
T KOG0129|consen  254 RSPRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGN  332 (520)
T ss_pred             CccccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccc
Confidence            3455678899999999999999999999999864 4433211 111  3667   99999999999988877632     


Q ss_pred             -----------cCcccceecc-----------cccCCCCceEEecCCCCCCHHHHHHHHh-hCCCeEEEEEeeCC-CCCc
Q psy4086         122 -----------DKGIHAQMAR-----------QQEQDPTNLYIANLPLNFKECDLESLLA-KYVTVVSTRILRDN-NNTS  177 (305)
Q Consensus       122 -----------g~~i~~~~~~-----------~~~~~~~~l~V~nlp~~~te~~l~~~F~-~~g~v~~v~i~~~~-~g~~  177 (305)
                                 .+.++++.+.           ......+|||||+||.-++.++|..+|+ .||.|..+-|-.|. -..+
T Consensus       333 ~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYP  412 (520)
T KOG0129|consen  333 YYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYP  412 (520)
T ss_pred             eEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCC
Confidence                       1223444333           2223458999999999999999999998 79999999999995 6789


Q ss_pred             ccEEEEEecCHHHHHHHHHH
Q psy4086         178 KGVGFARLESKDKCDQMIQL  197 (305)
Q Consensus       178 ~g~afV~f~~~~~A~~Ai~~  197 (305)
                      +|-|.|+|.+..+-.+||++
T Consensus       413 kGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  413 KGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CCcceeeecccHHHHHHHhh
Confidence            99999999999999999974

>KOG0113|consensus

Probab=99.51  E-value=1e-13  Score=117.20  Aligned_cols=82  Identities=23%  Similarity=0.381  Sum_probs=76.3

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      .+-+||||+-|+++++|..|+..|+.||.|+.|.|++|+ +|+++|||||+|++..+...|.+..+|..|++  +.|.|.
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idg--rri~VD  176 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDG--RRILVD  176 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecC--cEEEEE
Confidence            455899999999999999999999999999999999998 99999999999999999999999999999999  668888


Q ss_pred             eccCC
Q psy4086         214 FADSG  218 (305)
Q Consensus       214 ~a~~~  218 (305)
                      +....
T Consensus       177 vERgR  181 (335)
T KOG0113|consen  177 VERGR  181 (335)
T ss_pred             ecccc
Confidence            86554

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.51  E-value=5.6e-14  Score=118.99  Aligned_cols=70  Identities=17%  Similarity=0.180  Sum_probs=63.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .++|||+||++.+|+++|+++|+.||+|++|.|+.++.   .+|||||+|.++++|+.|+. |||..|.++.++
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~   73 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVT   73 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEE
Confidence            46799999999999999999999999999999998864   57899999999999999995 999888887766

>KOG1365|consensus

Probab=99.49  E-value=8e-13  Score=115.21  Aligned_cols=157  Identities=15%  Similarity=0.201  Sum_probs=119.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHh---cc-CCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhc---cCc-ccc--
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCS---QY-GPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ---DKG-IHA--  127 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~---~~-G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~---g~~-i~~--  127 (305)
                      .-.|-+++||+++++.|+.++|.   .. |..+.|-.++.. +|+..|-|||.|..+++|+.|+.+-.   |++ |..  
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFR  239 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFR  239 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            45588999999999999999995   22 245666666655 68999999999999999999997521   211 100  


Q ss_pred             -----------e--------------------ecccccCCCCceEEecCCCCCCHHHHHHHHhhCCC-eEE--EEEeeCC
Q psy4086         128 -----------Q--------------------MARQQEQDPTNLYIANLPLNFKECDLESLLAKYVT-VVS--TRILRDN  173 (305)
Q Consensus       128 -----------~--------------------~~~~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~-v~~--v~i~~~~  173 (305)
                                 +                    ...+......+|-+++||+..+.++|.++|..|.. |..  |.+..+.
T Consensus       240 STaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~  319 (508)
T KOG1365|consen  240 STAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG  319 (508)
T ss_pred             HhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC
Confidence                       0                    00022233567999999999999999999988865 333  7888888


Q ss_pred             CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         174 NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       174 ~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      .|++.|-|||+|.+.++|..|....+.+....  |-|.|--+..
T Consensus       320 qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~--RYiEvfp~S~  361 (508)
T KOG1365|consen  320 QGRPSGEAFIQMRNAERARAAAQKCHKKLMKS--RYIEVFPCSV  361 (508)
T ss_pred             CCCcChhhhhhhhhhHHHHHHHHHHHHhhccc--ceEEEeeccH
Confidence            89999999999999999999999888777756  6677765544

>KOG0126|consensus

Probab=99.47  E-value=5.1e-15  Score=116.48  Aligned_cols=101  Identities=23%  Similarity=0.458  Sum_probs=86.3

Q ss_pred             HHHHHhccCcccceec-----ccccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCH
Q psy4086         115 AAVKALQDKGIHAQMA-----RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESK  188 (305)
Q Consensus       115 ~a~~~l~g~~i~~~~~-----~~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~  188 (305)
                      +-|..||.+.++...+     +..-.++.-|||||||+.+||.||..+|++||+|+.|.+++|+ +|+++||||+.|++.
T Consensus         8 k~i~~lne~Elq~g~~~~~SWH~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQ   87 (219)
T KOG0126|consen    8 KNIQKLNERELQLGIADKKSWHQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQ   87 (219)
T ss_pred             HHHHHhhHHhhccccccccchhhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCc
Confidence            3455577666654433     2334456779999999999999999999999999999999999 999999999999999


Q ss_pred             HHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         189 DKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       189 ~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      .+..-|+..|||..|.|  |.|+|.....
T Consensus        88 RSTILAVDN~NGiki~g--RtirVDHv~~  114 (219)
T KOG0126|consen   88 RSTILAVDNLNGIKILG--RTIRVDHVSN  114 (219)
T ss_pred             cceEEEEeccCCceecc--eeEEeeeccc
Confidence            99999999999999999  7799987554

>KOG4207|consensus

Probab=99.47  E-value=9.5e-14  Score=111.53  Aligned_cols=78  Identities=26%  Similarity=0.349  Sum_probs=71.9

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +...-++|-|-||-+.++.++|+.+|++||.|-+|.|.+|+.|+.++|||||.|.+..+|+.|+++|||..|+++.++
T Consensus         9 dv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    9 DVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            333456799999999999999999999999999999999999999999999999999999999999999998887654

>KOG0114|consensus

Probab=99.46  E-value=3.9e-13  Score=96.26  Aligned_cols=74  Identities=24%  Similarity=0.289  Sum_probs=66.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++.|||.|||+++|.+++.++|.+||.|+.|+|=..+.   .+|.|||.|++..+|.+|++.|+|..+..+.+.
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~   88 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLV   88 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEE
Confidence            34567799999999999999999999999999999876554   589999999999999999999999998887764

>smart00362 RRM_2 RNA recognition motif

Probab=99.46  E-value=4.5e-13  Score=92.23  Aligned_cols=71  Identities=37%  Similarity=0.680  Sum_probs=65.7

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      +|||+|||..+++++|+++|.+||.|..+.+..+. +.++++|||+|.+.++|++|++.+++..+.+  +.|.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~--~~i~v   71 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALNGTKLGG--RPLRV   71 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhCCcEECC--EEEee
Confidence            58999999999999999999999999999999876 6788999999999999999999999999988  55766

>KOG4454|consensus

Probab=99.45  E-value=2e-14  Score=116.34  Aligned_cols=140  Identities=16%  Similarity=0.228  Sum_probs=125.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccccCCC
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDP  137 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~~~~  137 (305)
                      .+||||+|+...++|+-|.++|-+-|+|.+|.|..++ .++.| ||||.|+++-.+..|++.+||.++..+.+.      
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q------   80 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQ------   80 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhh------
Confidence            3679999999999999999999999999999998887 56777 999999999999999999999988877653      


Q ss_pred             CceEEec----CCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCC
Q psy4086         138 TNLYIAN----LPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPG  205 (305)
Q Consensus       138 ~~l~V~n----lp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  205 (305)
                      .+++.|+    |...++++.+.+.|+.-+.+..+++.++.+|+.+.+.|+++.-..+.-.++....+....-
T Consensus        81 ~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~  152 (267)
T KOG4454|consen   81 RTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQGLELFQ  152 (267)
T ss_pred             cccccCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhcccCcCC
Confidence            5677787    8888999999999999999999999999999999999999998888888888777666655

>KOG1190|consensus

Probab=99.45  E-value=4.1e-13  Score=117.93  Aligned_cols=152  Identities=16%  Similarity=0.235  Sum_probs=116.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHH-------hccCccccee
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA-------LQDKGIHAQM  129 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~-------l~g~~i~~~~  129 (305)
                      .++.|.++|||++++|+||.+++..||.|..+.+.+.++      .||++|.|++.|...+..       |.|+.|.+++
T Consensus        27 pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGkn------QAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq~  100 (492)
T KOG1190|consen   27 PSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKN------QAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQY  100 (492)
T ss_pred             CcceeEeccCCccccHHHHHHhcccccceeeeeeeccch------hhhhhhcchhhhhheeecccccCccccCcceeehh
Confidence            345699999999999999999999999999999987664      799999999998873321       2233332221


Q ss_pred             cc---------------------------------c------ccCCC---CceEEecCCCCCCHHHHHHHHhhCCCeEEE
Q psy4086         130 AR---------------------------------Q------QEQDP---TNLYIANLPLNFKECDLESLLAKYVTVVST  167 (305)
Q Consensus       130 ~~---------------------------------~------~~~~~---~~l~V~nlp~~~te~~l~~~F~~~g~v~~v  167 (305)
                      ..                                 .      ....+   -.++|+|+-+.++-+.|..+|++||.|.++
T Consensus       101 sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~VlKI  180 (492)
T KOG1190|consen  101 SNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVLKI  180 (492)
T ss_pred             hhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeEEE
Confidence            11                                 0      00001   136789999999999999999999999988


Q ss_pred             EEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         168 RILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       168 ~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      .-+.+..+   -.|+|+|.+.+.|+.|..+|+|..|......|+|.|.+-
T Consensus       181 iTF~Knn~---FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Skl  227 (492)
T KOG1190|consen  181 ITFTKNNG---FQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKL  227 (492)
T ss_pred             EEEecccc---hhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhc
Confidence            66654322   248999999999999999999998866556788888654

>KOG0146|consensus

Probab=99.45  E-value=1.7e-13  Score=114.06  Aligned_cols=99  Identities=27%  Similarity=0.494  Sum_probs=86.8

Q ss_pred             Ccccceeccc--ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCC
Q psy4086         123 KGIHAQMARQ--QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNG  200 (305)
Q Consensus       123 ~~i~~~~~~~--~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g  200 (305)
                      +.|.++.+..  +..+.++||||-|.+.-.|||++.+|..||.|++|.+.+..+|.+||||||.|.+..+|+.||..|+|
T Consensus         3 rpiqvkpadsesrg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHg   82 (371)
T KOG0146|consen    3 RPIQVKPADSESRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHG   82 (371)
T ss_pred             CCccccccccccCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcc
Confidence            4455555543  33367899999999999999999999999999999999999999999999999999999999999998


Q ss_pred             C-CCCCCCccEEEEeccCCCcC
Q psy4086         201 S-TLPGSKEPLLVKFADSGLKK  221 (305)
Q Consensus       201 ~-~~~g~~~~l~v~~a~~~~~~  221 (305)
                      . .+.|....|.|+|++..+.|
T Consensus        83 SqTmpGASSSLVVK~ADTdkER  104 (371)
T KOG0146|consen   83 SQTMPGASSSLVVKFADTDKER  104 (371)
T ss_pred             cccCCCCccceEEEeccchHHH
Confidence            6 57887778999999987665

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.44  E-value=6.5e-13  Score=110.77  Aligned_cols=78  Identities=12%  Similarity=0.171  Sum_probs=70.2

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ...+|||+||++.+||++|+++|+.||.|.+|+|+++.  ..++||||+|++.++|+.|+ .|+|..|.+  ++|.|..+
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~--et~gfAfVtF~d~~aaetAl-lLnGa~l~d--~~I~It~~   78 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG--EYACTAYVTFKDAYALETAV-LLSGATIVD--QRVCITRW   78 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC--CcceEEEEEECCHHHHHHHH-hcCCCeeCC--ceEEEEeC
Confidence            35789999999999999999999999999999999884  55689999999999999999 599999999  67998887


Q ss_pred             cCC
Q psy4086         216 DSG  218 (305)
Q Consensus       216 ~~~  218 (305)
                      ...
T Consensus        79 ~~y   81 (243)
T PLN03121         79 GQY   81 (243)
T ss_pred             ccc
Confidence            653

>smart00362 RRM_2 RNA recognition motif

Probab=99.44  E-value=6.6e-13  Score=91.39  Aligned_cols=69  Identities=35%  Similarity=0.569  Sum_probs=63.3

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      +|||+|||.++++++|+++|++||+|.++.+..++  +.++|+|||+|.+.++|++|++.+++..+.++.+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i   69 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPL   69 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEE
Confidence            49999999999999999999999999999999877  7789999999999999999999999888776544

>KOG0111|consensus

Probab=99.44  E-value=7.4e-14  Score=113.10  Aligned_cols=85  Identities=22%  Similarity=0.337  Sum_probs=80.3

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ..++||||+|..+++|..|...|-.||.|..|.++.|- +++.|||+||+|...|+|.+||..||+.++.|  |.|+|.+
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~G--rtirVN~   86 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFG--RTIRVNL   86 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcc--eeEEEee
Confidence            45789999999999999999999999999999999998 88999999999999999999999999999999  8899999


Q ss_pred             ccCCCcCC
Q psy4086         215 ADSGLKKR  222 (305)
Q Consensus       215 a~~~~~~~  222 (305)
                      |.+.+-+.
T Consensus        87 AkP~kike   94 (298)
T KOG0111|consen   87 AKPEKIKE   94 (298)
T ss_pred             cCCccccC
Confidence            99876654

>PLN03213 repressor of silencing 3; Provisional

Probab=99.44  E-value=4e-13  Score=120.55  Aligned_cols=79  Identities=15%  Similarity=0.251  Sum_probs=71.4

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCH--HHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESK--DKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~--~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....+||||||.+.+++++|+.+|..||.|.+|.|++. +|  ||||||+|.+.  +++.+||..|||..+.|  +.|+|
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAEWKG--R~LKV   82 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKG--GRLRL   82 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCeecC--ceeEE
Confidence            34578999999999999999999999999999999954 45  99999999987  78999999999999999  66999


Q ss_pred             EeccCC
Q psy4086         213 KFADSG  218 (305)
Q Consensus       213 ~~a~~~  218 (305)
                      ..|++.
T Consensus        83 NKAKP~   88 (759)
T PLN03213         83 EKAKEH   88 (759)
T ss_pred             eeccHH
Confidence            998873

>PLN03213 repressor of silencing 3; Provisional

Probab=99.43  E-value=4.4e-13  Score=120.33  Aligned_cols=73  Identities=16%  Similarity=0.281  Sum_probs=65.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecch--hhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESG--GYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~--~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .....+||||||++++++++|+.+|..||.|.+|.|+  +.+|  ||||||+|.+.  .++.+||..|||..+.++.++
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LK   81 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLR   81 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeE
Confidence            3445779999999999999999999999999999999  4467  99999999987  789999999999888877766

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.43  E-value=5.2e-13  Score=111.39  Aligned_cols=70  Identities=21%  Similarity=0.216  Sum_probs=62.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..+|||+||++.+|+++|+++|+.||+|++|+|++|.   +.+++|||+|.++++|+.|+. |+|..|..+.+.
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~   74 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVC   74 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEE
Confidence            3679999999999999999999999999999999985   456899999999999999995 999988777654

>KOG0108|consensus

Probab=99.42  E-value=3.8e-13  Score=122.95  Aligned_cols=83  Identities=24%  Similarity=0.476  Sum_probs=78.8

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      +.+||||+|++++|++|.++|+..|.|.+++++.|+ +|+++|||||+|.+.++|++|++.|||.++.|  ++|+|.|+.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~g--r~l~v~~~~   96 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNG--RKLRVNYAS   96 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCC--ceEEeeccc
Confidence            789999999999999999999999999999999999 99999999999999999999999999999999  779999998


Q ss_pred             CCCcCC
Q psy4086         217 SGLKKR  222 (305)
Q Consensus       217 ~~~~~~  222 (305)
                      ..+.+.
T Consensus        97 ~~~~~~  102 (435)
T KOG0108|consen   97 NRKNAE  102 (435)
T ss_pred             ccchhH
Confidence            766543

>KOG0108|consensus

Probab=99.41  E-value=1.4e-13  Score=125.74  Aligned_cols=73  Identities=22%  Similarity=0.534  Sum_probs=70.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +.|||||||++++|++|.++|+..|.|..++++.|+.||+++||||++|.+.++|+.|++.|||.++.++.++
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~   91 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLR   91 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEE
Confidence            6699999999999999999999999999999999999999999999999999999999999999988887766

>smart00360 RRM RNA recognition motif

Probab=99.40  E-value=1.2e-12  Score=89.76  Aligned_cols=68  Identities=34%  Similarity=0.548  Sum_probs=62.8

Q ss_pred             EcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          63 IRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        63 V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      |+|||.++++++|+++|+.||.|.++.+..++.++.++|+|||+|.+.++|.+|++.+++..+.++.+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~   68 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPL   68 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEE
Confidence            67999999999999999999999999999998889999999999999999999999999887766543

>KOG0132|consensus

Probab=99.40  E-value=3.9e-11  Score=113.19  Aligned_cols=69  Identities=23%  Similarity=0.412  Sum_probs=60.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      +.+||||||+|+.+++|.||.++|+.||+|.+|.++.      ++|||||++...++|++|+.+|+...+..+.+
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~I  487 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTI  487 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceee
Confidence            3688999999999999999999999999999999875      46799999999999999999988665554443

>smart00360 RRM RNA recognition motif

Probab=99.39  E-value=1.9e-12  Score=88.73  Aligned_cols=69  Identities=35%  Similarity=0.668  Sum_probs=63.8

Q ss_pred             EecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         142 IANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       142 V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      |+|||..+++++|+++|+.||.|..+.+..++ ++.++++|||+|.+.++|.+|++.|++..+.+  +.|+|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~--~~~~v   70 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDG--RPLKV   70 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCC--cEEEe
Confidence            57999999999999999999999999999987 68889999999999999999999999999988  55766

>KOG0130|consensus

Probab=99.39  E-value=1.8e-12  Score=97.33  Aligned_cols=83  Identities=17%  Similarity=0.250  Sum_probs=76.1

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ..--|||.++....+|++|.+.|..||+|+.+.+-.|+ +|..+|||+|+|++.++|++|+..|||..|-+  ..|.|.|
T Consensus        71 EGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~--q~v~VDw  148 (170)
T KOG0130|consen   71 EGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLG--QNVSVDW  148 (170)
T ss_pred             eeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhC--CceeEEE
Confidence            34569999999999999999999999999999999998 99999999999999999999999999999999  5599998


Q ss_pred             ccCCCc
Q psy4086         215 ADSGLK  220 (305)
Q Consensus       215 a~~~~~  220 (305)
                      +-.+..
T Consensus       149 ~Fv~gp  154 (170)
T KOG0130|consen  149 CFVKGP  154 (170)
T ss_pred             EEecCC
Confidence            876544

>KOG0131|consensus

Probab=99.38  E-value=7.6e-13  Score=104.42  Aligned_cols=81  Identities=28%  Similarity=0.432  Sum_probs=76.4

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....+|||+||+..++++.|.++|-+.|.|..++|.+|+ +...+|||||+|.++|+|+-||+.||...+.|  ++|+|+
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYg--rpIrv~   84 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYG--RPIRVN   84 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcC--ceeEEE
Confidence            345799999999999999999999999999999999999 77899999999999999999999999999999  889999


Q ss_pred             eccC
Q psy4086         214 FADS  217 (305)
Q Consensus       214 ~a~~  217 (305)
                      -+..
T Consensus        85 kas~   88 (203)
T KOG0131|consen   85 KASA   88 (203)
T ss_pred             eccc
Confidence            9883

>KOG1456|consensus

Probab=99.38  E-value=2.7e-10  Score=99.31  Aligned_cols=152  Identities=18%  Similarity=0.239  Sum_probs=116.7

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHh-------ccCcccceec-
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL-------QDKGIHAQMA-  130 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l-------~g~~i~~~~~-  130 (305)
                      -.|.|++|-..++|.||.+.++.||.|..+..+..+.      -|.|+|+|.+.|+.++.--       +|+.-..... 
T Consensus        32 pvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r------~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~NySt  105 (494)
T KOG1456|consen   32 PVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKR------QALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNYST  105 (494)
T ss_pred             ceEEEeccccccchhHHHHHHhcCCceEEEEeccccc------eeeeeeccccchhhheehhccCcccccCchhhcccch
Confidence            4599999999999999999999999998887765442      7999999999999988642       1211111111 


Q ss_pred             ----c---cccCCCCc---eEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCC
Q psy4086         131 ----R---QQEQDPTN---LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNG  200 (305)
Q Consensus       131 ----~---~~~~~~~~---l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g  200 (305)
                          +   ......++   +.|-|--+.+|.+.|..++...|.|..|.|++. +|   -.|.|+|++.+.|++|.++|||
T Consensus       106 sq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-ng---VQAmVEFdsv~~AqrAk~alNG  181 (494)
T KOG1456|consen  106 SQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-NG---VQAMVEFDSVEVAQRAKAALNG  181 (494)
T ss_pred             hhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-cc---eeeEEeechhHHHHHHHhhccc
Confidence                1   11112223   235566778999999999999999999998876 33   2699999999999999999999


Q ss_pred             CCCCCCCccEEEEeccCCCc
Q psy4086         201 STLPGSKEPLLVKFADSGLK  220 (305)
Q Consensus       201 ~~~~g~~~~l~v~~a~~~~~  220 (305)
                      ..|...-..|+|+||++.+.
T Consensus       182 ADIYsGCCTLKIeyAkP~rl  201 (494)
T KOG1456|consen  182 ADIYSGCCTLKIEYAKPTRL  201 (494)
T ss_pred             ccccccceeEEEEecCccee
Confidence            98865557899999998543

>KOG0114|consensus

Probab=99.38  E-value=3.1e-12  Score=91.70  Aligned_cols=78  Identities=23%  Similarity=0.366  Sum_probs=71.3

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      .+-|||.|||+++|.++..++|.+||.|..++|-..+  .-+|-|||.|++..+|.+|++.|+|..+.+  +.|.|-|..
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k--~TrGTAFVVYedi~dAk~A~dhlsg~n~~~--ryl~vlyyq   93 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK--ETRGTAFVVYEDIFDAKKACDHLSGYNVDN--RYLVVLYYQ   93 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCcc--CcCceEEEEehHhhhHHHHHHHhcccccCC--ceEEEEecC
Confidence            4669999999999999999999999999999998776  458899999999999999999999999999  889999876


Q ss_pred             CC
Q psy4086         217 SG  218 (305)
Q Consensus       217 ~~  218 (305)
                      ..
T Consensus        94 ~~   95 (124)
T KOG0114|consen   94 PE   95 (124)
T ss_pred             HH
Confidence            53

>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=99.37  E-value=5.7e-12  Score=87.13  Aligned_cols=74  Identities=38%  Similarity=0.715  Sum_probs=67.9

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      +|+|+|||..+++++|+++|+.+|.|..+.+..+..+..+++|||+|.+.++|..|++.+++..+.+  +.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~--~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGG--RPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECC--eEEEEeC
Confidence            5899999999999999999999999999999988755778999999999999999999999999998  6688764

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).

>KOG1456|consensus

Probab=99.35  E-value=1.2e-10  Score=101.49  Aligned_cols=158  Identities=18%  Similarity=0.228  Sum_probs=123.7

Q ss_pred             CCCCCCCeEEEcCCCCC-CcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          53 PEQLSKTNLYIRGLTQD-TTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        53 ~~~~~~~~l~V~~Lp~~-~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ......+.++|-+|... +.-+.|.++|..||.|++|+.++.+     .|.|.|++.|..+.++|+..||+..+.+..+.
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~  356 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLN  356 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEE
Confidence            33456788999999987 7788999999999999999999877     35899999999999999999987655443332


Q ss_pred             --------------------------------------------cccCCCCceEEecCCCCCCHHHHHHHHhhCCC-eEE
Q psy4086         132 --------------------------------------------QQEQDPTNLYIANLPLNFKECDLESLLAKYVT-VVS  166 (305)
Q Consensus       132 --------------------------------------------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~-v~~  166 (305)
                                                                  .-..+++.|..-|.|..+||+.|.++|...+. .++
T Consensus       357 v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~s  436 (494)
T KOG1456|consen  357 VCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTS  436 (494)
T ss_pred             EeeccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcce
Confidence                                                        11123467888999999999999999976644 467


Q ss_pred             EEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCC--CccEEEEecc
Q psy4086         167 TRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGS--KEPLLVKFAD  216 (305)
Q Consensus       167 v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~--~~~l~v~~a~  216 (305)
                      ++|+..++.++ .-+.++|++.++|.+||..||...|++-  +-+..++++-
T Consensus       437 vkvFp~kserS-ssGllEfe~~s~Aveal~~~NH~pi~~p~gs~PfilKlcf  487 (494)
T KOG1456|consen  437 VKVFPLKSERS-SSGLLEFENKSDAVEALMKLNHYPIEGPNGSFPFILKLCF  487 (494)
T ss_pred             EEeeccccccc-ccceeeeehHHHHHHHHHHhccccccCCCCCCCeeeeeee
Confidence            78777764333 3589999999999999999999988652  2455555543

>KOG0226|consensus

Probab=99.34  E-value=2.5e-12  Score=106.60  Aligned_cols=156  Identities=18%  Similarity=0.303  Sum_probs=130.4

Q ss_pred             eEEEcCCCCCCcHHH-H--HHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc-----
Q psy4086          60 NLYIRGLTQDTTDKD-L--INMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR-----  131 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~-L--~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~-----  131 (305)
                      ..+++++-..+..+- |  ...|+.+-.++..+++++. .+.-++++|+.|...+.-.++..+-+++.+....++     
T Consensus        98 ~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~-p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gt  176 (290)
T KOG0226|consen   98 RPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDR-PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGT  176 (290)
T ss_pred             cccccccccccCCCCCCcchhhhccchhhhhhhhhhcC-CCccCcccccCcchhhhhhhhccccccccccCcceeecccc
Confidence            367777777766555 4  6788888888888888887 477889999999998888888877777777665333     


Q ss_pred             --------cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCC
Q psy4086         132 --------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGST  202 (305)
Q Consensus       132 --------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~  202 (305)
                              ....+..+||+|.|..+++++.|-..|.+|-.....++++|+ +|+++||+||.|.+.+++.+|+..|||+.
T Consensus       177 swedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gky  256 (290)
T KOG0226|consen  177 SWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKY  256 (290)
T ss_pred             ccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccc
Confidence                    444556789999999999999999999999999999999998 99999999999999999999999999999


Q ss_pred             CCCCCccEEEEeccCC
Q psy4086         203 LPGSKEPLLVKFADSG  218 (305)
Q Consensus       203 ~~g~~~~l~v~~a~~~  218 (305)
                      ++.  ++|+++-...+
T Consensus       257 Vgs--rpiklRkS~wk  270 (290)
T KOG0226|consen  257 VGS--RPIKLRKSEWK  270 (290)
T ss_pred             ccc--chhHhhhhhHH
Confidence            998  67776655443

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

Probab=99.34  E-value=4.5e-12  Score=110.58  Aligned_cols=79  Identities=34%  Similarity=0.627  Sum_probs=75.3

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||..+++++|+++|..||.|..+.+..++ ++.++|||||+|.+.++|..|++.+++..|.+  ++|.|.++
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~--~~~~v~~~  192 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEG--RPLRVQKA  192 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECC--ceeEeecc
Confidence            5899999999999999999999999999999999997 89999999999999999999999999999999  77999997


Q ss_pred             cC
Q psy4086         216 DS  217 (305)
Q Consensus       216 ~~  217 (305)
                      ..
T Consensus       193 ~~  194 (306)
T COG0724         193 QP  194 (306)
T ss_pred             cc
Confidence            53

>KOG0132|consensus

Probab=99.34  E-value=4e-11  Score=113.12  Aligned_cols=78  Identities=17%  Similarity=0.396  Sum_probs=72.2

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      ++|||||.|+.+++|+||..+|+.||.|.+|.++     .+++||||......+|.+|+.+|+...+..  +.|+|.|+.
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li-----~~R~cAfI~M~~RqdA~kalqkl~n~kv~~--k~Iki~Wa~  493 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILI-----PPRGCAFIKMVRRQDAEKALQKLSNVKVAD--KTIKIAWAV  493 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeec-----cCCceeEEEEeehhHHHHHHHHHhcccccc--eeeEEeeec
Confidence            3789999999999999999999999999999998     568999999999999999999999999998  779999998


Q ss_pred             CCCcC
Q psy4086         217 SGLKK  221 (305)
Q Consensus       217 ~~~~~  221 (305)
                      .+..+
T Consensus       494 g~G~k  498 (894)
T KOG0132|consen  494 GKGPK  498 (894)
T ss_pred             cCCcc
Confidence            76655

>KOG0111|consensus

Probab=99.32  E-value=1.2e-12  Score=106.24  Aligned_cols=99  Identities=27%  Similarity=0.440  Sum_probs=79.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccccCC
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQD  136 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~~~  136 (305)
                      .+++||||+|..++||.-|...|-.||+|.+|.+..|..+.+.||||||+|...|||.+||..||+.++.++.++..-..
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            56789999999999999999999999999999999999999999999999999999999999998877777766644444


Q ss_pred             CCceEEecC-CCCCCHHHHH
Q psy4086         137 PTNLYIANL-PLNFKECDLE  155 (305)
Q Consensus       137 ~~~l~V~nl-p~~~te~~l~  155 (305)
                      +.+|--+.- |.+.+++.|+
T Consensus        89 P~kikegsqkPvWADDdWlk  108 (298)
T KOG0111|consen   89 PEKIKEGSQKPVWADDDWLK  108 (298)
T ss_pred             CccccCCCCCCcccCcHHHH
Confidence            433332222 3344444443

>KOG0109|consensus

Probab=99.31  E-value=2.3e-12  Score=108.68  Aligned_cols=73  Identities=32%  Similarity=0.516  Sum_probs=68.3

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      .+|||||||..+++.+|+.+|++||+|++|.|+++       |+||..++...|+.||+.|||..|.|  ..|.|+-+++
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN-------YgFVHiEdktaaedairNLhgYtLhg--~nInVeaSks   73 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN-------YGFVHIEDKTAAEDAIRNLHGYTLHG--VNINVEASKS   73 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc-------cceEEeecccccHHHHhhcccceecc--eEEEEEeccc
Confidence            57999999999999999999999999999999944       99999999999999999999999999  6699998887


Q ss_pred             CC
Q psy4086         218 GL  219 (305)
Q Consensus       218 ~~  219 (305)
                      +.
T Consensus        74 Ks   75 (346)
T KOG0109|consen   74 KS   75 (346)
T ss_pred             cC
Confidence            73

>KOG0120|consensus

Probab=99.31  E-value=4.3e-12  Score=116.77  Aligned_cols=156  Identities=22%  Similarity=0.411  Sum_probs=125.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcc-----------C-CeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQY-----------G-PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG  124 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~-----------G-~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~  124 (305)
                      ..+.++|+++++.++++++-.+|..-           | .+..+.+-..+      .|||++|.+.++|..|+. +++..
T Consensus       174 q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~------nfa~ie~~s~~~at~~~~-~~~~~  246 (500)
T KOG0120|consen  174 QARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEK------NFAFIEFRSISEATEAMA-LDGII  246 (500)
T ss_pred             hhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccc------cceeEEecCCCchhhhhc-ccchh
Confidence            34569999999999999999988643           3 25666655444      499999999999999987 44432


Q ss_pred             ccceecc------------------------------cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-
Q psy4086         125 IHAQMAR------------------------------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-  173 (305)
Q Consensus       125 i~~~~~~------------------------------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-  173 (305)
                      +.+...+                              ......+++||++||..+++++++++...||.+...+++.+. 
T Consensus       247 f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~  326 (500)
T KOG0120|consen  247 FEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSA  326 (500)
T ss_pred             hCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccc
Confidence            2222211                              112234779999999999999999999999999999999998 


Q ss_pred             CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCCCcC
Q psy4086         174 NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKK  221 (305)
Q Consensus       174 ~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~~~~  221 (305)
                      +|.++||||.+|.+......|+..|||..+.+  +.|.|..|......
T Consensus       327 ~g~skg~af~ey~dpsvtd~A~agLnGm~lgd--~~lvvq~A~~g~~~  372 (500)
T KOG0120|consen  327 TGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGD--KKLVVQRAIVGASN  372 (500)
T ss_pred             cccccceeeeeeeCCcchhhhhcccchhhhcC--ceeEeehhhccchh
Confidence            78999999999999999999999999999999  56999998875443

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.30  E-value=1.8e-11  Score=84.57  Aligned_cols=70  Identities=33%  Similarity=0.567  Sum_probs=63.4

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      +|+|+|||..+++++|+++|+.||.|..+.+..++.+ ..+|+|||+|.+.++|..|++.+++..+.++.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~   70 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPL   70 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            4899999999999999999999999999999988754 778999999999999999999999887666543

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).

>KOG4211|consensus

Probab=99.30  E-value=2.3e-10  Score=103.25  Aligned_cols=145  Identities=15%  Similarity=0.204  Sum_probs=107.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeE-EEEeeCCCCCCccceEEEEecchhhHHHHHHHhc----cCcccceecc-
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIIS-TKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ----DKGIHAQMAR-  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~-~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~----g~~i~~~~~~-  131 (305)
                      ...|-+++||+.||++||.++|+..-.|.. +.++.+. -+++.|-|||+|++.+.|++|+....    .+-|.+-.+. 
T Consensus       103 d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~Ss~  181 (510)
T KOG4211|consen  103 DGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRSSR  181 (510)
T ss_pred             CceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehhHH
Confidence            345999999999999999999997755544 4455665 47899999999999999999997521    1111110000 


Q ss_pred             ------------------------------------------------------------------------------cc
Q psy4086         132 ------------------------------------------------------------------------------QQ  133 (305)
Q Consensus       132 ------------------------------------------------------------------------------~~  133 (305)
                                                                                                    ..
T Consensus       182 ~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~~~  261 (510)
T KOG4211|consen  182 AEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNYPV  261 (510)
T ss_pred             HHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCccccccccccccccccccccCC
Confidence                                                                                          00


Q ss_pred             c----------------CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHH
Q psy4086         134 E----------------QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL  197 (305)
Q Consensus       134 ~----------------~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~  197 (305)
                      .                .....+...+||+..++.+|..+|+..- ...|.|-...+|+..|-|+|+|.+.++|..|+..
T Consensus       262 ~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~-p~~v~i~ig~dGr~TGEAdveF~t~edav~Amsk  340 (510)
T KOG4211|consen  262 SSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLN-PYRVHIEIGPDGRATGEADVEFATGEDAVGAMGK  340 (510)
T ss_pred             CCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCC-ceeEEEEeCCCCccCCcceeecccchhhHhhhcc
Confidence            0                0013466789999999999999998764 4478888888899999999999999999999863


Q ss_pred             hCCCCCCC
Q psy4086         198 FNGSTLPG  205 (305)
Q Consensus       198 l~g~~~~g  205 (305)
                       ++..+..
T Consensus       341 -d~anm~h  347 (510)
T KOG4211|consen  341 -DGANMGH  347 (510)
T ss_pred             -CCcccCc
Confidence             4455554

>KOG0130|consensus

Probab=99.29  E-value=6.2e-12  Score=94.43  Aligned_cols=76  Identities=25%  Similarity=0.448  Sum_probs=69.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      ....-.|||.++..++||++|.+.|..||+|+.+.+..|+.||-.||||+|+|.+.++|++|+..+||..|..+.+
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v  144 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNV  144 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCce
Confidence            3344579999999999999999999999999999999999999999999999999999999999999887766543

>KOG4210|consensus

Probab=99.29  E-value=7.4e-12  Score=109.53  Aligned_cols=162  Identities=15%  Similarity=0.256  Sum_probs=134.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec------
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA------  130 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~------  130 (305)
                      ..+++|++++...+.+.++..++..+|.+..+.+........++|++.+.|...+.+..|+.....+.+.....      
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            46789999999999999999999999988888888877788999999999999999999998532212111111      


Q ss_pred             -----------ccccCCCCceE-EecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHH
Q psy4086         131 -----------RQQEQDPTNLY-IANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQL  197 (305)
Q Consensus       131 -----------~~~~~~~~~l~-V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~  197 (305)
                                 +.......++| |++|+..+++++|+.+|..+|.|..+++..++ ++.+++||+|+|.....+..++..
T Consensus       167 ~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~  246 (285)
T KOG4210|consen  167 RRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND  246 (285)
T ss_pred             cccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc
Confidence                       11222335566 99999999999999999999999999999988 899999999999999999999987


Q ss_pred             hCCCCCCCCCccEEEEeccCCCcC
Q psy4086         198 FNGSTLPGSKEPLLVKFADSGLKK  221 (305)
Q Consensus       198 l~g~~~~g~~~~l~v~~a~~~~~~  221 (305)
                       +...+.+  +++.+.+.......
T Consensus       247 -~~~~~~~--~~~~~~~~~~~~~~  267 (285)
T KOG4210|consen  247 -QTRSIGG--RPLRLEEDEPRPKS  267 (285)
T ss_pred             -ccCcccC--cccccccCCCCccc
Confidence             7788888  78999998876444

>KOG0128|consensus

Probab=99.28  E-value=8.6e-13  Score=125.50  Aligned_cols=149  Identities=18%  Similarity=0.222  Sum_probs=128.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccccCC
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQD  136 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~~~  136 (305)
                      ..+++||.||+..+.+.+|...|..+|.+..+.+......++.+|+|+|+|.+++++.+||.-.++..+.          
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g----------  735 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG----------  735 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh----------
Confidence            3467999999999999999999999998887777766677999999999999999999999854433332          


Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      ...++|.|.|+..|.++|+.++..+|.+++++++..+.|+++|.|+|.|.+..++.+++...+...+...  .+.|...+
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~--~~~v~vsn  813 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKREN--NGEVQVSN  813 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhhhhc--CccccccC
Confidence            4579999999999999999999999999999999999999999999999999999999988777766663  36666655


Q ss_pred             C
Q psy4086         217 S  217 (305)
Q Consensus       217 ~  217 (305)
                      +
T Consensus       814 p  814 (881)
T KOG0128|consen  814 P  814 (881)
T ss_pred             C
Confidence            4

>PF13893 RRM_5: RNA recognition motif

Probab=99.28  E-value=1.4e-11  Score=81.25  Aligned_cols=56  Identities=29%  Similarity=0.581  Sum_probs=50.5

Q ss_pred             HHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         154 LESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       154 l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      |+++|++||.|.++.+..+.    +++|||+|.+.++|.+|++.|||..+.|  ++|+|.|+
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----RGFAFVEFASVEDAQKAIEQLNGRQFNG--RPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHHHHHHHHTTSEETT--EEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECC--cEEEEEEC
Confidence            68999999999999998663    5899999999999999999999999999  77999985

(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 ....

>smart00361 RRM_1 RNA recognition motif

Probab=99.27  E-value=1.5e-11  Score=85.12  Aligned_cols=60  Identities=22%  Similarity=0.338  Sum_probs=53.8

Q ss_pred             HHHHHHHHh----ccCCeeEEE-EeeCCCC--CCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          72 DKDLINMCS----QYGPIISTK-AILDKTT--NKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        72 ~~~L~~~f~----~~G~i~~~~-i~~~~~~--g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +++|+++|+    +||.|.++. |+.++.+  ++++|||||+|.+.++|.+|++.|||+.+.++.++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~   68 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVK   68 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            678999998    999999995 7777766  89999999999999999999999999999887654

>smart00361 RRM_1 RNA recognition motif

Probab=99.27  E-value=1.8e-11  Score=84.63  Aligned_cols=60  Identities=22%  Similarity=0.325  Sum_probs=53.2

Q ss_pred             HHHHHHHHh----hCCCeEEEE-EeeCC-C--CCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         151 ECDLESLLA----KYVTVVSTR-ILRDN-N--NTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       151 e~~l~~~F~----~~g~v~~v~-i~~~~-~--g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      +++|+++|+    +||.|.++. |..++ +  +.++||+||+|.+.++|.+|+..|||..+.|  +.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~g--r~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDG--RTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECC--EEEEe
Confidence            578888888    999999995 66665 5  8899999999999999999999999999999  66765

>KOG0112|consensus

Probab=99.26  E-value=5.6e-12  Score=120.52  Aligned_cols=162  Identities=14%  Similarity=0.120  Sum_probs=138.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          52 GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        52 ~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..+...+++||+|||+..+++.+|+..|..+|.|.+|.|-.-+ -+.-..|+||.|.+.+.+-.|+.++.+..|.....+
T Consensus       366 ~DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r  444 (975)
T KOG0112|consen  366 LDDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHR  444 (975)
T ss_pred             ccchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCccc
Confidence            3456678899999999999999999999999999999986654 355566999999999999999999888776544333


Q ss_pred             -----cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCC
Q psy4086         132 -----QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGS  206 (305)
Q Consensus       132 -----~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  206 (305)
                           .+....+.+|+++|..++....|...|..||.|..|.+-..     .-||+|.|++...|+.|++.|-|..|.+-
T Consensus       445 ~glG~~kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-----q~yayi~yes~~~aq~a~~~~rgap~G~P  519 (975)
T KOG0112|consen  445 IGLGQPKSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-----QPYAYIQYESPPAAQAATHDMRGAPLGGP  519 (975)
T ss_pred             ccccccccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-----CcceeeecccCccchhhHHHHhcCcCCCC
Confidence                 24455678999999999999999999999999998776643     45999999999999999999999999998


Q ss_pred             CccEEEEeccCCC
Q psy4086         207 KEPLLVKFADSGL  219 (305)
Q Consensus       207 ~~~l~v~~a~~~~  219 (305)
                      ++.|+|.|+....
T Consensus       520 ~~r~rvdla~~~~  532 (975)
T KOG0112|consen  520 PRRLRVDLASPPG  532 (975)
T ss_pred             CcccccccccCCC
Confidence            8899999998743

>KOG0415|consensus

Probab=99.14  E-value=7.7e-11  Score=102.03  Aligned_cols=84  Identities=23%  Similarity=0.392  Sum_probs=77.9

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      .+.+.|||-.|.+-+++++|.-+|+.||.|.+|.|++|+ +|.+-.||||+|++.+++++|.-.|++..|+.  +.|.|.
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDD--rRIHVD  314 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDD--RRIHVD  314 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeecc--ceEEee
Confidence            345789999999999999999999999999999999999 99999999999999999999999999999999  669999


Q ss_pred             eccCCCc
Q psy4086         214 FADSGLK  220 (305)
Q Consensus       214 ~a~~~~~  220 (305)
                      |.....+
T Consensus       315 FSQSVsk  321 (479)
T KOG0415|consen  315 FSQSVSK  321 (479)
T ss_pred             hhhhhhh
Confidence            9876544

>KOG4206|consensus

Probab=99.11  E-value=2.3e-10  Score=93.88  Aligned_cols=79  Identities=19%  Similarity=0.439  Sum_probs=72.3

Q ss_pred             CceEEecCCCCCCHHHHHH----HHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         138 TNLYIANLPLNFKECDLES----LLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~----~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      .||||.||+..+..++|+.    +|++||.|.+|......  +.||.|||.|.+.+.|..|+.+|+|..+.|  ++++|.
T Consensus        10 ~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~--KmRGQA~VvFk~~~~As~A~r~l~gfpFyg--K~mriq   85 (221)
T KOG4206|consen   10 GTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTP--KMRGQAFVVFKETEAASAALRALQGFPFYG--KPMRIQ   85 (221)
T ss_pred             ceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCC--CccCceEEEecChhHHHHHHHHhcCCcccC--chhhee
Confidence            3999999999999999888    99999999998877653  789999999999999999999999999999  889999


Q ss_pred             eccCCCc
Q psy4086         214 FADSGLK  220 (305)
Q Consensus       214 ~a~~~~~  220 (305)
                      ||..+..
T Consensus        86 yA~s~sd   92 (221)
T KOG4206|consen   86 YAKSDSD   92 (221)
T ss_pred             cccCccc
Confidence            9997654

>KOG4208|consensus

Probab=99.06  E-value=4.9e-10  Score=90.52  Aligned_cols=81  Identities=22%  Similarity=0.408  Sum_probs=71.1

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCcHHHHHHHHhcc-CCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccce
Q psy4086          50 PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQY-GPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ  128 (305)
Q Consensus        50 ~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~-G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~  128 (305)
                      ..........-+||..+|.-+.+.+|..+|.+| |.|..+++-+++.||.++|||||+|++++.|.-|-+.||++-+..+
T Consensus        41 ~~~p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~  120 (214)
T KOG4208|consen   41 REKPEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEH  120 (214)
T ss_pred             ccCCccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhh
Confidence            334445556669999999999999999999998 7888899889999999999999999999999999999999988776


Q ss_pred             ec
Q psy4086         129 MA  130 (305)
Q Consensus       129 ~~  130 (305)
                      .+
T Consensus       121 lL  122 (214)
T KOG4208|consen  121 LL  122 (214)
T ss_pred             ee
Confidence            54

>KOG4661|consensus

Probab=99.04  E-value=1.4e-09  Score=99.69  Aligned_cols=77  Identities=27%  Similarity=0.522  Sum_probs=67.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||.+|...+...+|++||++||+|+..+|+++..+--.+.|+||++.+.++|.+||+.|+-..++++++.
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmIS  478 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMIS  478 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeee
Confidence            33557899999999999999999999999999999999987777889999999999999999999776666665554

>PF13893 RRM_5: RNA recognition motif

Probab=99.04  E-value=7e-10  Score=73.08  Aligned_cols=52  Identities=27%  Similarity=0.485  Sum_probs=45.5

Q ss_pred             HHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          75 LINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        75 L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      |+++|++||+|.++.+..+.     +++|||+|.+.++|++|++.|||..+.++.++
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~   52 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLK   52 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            68999999999999997654     57999999999999999999999998887654

(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 ....

>KOG0116|consensus

Probab=99.04  E-value=2e-09  Score=98.20  Aligned_cols=81  Identities=17%  Similarity=0.320  Sum_probs=67.7

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      .+|||+|||.++++++|+++|..||.|+...|.... .++...||||+|.+.++++.||++- -..|++  +.|.|+-.+
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As-p~~ig~--~kl~Veek~  365 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS-PLEIGG--RKLNVEEKR  365 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC-ccccCC--eeEEEEecc
Confidence            459999999999999999999999999999888765 4455589999999999999999863 456666  679998877


Q ss_pred             CCCcC
Q psy4086         217 SGLKK  221 (305)
Q Consensus       217 ~~~~~  221 (305)
                      .....
T Consensus       366 ~~~~g  370 (419)
T KOG0116|consen  366 PGFRG  370 (419)
T ss_pred             ccccc
Confidence            64444

>KOG4208|consensus

Probab=99.03  E-value=9.3e-10  Score=88.95  Aligned_cols=82  Identities=21%  Similarity=0.319  Sum_probs=73.8

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhC-CCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKY-VTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~-g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      .....+||..+|..+.+.+|..+|.++ |.|+.+++-+++ +|.++|||||+|++.+.|.-|.+.||++.+.+  +.|.+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e--~lL~c  124 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLME--HLLEC  124 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhh--heeee
Confidence            334668999999999999999999888 778888887887 99999999999999999999999999999999  77999


Q ss_pred             EeccCC
Q psy4086         213 KFADSG  218 (305)
Q Consensus       213 ~~a~~~  218 (305)
                      .+-.+.
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            997664

>KOG0153|consensus

Probab=99.03  E-value=1.2e-09  Score=94.71  Aligned_cols=79  Identities=22%  Similarity=0.341  Sum_probs=68.2

Q ss_pred             cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhC-CCCCCCCCccE
Q psy4086         132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN-GSTLPGSKEPL  210 (305)
Q Consensus       132 ~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~~~g~~~~l  210 (305)
                      +.+..-.+|||++|-..++|.+|+++|.+||+|+++.+...     +++|||+|.+.++|+.|.+++- ...|+|  ..|
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lvI~G--~Rl  295 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLVING--FRL  295 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceeeecc--eEE
Confidence            45555688999999999999999999999999999999854     6799999999999999887654 446788  679


Q ss_pred             EEEeccC
Q psy4086         211 LVKFADS  217 (305)
Q Consensus       211 ~v~~a~~  217 (305)
                      .|.|..+
T Consensus       296 ~i~Wg~~  302 (377)
T KOG0153|consen  296 KIKWGRP  302 (377)
T ss_pred             EEEeCCC
Confidence            9999887

>KOG4660|consensus

Probab=98.96  E-value=1.3e-09  Score=99.84  Aligned_cols=151  Identities=17%  Similarity=0.190  Sum_probs=107.0

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        53 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ..+...++|+|-|||..|++++|+.+|+.||+|++|+.     +-..+|..||+|.|..+|++|+++|+++.|.++.++.
T Consensus        70 ~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~  144 (549)
T KOG4660|consen   70 EKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIKR  144 (549)
T ss_pred             cccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcC
Confidence            34567788999999999999999999999999998654     3445789999999999999999999999888776651


Q ss_pred             ccC-----------------------------CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEE
Q psy4086         133 QEQ-----------------------------DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFA  183 (305)
Q Consensus       133 ~~~-----------------------------~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV  183 (305)
                      ...                             ....+ ++.|.+..+...++..|.-+|.+.. +..    +.-+-.-|+
T Consensus       145 ~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~-~g~l~P~~s~~~~~~~~~~~~~~~~-~~~----~~~~hq~~~  218 (549)
T KOG4660|consen  145 PGGARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQL-FGMLSPTRSSILLEHISSVDGSSPG-RET----PLLNHQRFV  218 (549)
T ss_pred             CCcccccchhcccchhhhhccchhhcCCCCCCcCCcc-eeeeccchhhhhhhcchhccCcccc-ccc----cchhhhhhh
Confidence            110                             11223 3447777777666777777776654 211    112225578


Q ss_pred             EecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         184 RLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       184 ~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      .|.+..++..+.... |..+.+  ....+.+...
T Consensus       219 ~~~~~~s~a~~~~~~-G~~~s~--~~~v~t~S~~  249 (549)
T KOG4660|consen  219 EFADNRSYAFSEPRG-GFLISN--SSGVITFSGP  249 (549)
T ss_pred             hhccccchhhcccCC-ceecCC--CCceEEecCC
Confidence            888888886665533 566666  3466666554

>KOG4849|consensus

Probab=98.94  E-value=1.3e-08  Score=88.27  Aligned_cols=89  Identities=22%  Similarity=0.328  Sum_probs=71.1

Q ss_pred             ccceecccccCCCCceEEecCCCCCCHHHHHHHHhhCCC--eEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCC
Q psy4086         125 IHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVT--VVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGS  201 (305)
Q Consensus       125 i~~~~~~~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~--v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~  201 (305)
                      +..+.+...+...-++|||||-|.+|++||.+....-|.  +.+++++.++ +|.+||||+|...+..+..+-++.|-.+
T Consensus        68 ~~~~~~~s~~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k  147 (498)
T KOG4849|consen   68 IGAKPATSSEGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTK  147 (498)
T ss_pred             ccCCccccccCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccc
Confidence            333344444555567999999999999999998877664  6777888888 8999999999999999999999999999


Q ss_pred             CCCCCCccEEEEe
Q psy4086         202 TLPGSKEPLLVKF  214 (305)
Q Consensus       202 ~~~g~~~~l~v~~  214 (305)
                      +|.|.. +..+.|
T Consensus       148 ~iHGQ~-P~V~~~  159 (498)
T KOG4849|consen  148 TIHGQS-PTVLSY  159 (498)
T ss_pred             eecCCC-Ceeecc
Confidence            998853 444444

>KOG0415|consensus

Probab=98.94  E-value=1e-09  Score=95.16  Aligned_cols=73  Identities=27%  Similarity=0.395  Sum_probs=68.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..|||..|.+-+|+++|.-+|+.||+|..|.|++|..||.+..||||+|.+.+++++|.-.|++.-|+.+.++
T Consensus       240 NVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIH  312 (479)
T KOG0415|consen  240 NVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIH  312 (479)
T ss_pred             ceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEE
Confidence            4599999999999999999999999999999999999999999999999999999999999988877776655

>KOG4205|consensus

Probab=98.94  E-value=9.7e-10  Score=96.65  Aligned_cols=82  Identities=22%  Similarity=0.372  Sum_probs=72.7

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      +.++|||++|.|+++++.|++.|.+||+|.+|.+++|+ ++++++|+||+|.+.+...+++.. .-+.|++  +.|.++.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dg--r~ve~k~   81 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDG--RSVEPKR   81 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCC--cccccee
Confidence            67899999999999999999999999999999999999 899999999999999998888864 3467888  6688888


Q ss_pred             ccCCCc
Q psy4086         215 ADSGLK  220 (305)
Q Consensus       215 a~~~~~  220 (305)
                      |.+...
T Consensus        82 av~r~~   87 (311)
T KOG4205|consen   82 AVSRED   87 (311)
T ss_pred             ccCccc
Confidence            777553

>KOG0533|consensus

Probab=98.94  E-value=4.8e-09  Score=88.80  Aligned_cols=86  Identities=22%  Similarity=0.436  Sum_probs=77.2

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      +..+.+|+|.||++.++++||+++|+.||.++.+.+..++.|.+.|.|-|.|...++|++|++.+||..++|  +++++.
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG--~~mk~~  157 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDG--RPMKIE  157 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCC--ceeeeE
Confidence            344578999999999999999999999999999999999999999999999999999999999999999999  668887


Q ss_pred             eccCCCcC
Q psy4086         214 FADSGLKK  221 (305)
Q Consensus       214 ~a~~~~~~  221 (305)
                      ........
T Consensus       158 ~i~~~~~~  165 (243)
T KOG0533|consen  158 IISSPSQS  165 (243)
T ss_pred             EecCcccc
Confidence            76654443

>KOG4307|consensus

Probab=98.92  E-value=1.3e-08  Score=95.29  Aligned_cols=74  Identities=18%  Similarity=0.310  Sum_probs=64.8

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCe-EEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTV-VSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v-~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      +.|-|.|+|++++-+||.++|..|-.+ .+|.+.+..+|...|-|.|.|++.++|.+|.+.|+++.|..+.  +.+.
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~--V~l~  942 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRV--VSLR  942 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCccccee--EEEE
Confidence            468899999999999999999999655 4677777779999999999999999999999999999999844  5554

>KOG0533|consensus

Probab=98.89  E-value=5.3e-09  Score=88.56  Aligned_cols=79  Identities=18%  Similarity=0.277  Sum_probs=70.9

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ  133 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~  133 (305)
                      .+...++|+|.|||+.|+++||+++|+.||.+..+-|..++ +|++.|.|-|.|...+||++|++.++|..++++.++..
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~  157 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIE  157 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeE
Confidence            44455789999999999999999999999999999998888 69999999999999999999999999988888776533

>KOG0153|consensus

Probab=98.86  E-value=4.7e-09  Score=91.02  Aligned_cols=77  Identities=29%  Similarity=0.411  Sum_probs=63.7

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHh------ccC
Q psy4086          50 PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL------QDK  123 (305)
Q Consensus        50 ~~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l------~g~  123 (305)
                      -..+++..-++|||++|-..++|.+|++.|.+||+|+.+.++..+      ++|||+|.+.+.|+.|.++.      +|+
T Consensus       220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~  293 (377)
T KOG0153|consen  220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGF  293 (377)
T ss_pred             cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecce
Confidence            345567777889999999999999999999999999999998654      49999999999999999873      455


Q ss_pred             cccceeccc
Q psy4086         124 GIHAQMARQ  132 (305)
Q Consensus       124 ~i~~~~~~~  132 (305)
                      .|.+.|.+.
T Consensus       294 Rl~i~Wg~~  302 (377)
T KOG0153|consen  294 RLKIKWGRP  302 (377)
T ss_pred             EEEEEeCCC
Confidence            555555443

>KOG1457|consensus

Probab=98.85  E-value=2.1e-08  Score=82.03  Aligned_cols=86  Identities=19%  Similarity=0.323  Sum_probs=72.4

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC--CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCC-CccEEEE
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN--NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGS-KEPLLVK  213 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~--~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~-~~~l~v~  213 (305)
                      -+||||.+||.++..-+|..+|..|...+.+.+....  +..++.+|||+|.+..+|++|+.+|||..|+-. ...|+|+
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            5899999999999999999999999888877766654  335678999999999999999999999998653 2579999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      +|+...++.
T Consensus       114 lAKSNtK~k  122 (284)
T KOG1457|consen  114 LAKSNTKRK  122 (284)
T ss_pred             ehhcCcccc
Confidence            998755443

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

Probab=98.84  E-value=2e-08  Score=73.09  Aligned_cols=70  Identities=26%  Similarity=0.286  Sum_probs=63.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhc--cCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQ--YGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~--~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      +|||+|.|||...|.++|.+++..  .|..+.+.+..|-.++.+.|||||.|.+.+.|.+..+.++|+.+..
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~   72 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPN   72 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCcccc
Confidence            478999999999999999998864  3678889999999999999999999999999999999999988754

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

>KOG0226|consensus

Probab=98.81  E-value=6e-09  Score=86.73  Aligned_cols=75  Identities=23%  Similarity=0.407  Sum_probs=70.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +..+||.|.|..+++++-|...|.+|-.-...++++|+.||+++||+||.|.+..++..|++++||+-+..+.++
T Consensus       189 ~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpik  263 (290)
T KOG0226|consen  189 DDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIK  263 (290)
T ss_pred             ccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhH
Confidence            345699999999999999999999999889999999999999999999999999999999999999988887765

>KOG2193|consensus

Probab=98.80  E-value=1.1e-09  Score=97.00  Aligned_cols=148  Identities=24%  Similarity=0.318  Sum_probs=116.0

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCC-eeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhcc------Ccccceeccc
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGP-IISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQD------KGIHAQMARQ  132 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~-i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g------~~i~~~~~~~  132 (305)
                      .+||+||.+.++.++|..+|...-. ...-.++       -.||+||.+.+...|.+|++.++|      +.+.......
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~-------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceee-------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            4999999999999999999975411 1111222       246999999999999999998765      4445555556


Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      +....+++-|.|+|..+.++.|..+...||.++.|......  ...-..-|+|...+.+..||..|+|..+..  ..++|
T Consensus        76 kkqrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~--~etavvnvty~~~~~~~~ai~kl~g~Q~en--~~~k~  151 (584)
T KOG2193|consen   76 KKQRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTD--SETAVVNVTYSAQQQHRQAIHKLNGPQLEN--QHLKV  151 (584)
T ss_pred             HHHHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccc--hHHHHHHHHHHHHHHHHHHHHhhcchHhhh--hhhhc
Confidence            66677889999999999999999999999999998764332  122234578999999999999999999999  66999


Q ss_pred             EeccCC
Q psy4086         213 KFADSG  218 (305)
Q Consensus       213 ~~a~~~  218 (305)
                      .|-...
T Consensus       152 ~YiPde  157 (584)
T KOG2193|consen  152 GYIPDE  157 (584)
T ss_pred             ccCchh
Confidence            996553

>KOG4454|consensus

Probab=98.78  E-value=3.1e-09  Score=86.52  Aligned_cols=80  Identities=16%  Similarity=0.134  Sum_probs=72.7

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ..++|||+|+-..++|+.|.++|-.-|.|.+|.|..+++++.+ ||||.|+++....-|++.+||..+.+  ..|.|++-
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 MDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEE--DEEQRTLR   84 (267)
T ss_pred             hhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhcc--chhhcccc
Confidence            3578999999999999999999999999999999999988888 99999999999999999999999999  55777775


Q ss_pred             cCC
Q psy4086         216 DSG  218 (305)
Q Consensus       216 ~~~  218 (305)
                      ...
T Consensus        85 ~G~   87 (267)
T KOG4454|consen   85 CGN   87 (267)
T ss_pred             cCC
Confidence            543

>KOG0106|consensus

Probab=98.77  E-value=7.9e-09  Score=85.63  Aligned_cols=76  Identities=26%  Similarity=0.518  Sum_probs=67.9

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      ..+|||+||+.+.+.+|+.+|..||.+..+.+.       .+|+||+|.+..+|..||..||+..|.+..  +.|.++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk-------~gf~fv~fed~rda~Dav~~l~~~~l~~e~--~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK-------NGFGFVEFEDPRDADDAVHDLDGKELCGER--LVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee-------cccceeccCchhhhhcccchhcCceeccee--eeeecccc
Confidence            468999999999999999999999999999876       569999999999999999999999999964  99999886


Q ss_pred             CCcCC
Q psy4086         218 GLKKR  222 (305)
Q Consensus       218 ~~~~~  222 (305)
                      ....+
T Consensus        73 ~~~~~   77 (216)
T KOG0106|consen   73 KRRGR   77 (216)
T ss_pred             ccccc
Confidence            54433

>KOG4661|consensus

Probab=98.70  E-value=3.8e-08  Score=90.37  Aligned_cols=80  Identities=21%  Similarity=0.417  Sum_probs=72.5

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||.+|...+...+|+.+|++||.|+-.+|+++. +--.+.|+||++.+.++|.+||+.|+-+.|.|  +.|.|..+
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHG--rmISVEka  482 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHG--RMISVEKA  482 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcc--eeeeeeec
Confidence            4789999999999999999999999999999999986 44457899999999999999999999999999  77999988


Q ss_pred             cCC
Q psy4086         216 DSG  218 (305)
Q Consensus       216 ~~~  218 (305)
                      ++.
T Consensus       483 KNE  485 (940)
T KOG4661|consen  483 KNE  485 (940)
T ss_pred             ccC
Confidence            753

>KOG4209|consensus

Probab=98.70  E-value=5.4e-08  Score=82.62  Aligned_cols=84  Identities=17%  Similarity=0.370  Sum_probs=76.6

Q ss_pred             cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       132 ~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      ....+...+||+|+.+.+|.+++..+|+.||.|..+.|..|+ .+.+++|+||+|.+.+.++.|+. ||+..|.+  +.+
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~--~~i  172 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPG--PAI  172 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccc--ccc
Confidence            455667889999999999999999999999999999999999 67899999999999999999998 99999999  779


Q ss_pred             EEEeccCC
Q psy4086         211 LVKFADSG  218 (305)
Q Consensus       211 ~v~~a~~~  218 (305)
                      .|.+....
T Consensus       173 ~vt~~r~~  180 (231)
T KOG4209|consen  173 EVTLKRTN  180 (231)
T ss_pred             eeeeeeee
Confidence            99887764

>KOG1365|consensus

Probab=98.69  E-value=2.4e-07  Score=81.48  Aligned_cols=142  Identities=13%  Similarity=0.164  Sum_probs=100.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHH----hccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA----LQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~----l~g~~i~~~~~~  131 (305)
                      .+++.|-.++||+..++.+|..+|+..-...-...+-...-|+..|.+.|.|.|.|.-+.|++.    +.++.|.+-.+.
T Consensus        58 ~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~  137 (508)
T KOG1365|consen   58 DDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKAT  137 (508)
T ss_pred             CcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccC
Confidence            3455677899999999999999998553322222222233477789999999999999999876    223333332222


Q ss_pred             ------------------cccCCCCceEEecCCCCCCHHHHHHHHhhC----CCeEEEEEeeCCCCCcccEEEEEecCHH
Q psy4086         132 ------------------QQEQDPTNLYIANLPLNFKECDLESLLAKY----VTVVSTRILRDNNNTSKGVGFARLESKD  189 (305)
Q Consensus       132 ------------------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~----g~v~~v~i~~~~~g~~~g~afV~f~~~~  189 (305)
                                        ......--|-.++||++.++.++.++|..-    |..+.|.+++..+|+..|-|||.|..++
T Consensus       138 ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee  217 (508)
T KOG1365|consen  138 GEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEE  217 (508)
T ss_pred             chhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHH
Confidence                              001111235668999999999999999532    2355676777668999999999999999


Q ss_pred             HHHHHHHH
Q psy4086         190 KCDQMIQL  197 (305)
Q Consensus       190 ~A~~Ai~~  197 (305)
                      +|+.|+.+
T Consensus       218 ~aq~aL~k  225 (508)
T KOG1365|consen  218 DAQFALRK  225 (508)
T ss_pred             HHHHHHHH
Confidence            99999864

>KOG4209|consensus

Probab=98.63  E-value=3.7e-08  Score=83.57  Aligned_cols=77  Identities=17%  Similarity=0.206  Sum_probs=70.8

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .+.+.+.+||+|+.+.+|.+++...|+.||.|..+.|..|+.++.++||+||+|.+.+.++.++. |||..|..+.+.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~  173 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIE  173 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccce
Confidence            45566779999999999999999999999999999999999999999999999999999999999 999988887654

>KOG4307|consensus

Probab=98.61  E-value=1e-07  Score=89.44  Aligned_cols=156  Identities=11%  Similarity=-0.022  Sum_probs=117.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhc----cCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ----DKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~----g~~i~~~~~~  131 (305)
                      .+++.+-+.+.+++..+.|++++|... .|..+.|..+...+...|-++|+|....++.+|++.-+    .+.|+....-
T Consensus       309 ~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~~P~g  387 (944)
T KOG4307|consen  309 SDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQTGPPG  387 (944)
T ss_pred             chhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcceeecCCC
Confidence            456667788999999999999999744 35667777777666668999999999999999987511    1212111100


Q ss_pred             -----------------------------------------cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEE-EEE
Q psy4086         132 -----------------------------------------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVS-TRI  169 (305)
Q Consensus       132 -----------------------------------------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~-v~i  169 (305)
                                                               .......+|||..||..+++.++.++|...-.|++ |.|
T Consensus       388 ~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~l  467 (944)
T KOG4307|consen  388 NLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIEL  467 (944)
T ss_pred             ccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEe
Confidence                                                     11112367999999999999999999998777877 666


Q ss_pred             eeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         170 LRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       170 ~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      -+..+++.++.|||.|..++++..|+..-+...+..  +.|+|.-
T Consensus       468 t~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~--r~irv~s  510 (944)
T KOG4307|consen  468 TRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGH--RIIRVDS  510 (944)
T ss_pred             ccCCcccccchhhheeccccccchhhhcccccccCc--eEEEeec
Confidence            666688899999999999999999987666555655  6688765

>KOG0116|consensus

Probab=98.60  E-value=1.2e-07  Score=86.61  Aligned_cols=63  Identities=25%  Similarity=0.478  Sum_probs=53.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHH
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA  119 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~  119 (305)
                      ...+|||+|||+++++++|+++|+.||.|++..|....-.+....||||+|.+.+++..||++
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A  349 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA  349 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc
Confidence            344599999999999999999999999999988776543344458999999999999999984

>KOG4660|consensus

Probab=98.57  E-value=7.5e-08  Score=88.52  Aligned_cols=75  Identities=15%  Similarity=0.322  Sum_probs=65.0

Q ss_pred             ccccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       131 ~~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      .++.....+|+|-|||..+++++|+.+|+.||+|..|+.-..    .++..||+|.|..+|++|+++|++..|.+  +.|
T Consensus        69 ~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~--~~~  142 (549)
T KOG4660|consen   69 SEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN----KRGIVFVEFYDVRDAERALKALNRREIAG--KRI  142 (549)
T ss_pred             CcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc----cCceEEEEEeehHhHHHHHHHHHHHHhhh--hhh
Confidence            344556788999999999999999999999999999765544    47799999999999999999999999999  446


Q ss_pred             E
Q psy4086         211 L  211 (305)
Q Consensus       211 ~  211 (305)
                      +
T Consensus       143 k  143 (549)
T KOG4660|consen  143 K  143 (549)
T ss_pred             c
Confidence            5

>KOG1548|consensus

Probab=98.56  E-value=2.7e-07  Score=80.21  Aligned_cols=80  Identities=21%  Similarity=0.410  Sum_probs=73.3

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeE--------EEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCc
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVV--------STRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKE  208 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~--------~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~  208 (305)
                      ...|||.|||.++|.+++.++|++||.|.        .|++-++..|..+|=|+|.|--.++..-||..|++..|.|  +
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg--~  211 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRG--K  211 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccC--c
Confidence            45699999999999999999999999886        4889999999999999999999999999999999999999  6


Q ss_pred             cEEEEeccCC
Q psy4086         209 PLLVKFADSG  218 (305)
Q Consensus       209 ~l~v~~a~~~  218 (305)
                      .|+|..|+-.
T Consensus       212 ~~rVerAkfq  221 (382)
T KOG1548|consen  212 KLRVERAKFQ  221 (382)
T ss_pred             EEEEehhhhh
Confidence            6999988753

>KOG0151|consensus

Probab=98.50  E-value=1.8e-07  Score=88.15  Aligned_cols=80  Identities=16%  Similarity=0.336  Sum_probs=71.6

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCC----CCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN----NTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~----g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      ..++|||+||+..++++.|...|..||.|..++|++.++    .+.+.|+||.|-+..+|++|+..|+|..+..  ..++
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~--~e~K  250 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVME--YEMK  250 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeee--eeee
Confidence            347899999999999999999999999999999999873    3567899999999999999999999999998  5688


Q ss_pred             EEeccC
Q psy4086         212 VKFADS  217 (305)
Q Consensus       212 v~~a~~  217 (305)
                      +-|++.
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            888654

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

Probab=98.47  E-value=1.6e-06  Score=63.12  Aligned_cols=81  Identities=22%  Similarity=0.274  Sum_probs=68.6

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhC--CCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCC--CCccEEE
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKY--VTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPG--SKEPLLV  212 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~--g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~~~l~v  212 (305)
                      +||-|.|||...|.++|.+++...  |....+.++.|- ++.+.|||||.|.+.+.|.+-.+.++|..+..  +.+.+.|
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            578999999999999999998653  566777888886 67889999999999999999999999998863  3467889


Q ss_pred             EeccCC
Q psy4086         213 KFADSG  218 (305)
Q Consensus       213 ~~a~~~  218 (305)
                      .||+-.
T Consensus        82 ~yAriQ   87 (97)
T PF04059_consen   82 SYARIQ   87 (97)
T ss_pred             ehhHhh
Confidence            998753

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

>KOG4676|consensus

Probab=98.44  E-value=9.7e-08  Score=84.10  Aligned_cols=141  Identities=7%  Similarity=0.026  Sum_probs=105.4

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCC---CCccceEEEEecchhhHHHHHHHhccCcccceecc-----
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTT---NKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR-----  131 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~---g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~-----  131 (305)
                      .|-|.||.+.+|.++++.||...|+|.++.|+.+...   ......|||.|.|...+..|...-|-..|+.-.+.     
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~~   88 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYGD   88 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecCC
Confidence            5999999999999999999999999999999875432   23456899999999999988775443322211111     


Q ss_pred             ---------------------------------------------------------cccCCCCceEEecCCCCCCHHHH
Q psy4086         132 ---------------------------------------------------------QQEQDPTNLYIANLPLNFKECDL  154 (305)
Q Consensus       132 ---------------------------------------------------------~~~~~~~~l~V~nlp~~~te~~l  154 (305)
                                                                               ..+.-.++++|++|+..+...++
T Consensus        89 ~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~e~  168 (479)
T KOG4676|consen   89 EVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILPES  168 (479)
T ss_pred             CCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcchhh
Confidence                                                                     00011267999999999999999


Q ss_pred             HHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCC
Q psy4086         155 ESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLP  204 (305)
Q Consensus       155 ~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~  204 (305)
                      .++|+.+|+|....+...   ...-+|-|+|........|++ .+|..+.
T Consensus       169 ~e~f~r~Gev~ya~~ask---~~s~~c~~sf~~qts~~halr-~~gre~k  214 (479)
T KOG4676|consen  169 GESFERKGEVSYAHTASK---SRSSSCSHSFRKQTSSKHALR-SHGRERK  214 (479)
T ss_pred             hhhhhhcchhhhhhhhcc---CCCcchhhhHhhhhhHHHHHH-hcchhhh
Confidence            999999999988776544   334567799988888888876 4555554

>KOG0151|consensus

Probab=98.42  E-value=8.9e-07  Score=83.55  Aligned_cols=78  Identities=27%  Similarity=0.399  Sum_probs=67.2

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCC---CCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT---TNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~---~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      .+..+++|||+||++.++++.|...|..||+|..++|+.-+.   ..+.+-|+||-|-+..||++|++.|+|+.|....+
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~  249 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEM  249 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeee
Confidence            355678899999999999999999999999999999997652   34567799999999999999999999987765544


Q ss_pred             c
Q psy4086         131 R  131 (305)
Q Consensus       131 ~  131 (305)
                      +
T Consensus       250 K  250 (877)
T KOG0151|consen  250 K  250 (877)
T ss_pred             e
Confidence            4

>KOG4849|consensus

Probab=98.28  E-value=2.6e-05  Score=68.10  Aligned_cols=73  Identities=26%  Similarity=0.361  Sum_probs=64.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccC--CeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccccee
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYG--PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQM  129 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G--~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~  129 (305)
                      .+-.+|||||-|++|++||.+.+...|  .+.+++.+.++.+|.+||||+|...+.....+.++.|-.+.|+++.
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~  153 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQS  153 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCC
Confidence            344599999999999999999998777  5788899999999999999999999999999999988877777754

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.24  E-value=1e-05  Score=56.30  Aligned_cols=69  Identities=25%  Similarity=0.403  Sum_probs=47.7

Q ss_pred             CceEEecCCCCCCHH----HHHHHHhhCCC-eEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         138 TNLYIANLPLNFKEC----DLESLLAKYVT-VVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       138 ~~l~V~nlp~~~te~----~l~~~F~~~g~-v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ..|||.|||.+.+..    -|++++..||. |.+|.         .+.|+|.|.+.+.|.+|.+.|+|..+.|++  |.|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~---------~~tAilrF~~~~~A~RA~KRmegEdVfG~k--I~v   71 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS---------GGTAILRFPNQEFAERAQKRMEGEDVFGNK--ISV   71 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SSSS----EE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe---------CCEEEEEeCCHHHHHHHHHhhcccccccce--EEE
Confidence            358999999988765    56778888854 55542         457999999999999999999999999954  999


Q ss_pred             EeccC
Q psy4086         213 KFADS  217 (305)
Q Consensus       213 ~~a~~  217 (305)
                      +|...
T Consensus        72 ~~~~~   76 (90)
T PF11608_consen   72 SFSPK   76 (90)
T ss_dssp             ESS--
T ss_pred             EEcCC
Confidence            99754

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

>KOG1995|consensus

Probab=98.15  E-value=7.3e-06  Score=72.00  Aligned_cols=83  Identities=18%  Similarity=0.299  Sum_probs=73.3

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeE--------EEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCC
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVV--------STRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPG  205 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~--------~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  205 (305)
                      ....+|||-+|+..+++++|.++|.+++.|.        .|.|-+++ ++.+|+-|.|.|++...|+.||+-+++..+.+
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            3456899999999999999999999999875        35677777 88999999999999999999999999999999


Q ss_pred             CCccEEEEeccCCC
Q psy4086         206 SKEPLLVKFADSGL  219 (305)
Q Consensus       206 ~~~~l~v~~a~~~~  219 (305)
                        .+|+|.+|....
T Consensus       144 --n~ikvs~a~~r~  155 (351)
T KOG1995|consen  144 --NTIKVSLAERRT  155 (351)
T ss_pred             --CCchhhhhhhcc
Confidence              559999988755

>KOG1995|consensus

Probab=98.00  E-value=8.9e-06  Score=71.46  Aligned_cols=78  Identities=21%  Similarity=0.267  Sum_probs=68.9

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCee--------EEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPII--------STKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH  126 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~--------~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~  126 (305)
                      ....-+|||-+|+..+++++|.++|.+||.|.        .|+|.+|+.|+++||-|.|.|.+...|+.||.-++++.+.
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            33445699999999999999999999999885        3788899999999999999999999999999999999888


Q ss_pred             ceeccc
Q psy4086         127 AQMARQ  132 (305)
Q Consensus       127 ~~~~~~  132 (305)
                      ...++.
T Consensus       143 gn~ikv  148 (351)
T KOG1995|consen  143 GNTIKV  148 (351)
T ss_pred             CCCchh
Confidence            865553

>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=97.95  E-value=2.1e-05  Score=58.50  Aligned_cols=59  Identities=25%  Similarity=0.362  Sum_probs=39.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccC
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDK  123 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~  123 (305)
                      +.|.|.++...++.++|+++|+.||.|..|.+.+...      .|+|.|.+.+.|++|++.+...
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHHHhc
Confidence            5688999999999999999999999999999876553      6999999999999999986533

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

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.86  E-value=2.2e-05  Score=68.26  Aligned_cols=77  Identities=13%  Similarity=0.295  Sum_probs=60.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHH------HHHHhccCCeeEEEEeeCCCC-CCccceE--EEEecchhhHHHHHHHhccCcc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDL------INMCSQYGPIISTKAILDKTT-NKCRGYG--FVDFESGGYALAAVKALQDKGI  125 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L------~~~f~~~G~i~~~~i~~~~~~-g~~~G~a--fV~f~~~~~A~~a~~~l~g~~i  125 (305)
                      ...+.-+||-+|++.+..++.      .++|.+||+|.+|.|-+.-.+ ....+.+  ||+|.+.|+|.+||.+++|..+
T Consensus       111 VvQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~  190 (480)
T COG5175         111 VVQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLL  190 (480)
T ss_pred             eeecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccc
Confidence            334556999999999887773      569999999998887654311 1122333  9999999999999999999999


Q ss_pred             cceecc
Q psy4086         126 HAQMAR  131 (305)
Q Consensus       126 ~~~~~~  131 (305)
                      +++.++
T Consensus       191 DGr~lk  196 (480)
T COG5175         191 DGRVLK  196 (480)
T ss_pred             cCceEe
Confidence            988877

>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=97.84  E-value=5.1e-05  Score=56.46  Aligned_cols=59  Identities=12%  Similarity=0.240  Sum_probs=38.8

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCC
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGS  201 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~  201 (305)
                      +.|.|.++...++.++|++.|+.||.|..|.+...     ..-|+|+|.+.+.|++|++.+...
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G-----~~~g~VRf~~~~~A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG-----DTEGYVRFKTPEAAQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC-----CCEEEEEECCcchHHHHHHHHHhc
Confidence            45788889999999999999999999999888754     347999999999999999877644

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

>KOG0115|consensus

Probab=97.81  E-value=6.8e-05  Score=63.02  Aligned_cols=107  Identities=15%  Similarity=0.152  Sum_probs=85.9

Q ss_pred             hhHHHHHHHhccCcccceecccccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHH
Q psy4086         111 GYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK  190 (305)
Q Consensus       111 ~~A~~a~~~l~g~~i~~~~~~~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~  190 (305)
                      .-|+.|..+|++.....+.++........|||.||...+.-+.|++.|+.||.|....++.|..++..+-++|.|...-.
T Consensus         5 t~ae~ak~eLd~~~~~~~~lr~rfa~~a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~   84 (275)
T KOG0115|consen    5 TLAEIAKRELDGRFPKGRSLRVRFAMHAELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPN   84 (275)
T ss_pred             cHHHHHHHhcCCCCCCCCceEEEeeccceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchh
Confidence            45778888899988888887766666688999999999999999999999999999988888888888899999999999


Q ss_pred             HHHHHHHhCCCCCCC--CCccEEEEeccC
Q psy4086         191 CDQMIQLFNGSTLPG--SKEPLLVKFADS  217 (305)
Q Consensus       191 A~~Ai~~l~g~~~~g--~~~~l~v~~a~~  217 (305)
                      |.+|+..+.-.-+.+  ..++.-|.-..-
T Consensus        85 a~~a~rr~~~~g~~~~~~~~p~~VeP~eq  113 (275)
T KOG0115|consen   85 ARKAARRCREGGFGGTTGGRPVGVEPMEQ  113 (275)
T ss_pred             HHHHHHHhccCccccCCCCCccCCChhhc
Confidence            999998874332222  224555554443

>KOG2314|consensus

Probab=97.81  E-value=4.4e-05  Score=70.67  Aligned_cols=78  Identities=17%  Similarity=0.235  Sum_probs=64.9

Q ss_pred             CCceEEecCCCCCC------HHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         137 PTNLYIANLPLNFK------ECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       137 ~~~l~V~nlp~~~t------e~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      ...|+|-|+|.--.      ...|..+|+++|+|....++.+..|..+||.|++|.+..+|+.|++.|||+.|+.. +.+
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldkn-Htf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKN-HTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceeccc-ceE
Confidence            45677888876322      24578899999999999999998777999999999999999999999999999876 567


Q ss_pred             EEEec
Q psy4086         211 LVKFA  215 (305)
Q Consensus       211 ~v~~a  215 (305)
                      .|..-
T Consensus       137 ~v~~f  141 (698)
T KOG2314|consen  137 FVRLF  141 (698)
T ss_pred             Eeehh
Confidence            77653

>KOG0128|consensus

Probab=97.80  E-value=2.1e-06  Score=82.76  Aligned_cols=146  Identities=10%  Similarity=0.080  Sum_probs=107.4

Q ss_pred             CCCeEEEcCCCCCCcHH-HHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc---
Q psy4086          57 SKTNLYIRGLTQDTTDK-DLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ---  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~-~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~---  132 (305)
                      ..+...+.++.+..... ..+..|+.+|.|+.+++......-...-+.++.+....+++.|.. ..+..+.++.+..   
T Consensus       570 ~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~-pa~~~~a~~~~av~~a  648 (881)
T KOG0128|consen  570 ERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATV-PAGGALANRSAAVGLA  648 (881)
T ss_pred             hhhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhccc-ccccccCCccccCCCC
Confidence            34557788888887666 567889999999999987633222222388899999999988876 3333333332220   


Q ss_pred             --------------ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHH
Q psy4086         133 --------------QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQL  197 (305)
Q Consensus       133 --------------~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~  197 (305)
                                    ...+..++||.||+..+.+++|...|..++.+..+++.... .++.+|+|+|.|...+++.+||..
T Consensus       649 d~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f  728 (881)
T KOG0128|consen  649 DAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAF  728 (881)
T ss_pred             CchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhh
Confidence                          00123579999999999999999999999998888777444 678999999999999999999975


Q ss_pred             hCCCCC
Q psy4086         198 FNGSTL  203 (305)
Q Consensus       198 l~g~~~  203 (305)
                      .+.+.+
T Consensus       729 ~d~~~~  734 (881)
T KOG0128|consen  729 RDSCFF  734 (881)
T ss_pred             hhhhhh
Confidence            544433

>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=97.79  E-value=0.00013  Score=50.82  Aligned_cols=62  Identities=16%  Similarity=0.359  Sum_probs=41.7

Q ss_pred             CeEEEcCCCCCCcHHHH----HHHHhccC-CeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          59 TNLYIRGLTQDTTDKDL----INMCSQYG-PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L----~~~f~~~G-~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      +.|+|.|||.+.+...|    +.|+..|| +|.+|.          .+.|+|.|.+.+.|++|.+.|+|..+.+..+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI   69 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKI   69 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceE
Confidence            46999999999987765    55667887 444431          2479999999999999999999888776543

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

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

Probab=97.77  E-value=6.2e-05  Score=48.57  Aligned_cols=52  Identities=17%  Similarity=0.280  Sum_probs=41.7

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHH
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV  117 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~  117 (305)
                      ++|-|.+.+.+..+.-|+ .|..||+|.++.+-...      -+.+|+|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~vl~-~F~~fGeI~~~~~~~~~------~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEEVLE-HFASFGEIVDIYVPEST------NWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHHHHH-HHHhcCCEEEEEcCCCC------cEEEEEECCHHHHHhhC
Confidence            568899999777655554 78899999998876322      28999999999999985

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.56  E-value=0.00021  Score=62.32  Aligned_cols=80  Identities=14%  Similarity=0.302  Sum_probs=62.6

Q ss_pred             CCceEEecCCCCCCHHH----H--HHHHhhCCCeEEEEEeeCC-CC-CcccE--EEEEecCHHHHHHHHHHhCCCCCCCC
Q psy4086         137 PTNLYIANLPLNFKECD----L--ESLLAKYVTVVSTRILRDN-NN-TSKGV--GFARLESKDKCDQMIQLFNGSTLPGS  206 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~----l--~~~F~~~g~v~~v~i~~~~-~g-~~~g~--afV~f~~~~~A~~Ai~~l~g~~~~g~  206 (305)
                      ..-+||-+|+..+..++    |  .++|.+||.|..+.|-+.. .. .-.+.  .+|+|.+.++|.+||.+.+|..++| 
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG-  192 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG-  192 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC-
Confidence            45689999988876554    2  6789999999998877654 11 11122  3999999999999999999999999 


Q ss_pred             CccEEEEeccCC
Q psy4086         207 KEPLLVKFADSG  218 (305)
Q Consensus       207 ~~~l~v~~a~~~  218 (305)
                       |.|+..|...+
T Consensus       193 -r~lkatYGTTK  203 (480)
T COG5175         193 -RVLKATYGTTK  203 (480)
T ss_pred             -ceEeeecCchH
Confidence             77999986653

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

Probab=97.54  E-value=0.00026  Score=45.68  Aligned_cols=52  Identities=13%  Similarity=0.271  Sum_probs=41.0

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHH
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI  195 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai  195 (305)
                      +.|-|.+.+.+..+. +..+|..||+|+.+.+.     ....+.+|+|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~-----~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVP-----ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcC-----CCCcEEEEEECCHHHHHhhC
Confidence            456777777766544 55589999999998876     23558999999999999985

>KOG0129|consensus

Probab=97.50  E-value=0.0003  Score=64.79  Aligned_cols=63  Identities=19%  Similarity=0.327  Sum_probs=58.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHh-ccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHH
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCS-QYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA  119 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~-~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~  119 (305)
                      .++|||||+||.-++.++|..+|+ .||.|..+-|=+|++-+-++|-|=|.|.+...-.+||..
T Consensus       369 prrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  369 PRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             ccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            456799999999999999999999 899999999999977788999999999999999999985

>KOG1855|consensus

Probab=97.49  E-value=0.00015  Score=65.19  Aligned_cols=67  Identities=18%  Similarity=0.280  Sum_probs=56.9

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeC---C-C--CC--------cccEEEEEecCHHHHHHHHHHhCC
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD---N-N--NT--------SKGVGFARLESKDKCDQMIQLFNG  200 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~---~-~--g~--------~~g~afV~f~~~~~A~~Ai~~l~g  200 (305)
                      ...++|.+-|||.+-.-+.|.++|..+|.|..|+|+..   . +  +.        .+-+|+|+|+..+.|.+|.+.|+.
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            45688999999999888999999999999999999887   3 2  21        145799999999999999998864


Q ss_pred             C
Q psy4086         201 S  201 (305)
Q Consensus       201 ~  201 (305)
                      .
T Consensus       309 e  309 (484)
T KOG1855|consen  309 E  309 (484)
T ss_pred             h
Confidence            4

>KOG2314|consensus

Probab=97.49  E-value=0.00013  Score=67.70  Aligned_cols=68  Identities=25%  Similarity=0.336  Sum_probs=56.8

Q ss_pred             CCeEEEcCCCCCCcHH-------HHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          58 KTNLYIRGLTQDTTDK-------DLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~-------~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      ...|+|-|+|. +-.+       -|..+|+++|+|....+..+..+| .+||.|++|.+..+|+.|++.|||+.++-
T Consensus        58 D~vVvv~g~Pv-V~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldk  132 (698)
T KOG2314|consen   58 DSVVVVDGAPV-VGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDK  132 (698)
T ss_pred             ceEEEECCCcc-cChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecc
Confidence            34599999985 3332       246689999999999998888655 99999999999999999999999998764

>KOG4210|consensus

Probab=97.42  E-value=9.5e-05  Score=65.03  Aligned_cols=69  Identities=23%  Similarity=0.394  Sum_probs=60.7

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        61 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      .+|++|+.++++++|+..|..+|.|..+++..++.++.++|||+|.|.+...+..++.. +...+....+
T Consensus       188 ~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~  256 (285)
T KOG4210|consen  188 FFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPL  256 (285)
T ss_pred             eeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCccc
Confidence            44999999999999999999999999999999999999999999999999999988885 5555544433

>KOG2202|consensus

Probab=97.35  E-value=0.00013  Score=61.53  Aligned_cols=64  Identities=14%  Similarity=0.262  Sum_probs=52.2

Q ss_pred             HHHHHHHh-hCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         152 CDLESLLA-KYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       152 ~~l~~~F~-~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      +++...|+ +||+|++++|..+-.-.-+|-++|.|...++|++|++.||+.++.|  ++|...+..-
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G--~pi~ae~~pv  147 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNG--RPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccC--CcceeeecCc
Confidence            34555555 9999999987766533457789999999999999999999999999  7898888553

>KOG1996|consensus

Probab=97.32  E-value=0.00067  Score=58.18  Aligned_cols=65  Identities=17%  Similarity=0.133  Sum_probs=53.5

Q ss_pred             HHHHHHHHhhCCCeEEEEEeeCCCC--CcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         151 ECDLESLLAKYVTVVSTRILRDNNN--TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       151 e~~l~~~F~~~g~v~~v~i~~~~~g--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      ++++++.+++||.|..|.|+...+.  ...---||+|+..++|.+|+-.|||..|.|  +.+...|.+-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGG--r~v~A~Fyn~  366 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGG--RVVSACFYNL  366 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecc--eeeeheeccH
Confidence            4678999999999999998887621  112236999999999999999999999999  6688888664

>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=97.32  E-value=0.00076  Score=49.50  Aligned_cols=78  Identities=17%  Similarity=0.173  Sum_probs=52.6

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEE-EeeC-------CCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCC
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTR-ILRD-------NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSK  207 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~-i~~~-------~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~  207 (305)
                      ..+.|.|-+.|.. ....+.+.|++||.|++.. +.++       ..-....+..|+|.+..+|++||. -||..|.|. 
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~-   81 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGS-   81 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTC-
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCc-
Confidence            3455778888887 5567788999999998764 1111       101345699999999999999997 599999885 


Q ss_pred             ccEEEEecc
Q psy4086         208 EPLLVKFAD  216 (305)
Q Consensus       208 ~~l~v~~a~  216 (305)
                      ..+-|.+.+
T Consensus        82 ~mvGV~~~~   90 (100)
T PF05172_consen   82 LMVGVKPCD   90 (100)
T ss_dssp             EEEEEEE-H
T ss_pred             EEEEEEEcH
Confidence            456688764

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG3152|consensus

Probab=97.32  E-value=0.00021  Score=60.07  Aligned_cols=75  Identities=17%  Similarity=0.193  Sum_probs=63.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCC--------CCccce----EEEEecchhhHHHHHHHhccCc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTT--------NKCRGY----GFVDFESGGYALAAVKALQDKG  124 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~--------g~~~G~----afV~f~~~~~A~~a~~~l~g~~  124 (305)
                      ..-.||+++||+.+.-.-|+++|++||.|-.|.+.....+        |.++.+    |.|+|.+...|.++...||+..
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            4457999999999999999999999999999998877655        333333    5599999999999999999999


Q ss_pred             ccceecc
Q psy4086         125 IHAQMAR  131 (305)
Q Consensus       125 i~~~~~~  131 (305)
                      |.++...
T Consensus       153 Iggkk~S  159 (278)
T KOG3152|consen  153 IGGKKKS  159 (278)
T ss_pred             cCCCCCC
Confidence            9987654

>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=97.12  E-value=0.0015  Score=47.92  Aligned_cols=71  Identities=11%  Similarity=0.163  Sum_probs=45.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEE-EeeCCC------CCCccceEEEEecchhhHHHHHHHhccCcccce
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTK-AILDKT------TNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ  128 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~-i~~~~~------~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~  128 (305)
                      .+.+.|.|-+.|+. ....|.+.|++||.|.+.. +.++..      .-.....-.|+|.++.+|.+||. -||..+.+.
T Consensus         4 ~~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~   81 (100)
T PF05172_consen    4 DSETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGS   81 (100)
T ss_dssp             GGCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTC
T ss_pred             cCCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCc
Confidence            34567999999988 5566677899999997765 111000      01123388999999999999999 677766543

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>KOG3152|consensus

Probab=97.08  E-value=0.00055  Score=57.67  Aligned_cols=72  Identities=19%  Similarity=0.383  Sum_probs=60.4

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-C--------CCccc----EEEEEecCHHHHHHHHHHhCCCC
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-N--------NTSKG----VGFARLESKDKCDQMIQLFNGST  202 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~--------g~~~g----~afV~f~~~~~A~~Ai~~l~g~~  202 (305)
                      ..-.||+++||+.+...-|+++|+.||.|-.|.+.... .        |..+.    -+.|+|.+...|.++.+.||+..
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            45679999999999999999999999999998877664 2        22221    26799999999999999999999


Q ss_pred             CCCCC
Q psy4086         203 LPGSK  207 (305)
Q Consensus       203 ~~g~~  207 (305)
                      |.|.+
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99865

>KOG0115|consensus

Probab=97.07  E-value=0.0017  Score=54.87  Aligned_cols=62  Identities=26%  Similarity=0.365  Sum_probs=56.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ  121 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~  121 (305)
                      ..|||.||..-+..|.|..-|+.||+|+...++-|. .++..+-++|+|...-.|.+|++.+.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhc
Confidence            569999999999999999999999999988887776 47888899999999999999998863

>KOG1855|consensus

Probab=97.05  E-value=0.00097  Score=60.10  Aligned_cols=71  Identities=18%  Similarity=0.225  Sum_probs=59.3

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeC---CCCCC----------ccceEEEEecchhhHHHHH
Q psy4086          51 TGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILD---KTTNK----------CRGYGFVDFESGGYALAAV  117 (305)
Q Consensus        51 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~---~~~g~----------~~G~afV~f~~~~~A~~a~  117 (305)
                      ...++...++|.+-|||.+-.-+.|.++|..+|.|..|+|++-   +.+.+          .+-+|+|+|...+.|.+|.
T Consensus       224 ~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~  303 (484)
T KOG1855|consen  224 FDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAR  303 (484)
T ss_pred             ccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHH
Confidence            3344567889999999999888999999999999999999876   33221          3568999999999999999


Q ss_pred             HHhc
Q psy4086         118 KALQ  121 (305)
Q Consensus       118 ~~l~  121 (305)
                      +.|+
T Consensus       304 e~~~  307 (484)
T KOG1855|consen  304 ELLN  307 (484)
T ss_pred             Hhhc
Confidence            9875

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

Probab=96.98  E-value=0.0053  Score=42.90  Aligned_cols=54  Identities=19%  Similarity=0.309  Sum_probs=41.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ  121 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~  121 (305)
                      ...+|+ +|.+....||.++|+.||.|. |..+.|-       .|||...+.+.|..++..++
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            435555 999999999999999999975 6666554       69999999999999998875

; 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.

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

Probab=96.95  E-value=0.0054  Score=40.63  Aligned_cols=54  Identities=28%  Similarity=0.308  Sum_probs=45.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcc----CCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHh
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQY----GPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL  120 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~----G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l  120 (305)
                      ..+|+|.+++ +++.++|+.+|..|    + ...|..+-|.       .|-|.|.+.+.|.+|+..|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~-~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEG-PFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCC-CceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            3459999997 69999999999999    5 4578888776       5899999999999999764

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

Probab=96.90  E-value=0.0069  Score=40.12  Aligned_cols=56  Identities=9%  Similarity=0.220  Sum_probs=45.8

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhC---CCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHh
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKY---VTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF  198 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~---g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l  198 (305)
                      .+.+|+|.++. +++.++|+.+|..|   .....|.++.|.      -|-|.|.+.+.|.+|+.+|
T Consensus         4 rpeavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    4 RPEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eeceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC------cEEEEECCHHHHHHHHHcC
Confidence            45689999985 58889999999988   236688888774      4789999999999999765

>KOG2202|consensus

Probab=96.79  E-value=0.00053  Score=57.88  Aligned_cols=50  Identities=22%  Similarity=0.258  Sum_probs=43.4

Q ss_pred             ccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          81 QYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        81 ~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +||+|++++|..+.. -.-+|-++|.|..+++|++|++.||+..+.++.+.
T Consensus        92 kygEiee~~Vc~Nl~-~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~  141 (260)
T KOG2202|consen   92 KYGEIEELNVCDNLG-DHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIH  141 (260)
T ss_pred             Hhhhhhhhhhhcccc-hhhhhhhhhhcccHHHHHHHHHHHcCccccCCcce
Confidence            899999998776652 35678999999999999999999999999988763

>KOG2416|consensus

Probab=96.62  E-value=0.0024  Score=59.90  Aligned_cols=81  Identities=19%  Similarity=0.192  Sum_probs=64.0

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHh-hCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCC-CCccEEEE
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLA-KYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPG-SKEPLLVK  213 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~-~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-~~~~l~v~  213 (305)
                      ..+.|||.||-.-+|.-+|++++. .+|.|++. ++ |   +-+..|||.|.+.++|.+.+.+|||..+.. +.+.|.+.
T Consensus       443 ~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-D---kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~ad  517 (718)
T KOG2416|consen  443 PSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-D---KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIAD  517 (718)
T ss_pred             ccceEeeecccccchHHHHHHHHhhccCchHHH-HH-H---HhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEee
Confidence            356799999999999999999998 56667666 22 2   335579999999999999999999987643 33679999


Q ss_pred             eccCCCcC
Q psy4086         214 FADSGLKK  221 (305)
Q Consensus       214 ~a~~~~~~  221 (305)
                      |+....-.
T Consensus       518 f~~~deld  525 (718)
T KOG2416|consen  518 FVRADELD  525 (718)
T ss_pred             ecchhHHH
Confidence            98765443

>KOG2591|consensus

Probab=96.55  E-value=0.055  Score=50.71  Aligned_cols=73  Identities=10%  Similarity=0.185  Sum_probs=53.6

Q ss_pred             ccCcccceecccccCCC-CceEEecCCCCCCHHHHHHHHh--hCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHH
Q psy4086         121 QDKGIHAQMARQQEQDP-TNLYIANLPLNFKECDLESLLA--KYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL  197 (305)
Q Consensus       121 ~g~~i~~~~~~~~~~~~-~~l~V~nlp~~~te~~l~~~F~--~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~  197 (305)
                      -+..++.+..+.+.... |-+.++.||..+-+|+++.+|.  .|-.+++|.+-.+.     ++ ||+|++..+|+.|...
T Consensus       158 p~VqvDekgekVrp~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-----nW-yITfesd~DAQqAyky  231 (684)
T KOG2591|consen  158 PNVQVDEKGEKVRPNHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-----NW-YITFESDTDAQQAYKY  231 (684)
T ss_pred             CCceeccCccccccCcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-----ce-EEEeecchhHHHHHHH
Confidence            34444444444443334 4467799999999999999995  57889999887653     23 9999999999999876


Q ss_pred             hC
Q psy4086         198 FN  199 (305)
Q Consensus       198 l~  199 (305)
                      |.
T Consensus       232 lr  233 (684)
T KOG2591|consen  232 LR  233 (684)
T ss_pred             HH
Confidence            54

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.53  E-value=0.0072  Score=47.16  Aligned_cols=55  Identities=18%  Similarity=0.343  Sum_probs=44.8

Q ss_pred             HHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         153 DLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       153 ~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      +|.+.|..||++.-+++..+       .-.|+|.+-+.|.+|+. |+|.++.|  +.|+|+...+
T Consensus        52 ~ll~~~~~~GevvLvRfv~~-------~mwVTF~dg~sALaals-~dg~~v~g--~~l~i~LKtp  106 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD-------TMWVTFRDGQSALAALS-LDGIQVNG--RTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT-------CEEEEESSCHHHHHHHH-GCCSEETT--EEEEEEE---
T ss_pred             HHHHHHHhCCceEEEEEeCC-------eEEEEECccHHHHHHHc-cCCcEECC--EEEEEEeCCc
Confidence            67888999999998888754       47999999999999996 89999999  7799988665

; PDB: 1UFW_A 2DNR_A.

>KOG2193|consensus

Probab=96.47  E-value=0.0026  Score=57.35  Aligned_cols=77  Identities=23%  Similarity=0.346  Sum_probs=59.1

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCC-CCCCCCccEEEEecc
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGS-TLPGSKEPLLVKFAD  216 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~~~l~v~~a~  216 (305)
                      ++||++||...++..+|+.+|...-.-.+-.++     ...||+||.+.+...|.+|++.|+|+ ++.|  +++.|...-
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl-----~k~gyafvd~pdq~wa~kaie~~sgk~elqG--kr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFL-----VKSGYAFVDCPDQQWANKAIETLSGKVELQG--KRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCccee-----eecceeeccCCchhhhhhhHHhhchhhhhcC--ceeeccchh
Confidence            479999999999999999999654111111122     23579999999999999999999987 5777  668888877


Q ss_pred             CCCcC
Q psy4086         217 SGLKK  221 (305)
Q Consensus       217 ~~~~~  221 (305)
                      .+..+
T Consensus        75 ~kkqr   79 (584)
T KOG2193|consen   75 PKKQR   79 (584)
T ss_pred             hHHHH
Confidence            76554

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=95.98  E-value=0.087  Score=39.42  Aligned_cols=65  Identities=15%  Similarity=0.082  Sum_probs=48.5

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccC-CeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          61 LYIRGLTQDTTDKDLINMCSQYG-PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        61 l~V~~Lp~~~t~~~L~~~f~~~G-~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      +.+...|..++.++|..+.+.+- .|..++|++|..  .++=-+.++|.+.++|+...+.+||+.+..
T Consensus        16 ~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   16 CCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             EEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            44444555566677776666554 478899998753  355568899999999999999999998753

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=95.73  E-value=0.11  Score=38.89  Aligned_cols=65  Identities=18%  Similarity=0.267  Sum_probs=49.3

Q ss_pred             eEEecCCCCCCHHHHHHHHhhCCC-eEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCC
Q psy4086         140 LYIANLPLNFKECDLESLLAKYVT-VVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPG  205 (305)
Q Consensus       140 l~V~nlp~~~te~~l~~~F~~~g~-v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  205 (305)
                      +.+...|+.++.++|..+.+.+-. |..++|++|.. .++-.++++|.+.++|.+-.+.+||+.++-
T Consensus        16 ~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~-pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   16 CCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT-PNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             EEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC-CceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            444555666666777766666543 77889988753 367789999999999999999999998753

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0112|consensus

Probab=95.62  E-value=0.018  Score=56.74  Aligned_cols=67  Identities=21%  Similarity=0.257  Sum_probs=57.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH  126 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~  126 (305)
                      .....+.+||++|..|+....|...|..||.|..|.+-...      -||+|.|.+...++.|++.|-|..|.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq------~yayi~yes~~~aq~a~~~~rgap~G  517 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQ------PYAYIQYESPPAAQAATHDMRGAPLG  517 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCC------cceeeecccCccchhhHHHHhcCcCC
Confidence            34456789999999999999999999999999987765433      39999999999999999998876654

>KOG2068|consensus

Probab=95.62  E-value=0.015  Score=51.31  Aligned_cols=76  Identities=17%  Similarity=0.235  Sum_probs=58.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHH---HHHHhccCCeeEEEEeeCCC--CCC-ccceEEEEecchhhHHHHHHHhccCccccee
Q psy4086          56 LSKTNLYIRGLTQDTTDKDL---INMCSQYGPIISTKAILDKT--TNK-CRGYGFVDFESGGYALAAVKALQDKGIHAQM  129 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L---~~~f~~~G~i~~~~i~~~~~--~g~-~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~  129 (305)
                      +.+.-+||-+|+..+..+++   .+.|.+||.|..|.+.++..  .+. .-.-++|+|...++|..||...+|...+++.
T Consensus        75 Vqknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~  154 (327)
T KOG2068|consen   75 VQKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRA  154 (327)
T ss_pred             hhhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhh
Confidence            44556899999988766655   34899999999999888762  111 1123899999999999999999988888776


Q ss_pred             cc
Q psy4086         130 AR  131 (305)
Q Consensus       130 ~~  131 (305)
                      ++
T Consensus       155 lk  156 (327)
T KOG2068|consen  155 LK  156 (327)
T ss_pred             hH
Confidence            44

>KOG1996|consensus

Probab=95.62  E-value=0.033  Score=48.11  Aligned_cols=60  Identities=18%  Similarity=0.223  Sum_probs=48.0

Q ss_pred             HHHHHHHHhccCCeeEEEEeeCCCCCCc-cceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          72 DKDLINMCSQYGPIISTKAILDKTTNKC-RGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        72 ~~~L~~~f~~~G~i~~~~i~~~~~~g~~-~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ++++++.+++||.|..|.|..++.--.. .---||+|...++|.+|+-.|||+-+.++..+
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~  360 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVS  360 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeee
Confidence            3567788899999999999887632211 12379999999999999999999999988764

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=95.55  E-value=0.014  Score=47.69  Aligned_cols=72  Identities=13%  Similarity=0.111  Sum_probs=45.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhc-cCCe---eEEEEeeCCC-CCC-ccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQ-YGPI---ISTKAILDKT-TNK-CRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~-~G~i---~~~~i~~~~~-~g~-~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      ...++|.|++||+++||+++.+.++. ++..   ..+.-..... ... .-.-|||.|.+.+++......++|+.+..
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D   82 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVD   82 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEEC
Confidence            34568999999999999999987776 6654   2232112221 111 22358999999999999999999976543

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=95.16  E-value=0.06  Score=49.52  Aligned_cols=71  Identities=10%  Similarity=0.203  Sum_probs=55.4

Q ss_pred             ceEEecCCCCC-CHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         139 NLYIANLPLNF-KECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       139 ~l~V~nlp~~~-te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      .|-+.-.+..+ +-++|..+|.+||+|..|.|-..     .--|.|+|.+..+|-+|.. .++..|++  +.|+|.|-++
T Consensus       374 ~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~-----~~~a~vTF~t~aeag~a~~-s~~avlnn--r~iKl~whnp  445 (526)
T KOG2135|consen  374 PLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS-----SLHAVVTFKTRAEAGEAYA-SHGAVLNN--RFIKLFWHNP  445 (526)
T ss_pred             hhhhhccCCCCchHhhhhhhhhhcCccccccccCc-----hhhheeeeeccccccchhc-cccceecC--ceeEEEEecC
Confidence            34444445554 45789999999999999987644     3368999999999977764 68899999  7799999776

>KOG4574|consensus

Probab=95.00  E-value=0.02  Score=56.10  Aligned_cols=77  Identities=21%  Similarity=0.288  Sum_probs=65.8

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCC
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSG  218 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~  218 (305)
                      +.++.|.+..++...|..+|+.||.|.+++.+++     -..|.|+|.+.+.|..|+++|+|+++-...-+.+|.||+.-
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~-----~N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRD-----LNMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccc-----ccchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            4566777778888999999999999999998876     44799999999999999999999988655578999999875


Q ss_pred             Cc
Q psy4086         219 LK  220 (305)
Q Consensus       219 ~~  220 (305)
                      .-
T Consensus       375 ~~  376 (1007)
T KOG4574|consen  375 PM  376 (1007)
T ss_pred             cc
Confidence            43

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=95.00  E-value=1.2  Score=38.76  Aligned_cols=149  Identities=13%  Similarity=0.151  Sum_probs=95.6

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCC-------CCCccceEEEEecchhhHHHHHHH----
Q psy4086          51 TGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT-------TNKCRGYGFVDFESGGYALAAVKA----  119 (305)
Q Consensus        51 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~-------~g~~~G~afV~f~~~~~A~~a~~~----  119 (305)
                      .+.|.-..|.|...|+..+++--++...|-+||+|+.|.++.+..       .-.......+.|-+.+.+......    
T Consensus         8 kGdD~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQr   87 (309)
T PF10567_consen    8 KGDDEYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQR   87 (309)
T ss_pred             CCCccceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHH
Confidence            455666778899999999999999999999999999999998761       112335688999998887665432    


Q ss_pred             -------hccCcccceecc----------------------------cccCCCCceEEecCCCCCCHHHHHHHH---hhC
Q psy4086         120 -------LQDKGIHAQMAR----------------------------QQEQDPTNLYIANLPLNFKECDLESLL---AKY  161 (305)
Q Consensus       120 -------l~g~~i~~~~~~----------------------------~~~~~~~~l~V~nlp~~~te~~l~~~F---~~~  161 (305)
                             |+...+...+..                            ......+.|.|.--....+++-+.+.+   ..-
T Consensus        88 LsEfK~~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~IeF~~~~~~~dl~~~kL~fL~~~  167 (309)
T PF10567_consen   88 LSEFKTKLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIEFKDPVDKDDLIEKKLPFLKNS  167 (309)
T ss_pred             HHHHHHhcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEEecCccchhHHHHHhhhhhccC
Confidence                   233333222221                            111223556654332222333333332   111


Q ss_pred             C----CeEEEEEeeCC---CCCcccEEEEEecCHHHHHHHHHHhC
Q psy4086         162 V----TVVSTRILRDN---NNTSKGVGFARLESKDKCDQMIQLFN  199 (305)
Q Consensus       162 g----~v~~v~i~~~~---~g~~~g~afV~f~~~~~A~~Ai~~l~  199 (305)
                      +    .+++|.|+...   ..-++.||.++|-+...|.+.++-|.
T Consensus       168 ~n~RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk  212 (309)
T PF10567_consen  168 NNKRYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLK  212 (309)
T ss_pred             CCceEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHH
Confidence            2    26777777654   34567899999999999999887665

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>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=94.77  E-value=0.034  Score=45.46  Aligned_cols=82  Identities=16%  Similarity=0.204  Sum_probs=51.4

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhh-CCCe---EEEEEeeCC--CC-CcccEEEEEecCHHHHHHHHHHhCCCCCCCC--
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAK-YVTV---VSTRILRDN--NN-TSKGVGFARLESKDKCDQMIQLFNGSTLPGS--  206 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~-~g~v---~~v~i~~~~--~g-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~--  206 (305)
                      ...+|.|++||+++||+++.+.++. ++.-   ..+.-....  .. ....-|+|.|.+.+++..-+..++|+.|.+.  
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4568999999999999999886665 4443   344322222  11 1223589999999999999999999876432  


Q ss_pred             -CccEEEEeccC
Q psy4086         207 -KEPLLVKFADS  217 (305)
Q Consensus       207 -~~~l~v~~a~~  217 (305)
                       ..+..|.+|--
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence             24567888765

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.

>KOG4676|consensus

Probab=94.76  E-value=0.035  Score=49.79  Aligned_cols=77  Identities=9%  Similarity=0.220  Sum_probs=58.9

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCC----CCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE-
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN----NTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV-  212 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~----g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v-  212 (305)
                      ..|-|.||..++|.++++.+|...|.|.++.|....+    ......|||.|.|...+..|-. |.++.|-+  +.|.| 
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvd--raliv~   84 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVD--RALIVR   84 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeee--eeEEEE
Confidence            4688999999999999999999999999999887442    2334589999999999988876 55565555  33444 


Q ss_pred             EeccC
Q psy4086         213 KFADS  217 (305)
Q Consensus       213 ~~a~~  217 (305)
                      -|.+.
T Consensus        85 p~~~~   89 (479)
T KOG4676|consen   85 PYGDE   89 (479)
T ss_pred             ecCCC
Confidence            44443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.67  E-value=0.22  Score=38.64  Aligned_cols=75  Identities=12%  Similarity=0.208  Sum_probs=55.8

Q ss_pred             ccCCCCceEEecCCCCCC-HHH---HHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCc
Q psy4086         133 QEQDPTNLYIANLPLNFK-ECD---LESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKE  208 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~t-e~~---l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~  208 (305)
                      .+..-.+|.|.=|..++. .+|   +...++.||.|.+|.+.      .+.-|.|.|.|..+|-+|+.+++. ...|  .
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c------GrqsavVvF~d~~SAC~Av~Af~s-~~pg--t  152 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC------GRQSAVVVFKDITSACKAVSAFQS-RAPG--T  152 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec------CCceEEEEehhhHHHHHHHHhhcC-CCCC--c
Confidence            445567888887766653 344   44556889999999886      345799999999999999999875 6667  4


Q ss_pred             cEEEEecc
Q psy4086         209 PLLVKFAD  216 (305)
Q Consensus       209 ~l~v~~a~  216 (305)
                      .+...|..
T Consensus       153 m~qCsWqq  160 (166)
T PF15023_consen  153 MFQCSWQQ  160 (166)
T ss_pred             eEEeeccc
Confidence            47777744

>KOG2591|consensus

Probab=94.54  E-value=0.11  Score=48.71  Aligned_cols=57  Identities=19%  Similarity=0.217  Sum_probs=49.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHh--ccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHh
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCS--QYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL  120 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~--~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l  120 (305)
                      ++|.|.|+.||.++-.|+++.||+  .|-++.+|..-.+..       =||+|+++.||+.|.+.|
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-------WyITfesd~DAQqAykyl  232 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-------WYITFESDTDAQQAYKYL  232 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-------eEEEeecchhHHHHHHHH
Confidence            678899999999999999999997  477888888776653       499999999999998764

>KOG2416|consensus

Probab=94.48  E-value=0.028  Score=53.02  Aligned_cols=64  Identities=19%  Similarity=0.067  Sum_probs=51.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHh-ccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCS-QYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~-~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      ...|+|.||=.-+|.-+|++|+. .+|.|++..|=+-      |-.|||.|.+.++|.+.+.+|||..+..
T Consensus       444 SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkI------KShCyV~yss~eEA~atr~AlhnV~WP~  508 (718)
T KOG2416|consen  444 SNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKI------KSHCYVSYSSVEEAAATREALHNVQWPP  508 (718)
T ss_pred             cceEeeecccccchHHHHHHHHhhccCchHHHHHHHh------hcceeEecccHHHHHHHHHHHhccccCC
Confidence            45599999999999999999998 5566766633222      3379999999999999999999876543

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=94.48  E-value=0.13  Score=40.26  Aligned_cols=53  Identities=25%  Similarity=0.424  Sum_probs=41.4

Q ss_pred             HHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccccC
Q psy4086          74 DLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQ  135 (305)
Q Consensus        74 ~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~~  135 (305)
                      +|.+.|..||++.=++.+.+        .-+|+|.+-+.|.+|+. ++|..|.++.++.+.+
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LK  104 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLK  104 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE-
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeC
Confidence            56778889999887777654        47999999999999998 9999998887654333

; PDB: 1UFW_A 2DNR_A.

>KOG2068|consensus

Probab=94.27  E-value=0.019  Score=50.65  Aligned_cols=79  Identities=15%  Similarity=0.300  Sum_probs=59.8

Q ss_pred             CceEEecCCCCCCHHHH---HHHHhhCCCeEEEEEeeCCC--CC--cccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         138 TNLYIANLPLNFKECDL---ESLLAKYVTVVSTRILRDNN--NT--SKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l---~~~F~~~g~v~~v~i~~~~~--g~--~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      ..+||-+|+..+..+.+   .+.|.+||.|.+|.+..+..  ..  ...-++|+|+..++|..||...+|..+++  +.|
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg--~~l  155 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDG--RAL  155 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhh--hhh
Confidence            45788888887765544   35688899999998888651  11  11238999999999999999999999998  557


Q ss_pred             EEEeccCC
Q psy4086         211 LVKFADSG  218 (305)
Q Consensus       211 ~v~~a~~~  218 (305)
                      +..+...+
T Consensus       156 ka~~gttk  163 (327)
T KOG2068|consen  156 KASLGTTK  163 (327)
T ss_pred             HHhhCCCc
Confidence            77776654

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

Probab=94.20  E-value=0.17  Score=35.50  Aligned_cols=54  Identities=15%  Similarity=0.421  Sum_probs=40.1

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhC
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN  199 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~  199 (305)
                      .+|--..|..+...||.++|+.||.|. |.++.|.      -|||...+.+.|..|+..+.
T Consensus        10 HVFhltFPkeWK~~DI~qlFspfG~I~-VsWi~dT------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLTFPKEWKTSDIYQLFSPFGQIY-VSWINDT------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE--TT--HHHHHHHCCCCCCEE-EEEECTT------EEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEeCchHhhhhhHHHHhccCCcEE-EEEEcCC------cEEEEeecHHHHHHHHHHhc
Confidence            344444999999999999999999775 5555442      69999999999999998875

; 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.

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=94.05  E-value=0.13  Score=42.19  Aligned_cols=61  Identities=26%  Similarity=0.330  Sum_probs=44.6

Q ss_pred             CHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhC--CCCCCCCCccEEEEeccC
Q psy4086         150 KECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN--GSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       150 te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~--g~~~~g~~~~l~v~~a~~  217 (305)
                      ..+.|+++|..++.+....++.     +-+-..|.|.+.++|.+|...|+  +..+.|  ..|+|-|+..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~-----sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g--~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLK-----SFRRIRVVFESPESAQRARQLLHWDGTSFNG--KRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEET-----TTTEEEEE-SSTTHHHHHHHTST--TSEETT--EE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcC-----CCCEEEEEeCCHHHHHHHHHHhcccccccCC--CceEEEEccc
Confidence            3478999999999988887774     33458999999999999999999  899999  5599999854

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.

>KOG2318|consensus

Probab=94.04  E-value=0.22  Score=47.04  Aligned_cols=131  Identities=14%  Similarity=0.142  Sum_probs=79.1

Q ss_pred             CCCCeEEEcCCCCC-CcHHHHHHHHhcc----CCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          56 LSKTNLYIRGLTQD-TTDKDLINMCSQY----GPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~-~t~~~L~~~f~~~----G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      ..+++|-|-||.|. +...+|.-+|..|    |.|.+|.|....       ||-     .   +.+-+..+|-.+..-..
T Consensus       172 ~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSe-------FGk-----e---RM~eEeV~GP~~el~~~  236 (650)
T KOG2318|consen  172 EETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSE-------FGK-----E---RMKEEEVHGPPKELFKP  236 (650)
T ss_pred             cccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhh-------hhH-----H---HhhhhcccCChhhhccc
Confidence            34566999999998 8899999999876    578888887543       221     1   11223344443322111


Q ss_pred             ccccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       131 ~~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      ........      ......++..++-+..|+ +...         ...||.|+|.+.+.|.+..+.++|..+..+.-.|
T Consensus       237 ~e~~~~s~------sD~ee~~~~~~~kLR~Yq-~~rL---------kYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~  300 (650)
T KOG2318|consen  237 VEEYKESE------SDDEEEEDVDREKLRQYQ-LNRL---------KYYYAVVECDSIETAKAVYEECDGIEFESSANKL  300 (650)
T ss_pred             cccCcccc------cchhhhhhHHHHHHHHHH-hhhh---------eeEEEEEEecCchHHHHHHHhcCcceecccccee
Confidence            11111110      111111222344445553 2222         2348999999999999999999999998766667


Q ss_pred             EEEeccC
Q psy4086         211 LVKFADS  217 (305)
Q Consensus       211 ~v~~a~~  217 (305)
                      .++|-..
T Consensus       301 DLRFIPD  307 (650)
T KOG2318|consen  301 DLRFIPD  307 (650)
T ss_pred             eeeecCC
Confidence            7777543

>KOG2253|consensus

Probab=94.01  E-value=0.016  Score=55.25  Aligned_cols=62  Identities=18%  Similarity=0.230  Sum_probs=51.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccce
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ  128 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~  128 (305)
                      .-+|||+||...+.++-++.++..||-|-.++...         |+|+.|.....+..|+..++-..+.+.
T Consensus        40 ~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~  101 (668)
T KOG2253|consen   40 RDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQ  101 (668)
T ss_pred             CceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcc
Confidence            34599999999999999999999999888776553         999999999999999988765444433

>KOG4285|consensus

Probab=93.88  E-value=0.14  Score=44.60  Aligned_cols=78  Identities=17%  Similarity=0.141  Sum_probs=57.9

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      .-|.|-+++..-. .-|..+|++||+|++....     ..-.|-.|+|.++.+|++||. .||+.|++. ..|-|+.+.+
T Consensus       198 ~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~-----~ngNwMhirYssr~~A~KALs-kng~ii~g~-vmiGVkpCtD  269 (350)
T KOG4285|consen  198 TWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP-----SNGNWMHIRYSSRTHAQKALS-KNGTIIDGD-VMIGVKPCTD  269 (350)
T ss_pred             ceEEEeccCccch-hHHHHHHHhhCeeeeeecC-----CCCceEEEEecchhHHHHhhh-hcCeeeccc-eEEeeeecCC
Confidence            3455656666533 4567899999999876544     224589999999999999997 589999886 5677888777


Q ss_pred             CCcCCC
Q psy4086         218 GLKKRG  223 (305)
Q Consensus       218 ~~~~~~  223 (305)
                      +....+
T Consensus       270 ksvi~~  275 (350)
T KOG4285|consen  270 KSVING  275 (350)
T ss_pred             HHHhcc
Confidence            666553

>KOG0804|consensus

Probab=93.45  E-value=0.33  Score=44.58  Aligned_cols=67  Identities=19%  Similarity=0.262  Sum_probs=56.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccC-CeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYG-PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH  126 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G-~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~  126 (305)
                      .+.|+|-.+|-.+|-.||..|...+- .|.+++|++|...  ++=-.+|+|.+.++|....+++||+.+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p--nrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP--NRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC--ceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            67899999999999999999887664 5899999996532  3335889999999999999999999764

>KOG4285|consensus

Probab=93.00  E-value=0.33  Score=42.26  Aligned_cols=64  Identities=14%  Similarity=0.209  Sum_probs=47.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccce
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ  128 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~  128 (305)
                      ..+.|-|-++|+.-+. -|..+|++||.|++...-.+   |   -+-.|.|.+.-+|++||. -||+.|.+.
T Consensus       196 ~D~WVTVfGFppg~~s-~vL~~F~~cG~Vvkhv~~~n---g---NwMhirYssr~~A~KALs-kng~ii~g~  259 (350)
T KOG4285|consen  196 ADTWVTVFGFPPGQVS-IVLNLFSRCGEVVKHVTPSN---G---NWMHIRYSSRTHAQKALS-KNGTIIDGD  259 (350)
T ss_pred             ccceEEEeccCccchh-HHHHHHHhhCeeeeeecCCC---C---ceEEEEecchhHHHHhhh-hcCeeeccc
Confidence            3677888888876554 45667999999987665422   2   289999999999999998 566666553

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=92.81  E-value=0.086  Score=37.62  Aligned_cols=56  Identities=20%  Similarity=0.338  Sum_probs=39.8

Q ss_pred             EEEEecchhhHHHHHHH------hccCcccceecc-----------cccCCCCceEEecCCCCCCHHHHHHHH
Q psy4086         103 GFVDFESGGYALAAVKA------LQDKGIHAQMAR-----------QQEQDPTNLYIANLPLNFKECDLESLL  158 (305)
Q Consensus       103 afV~f~~~~~A~~a~~~------l~g~~i~~~~~~-----------~~~~~~~~l~V~nlp~~~te~~l~~~F  158 (305)
                      |+|+|.++.-|++.++.      +++..+.++..-           ......++|-|.|||..+.+++|++..
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~L   73 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKL   73 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeE
Confidence            68999999999998875      333333222111           233456889999999999999998754

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=92.44  E-value=0.29  Score=37.95  Aligned_cols=59  Identities=27%  Similarity=0.284  Sum_probs=45.0

Q ss_pred             CCCeEEEcCCCCCCc-HHHHHH---HHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhcc
Q psy4086          57 SKTNLYIRGLTQDTT-DKDLIN---MCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQD  122 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t-~~~L~~---~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g  122 (305)
                      .-.||.|.=|..++. .+||+.   .++.||+|.+|.+.-.       -.|.|.|.|..+|-+|+.++..
T Consensus        85 PMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGr-------qsavVvF~d~~SAC~Av~Af~s  147 (166)
T PF15023_consen   85 PMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGR-------QSAVVVFKDITSACKAVSAFQS  147 (166)
T ss_pred             CceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCC-------ceEEEEehhhHHHHHHHHhhcC
Confidence            335688988777753 345544   5678999999987532       2699999999999999999874

>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=92.05  E-value=0.59  Score=31.45  Aligned_cols=50  Identities=18%  Similarity=0.276  Sum_probs=40.0

Q ss_pred             CCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCC
Q psy4086         148 NFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPG  205 (305)
Q Consensus       148 ~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  205 (305)
                      .++-++|+..+..|. ..  +|..|+    .|| ||.|.+..+|+++....+|..+..
T Consensus        11 ~~~v~d~K~~Lr~y~-~~--~I~~d~----tGf-YIvF~~~~Ea~rC~~~~~~~~~f~   60 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WD--RIRDDR----TGF-YIVFNDSKEAERCFRAEDGTLFFT   60 (66)
T ss_pred             CccHHHHHHHHhcCC-cc--eEEecC----CEE-EEEECChHHHHHHHHhcCCCEEEE
Confidence            467899999999996 33  344554    345 999999999999999999988766

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG0804|consensus

Probab=91.38  E-value=0.72  Score=42.49  Aligned_cols=68  Identities=22%  Similarity=0.378  Sum_probs=57.7

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhC-CCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCC
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKY-VTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPG  205 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~-g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  205 (305)
                      ...|+|-.+|..++--||..+...+ -.|.+++|++|.. ..+-..+|.|.+.++|..-.+.+||+.|..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~-pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM-PNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC-CceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            5678999999999999999998765 4488999999653 345678999999999999999999998854

>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=91.03  E-value=1.4  Score=30.23  Aligned_cols=59  Identities=14%  Similarity=0.302  Sum_probs=35.7

Q ss_pred             CCCCHHHHHHHHhhCCC-----eEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         147 LNFKECDLESLLAKYVT-----VVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       147 ~~~te~~l~~~F~~~g~-----v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ..++..+|..++...+.     |-.++|..+       |+||+-.. +.|..+++.|++..+.|  +.|+|+.|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~-------~S~vev~~-~~a~~v~~~l~~~~~~g--k~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN-------FSFVEVPE-EVAEKVLEALNGKKIKG--KKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS--------EEEEE-T-T-HHHHHHHHTT--SSS------EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee-------EEEEEECH-HHHHHHHHHhcCCCCCC--eeEEEEEC
Confidence            35788888888877655     446776643       89999765 47889999999999999  66888764

; PDB: 2G0C_A 3MOJ_B.

>KOG2253|consensus

Probab=90.76  E-value=0.18  Score=48.48  Aligned_cols=72  Identities=17%  Similarity=0.141  Sum_probs=60.6

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ...+..++||+|+-..+..+-++.+...||.|.+++...        |+|+.|..+..+.+|+..|+-..+++.+  |.+
T Consensus        36 ~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~--------fgf~~f~~~~~~~ra~r~~t~~~~~~~k--l~~  105 (668)
T KOG2253|consen   36 PLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK--------FGFCEFLKHIGDLRASRLLTELNIDDQK--LIE  105 (668)
T ss_pred             CCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh--------hcccchhhHHHHHHHHHHhcccCCCcch--hhc
Confidence            334567899999999999999999999999998876542        9999999999999999999988888854  554


Q ss_pred             Ee
Q psy4086         213 KF  214 (305)
Q Consensus       213 ~~  214 (305)
                      .-
T Consensus       106 ~~  107 (668)
T KOG2253|consen  106 NV  107 (668)
T ss_pred             cc
Confidence            44

>KOG2135|consensus

Probab=89.75  E-value=0.14  Score=47.22  Aligned_cols=70  Identities=19%  Similarity=0.138  Sum_probs=51.8

Q ss_pred             CCCCeEEEcCCCCCC-cHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHH----hccCcccceec
Q psy4086          56 LSKTNLYIRGLTQDT-TDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA----LQDKGIHAQMA  130 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~-t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~----l~g~~i~~~~~  130 (305)
                      .+.+.|-+.-.|+.. |-++|...|.+||+|+.|.|-....      .|.|+|.+..+|-.|...    ||++.|.+.|.
T Consensus       370 ~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~------~a~vTF~t~aeag~a~~s~~avlnnr~iKl~wh  443 (526)
T KOG2135|consen  370 VDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSL------HAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWH  443 (526)
T ss_pred             cccchhhhhccCCCCchHhhhhhhhhhcCccccccccCchh------hheeeeeccccccchhccccceecCceeEEEEe
Confidence            345556666677774 6688999999999999999866533      689999999999666552    56666665555


Q ss_pred             c
Q psy4086         131 R  131 (305)
Q Consensus       131 ~  131 (305)
                      .
T Consensus       444 n  444 (526)
T KOG2135|consen  444 N  444 (526)
T ss_pred             c
Confidence            4

>KOG4574|consensus

Probab=87.56  E-value=1.3  Score=43.94  Aligned_cols=60  Identities=28%  Similarity=0.419  Sum_probs=53.0

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccc
Q psy4086          61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH  126 (305)
Q Consensus        61 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~  126 (305)
                      .++-|.+-..+..-|..+|.+||.|.+++..++-+      .|.|+|...+.|..|+.+|+|+++-
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl~gkevs  360 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVS  360 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCccc
Confidence            55667777888899999999999999999988875      7999999999999999999998764

>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=86.57  E-value=2.7  Score=28.30  Aligned_cols=50  Identities=18%  Similarity=0.226  Sum_probs=39.3

Q ss_pred             CCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          69 DTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        69 ~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      .++-++|+..+..|+-   .+|..|+ |    || ||.|.+..+|+++....||+.+..
T Consensus        11 ~~~v~d~K~~Lr~y~~---~~I~~d~-t----Gf-YIvF~~~~Ea~rC~~~~~~~~~f~   60 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW---DRIRDDR-T----GF-YIVFNDSKEAERCFRAEDGTLFFT   60 (66)
T ss_pred             CccHHHHHHHHhcCCc---ceEEecC-C----EE-EEEECChHHHHHHHHhcCCCEEEE
Confidence            4788999999999963   3344454 3    34 899999999999999999886643

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>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=85.98  E-value=1.8  Score=35.65  Aligned_cols=55  Identities=22%  Similarity=0.176  Sum_probs=40.9

Q ss_pred             cHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhc--cCcccceecc
Q psy4086          71 TDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ--DKGIHAQMAR  131 (305)
Q Consensus        71 t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~--g~~i~~~~~~  131 (305)
                      ..+.|+++|..|+.+..+..++.-      +-..|.|.+.++|.+|...|+  +..+.+..++
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~   64 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLR   64 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-E
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceE
Confidence            347899999999998887777543      258999999999999999998  7777766543

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.

>KOG2295|consensus

Probab=82.39  E-value=0.45  Score=44.83  Aligned_cols=77  Identities=13%  Similarity=0.191  Sum_probs=59.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ...|+||+.|++++++-.+|..+++.+-.+..+.+-....-.+...+..|.|.-.-...-|+.+||+..+.......
T Consensus       229 hke~sll~rni~Pnis~aeIe~~ck~i~~~lrfals~~~aek~~~r~lwv~fk~~~ni~~a~~aLn~irl~s~~~se  305 (648)
T KOG2295|consen  229 HKECSLLVRNILPNISVAEIENLCKGIPGFLRFALSTINAEKNFERRLWVTFKRGTNIKEACWALNGIRLRSNFLSE  305 (648)
T ss_pred             hHHHHHHHhccCCcccHHHHHHHhccCchheeeeccCchHHHHHHHHhhHhhccccchHHHHHHhhhcccccccccc
Confidence            35678999999999999999999998876666665544433445567889999888888899999988776655543

>KOG4410|consensus

Probab=81.54  E-value=6  Score=34.42  Aligned_cols=53  Identities=21%  Similarity=0.193  Sum_probs=37.6

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchh
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG  111 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~  111 (305)
                      +....+-|+|+||+.++.-.||+..+.+-+- .-..|-.    .-+.|-||+.|.+..
T Consensus       326 ~a~~~~di~~~nl~rd~rv~dlk~~lr~~~~-~pm~isw----kg~~~k~flh~~~~~  378 (396)
T KOG4410|consen  326 EAGAKTDIKLTNLSRDIRVKDLKSELRKREC-TPMSISW----KGHFGKCFLHFGNRK  378 (396)
T ss_pred             cCccccceeeccCccccchHHHHHHHHhcCC-CceeEee----ecCCcceeEecCCcc
Confidence            3334566999999999999999999987653 2233322    225678999998743

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	305
1x5o_A	114	Solution Structure Of Rrm Domain In Rna Binding Mot		2e-26
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		5e-22
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-20
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		7e-20
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		1e-18
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		2e-18
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		6e-17
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		7e-17
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		3e-10
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		4e-10
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		4e-10
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		8e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		5e-10
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		6e-10
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		9e-09
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		7e-08
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		8e-08
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		8e-08
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		9e-08
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		9e-08
1sxl_A	97	Resonance Assignments And Solution Structure Of The		2e-07
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		4e-07
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		5e-07
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		5e-07
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		7e-07
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		1e-06
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		2e-06
2khc_A	118	Bruno Rrm3+ Length = 118		2e-06
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		3e-06
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		4e-06
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		1e-05
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		2e-05
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		2e-05
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		2e-05
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		2e-05
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		3e-05
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		3e-05
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		4e-05
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		5e-05
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		5e-05
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		6e-05
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		8e-05
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		8e-05
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		1e-04
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		1e-04
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		1e-04
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		1e-04
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		2e-04
2dnh_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		2e-04
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-04
2dno_A	102	Solution Structure Of Rna Binding Domain In Trinucl		2e-04
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		2e-04
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		3e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		3e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		3e-04
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		4e-04
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		5e-04
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		5e-04
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		5e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		5e-04
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		5e-04
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		5e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		5e-04
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		6e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		6e-04
3nnh_A	88	Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuug		6e-04
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		6e-04
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		7e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		7e-04
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		8e-04

>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 1 Length = 114

Iteration: 1
 Score =  116 bits (290), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 58/103 (56%), Positives = 76/103 (73%), Gaps = 6/103 (5%)
Query: 119 ALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSK 178
            L+  G+ AQMA+QQEQDPTNLYI+NLPL+  E +LE++L  +  V+STRILRD++ TS+
Sbjct: 7   GLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSR 66
Query: 179 GVGFARLESKDKCDQMIQLFNG---STLPGSK---EPLLVKFA 215
           GVGFAR+ES +KC+ +I  FNG    T PG     EPLL KF+
Sbjct: 67  GVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFS 109

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score =  101 bits (251), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 47/74 (63%), Positives = 57/74 (77%)
Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           + LYIRGL   TTD+DL+ +C  YG I+STKAILDKTTNKC+GYGFVDF+S   A  AV 
Sbjct: 6   SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 119 ALQDKGIHAQMARQ 132
           AL+  G+ AQMA+Q
Sbjct: 66  ALKASGVQAQMAKQ 79

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 96.7 bits (239), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 56/166 (33%), Positives = 87/166 (52%), Gaps = 8/166 (4%)
Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           +TNL +  L Q+ T  +L ++ S  G + S K I DK      GYGFV++ +   A  A+
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 118 KA-----LQDKGIHAQMARQQEQ--DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRIL 170
                  LQ K I    AR   +     NLYI+ LP    + D+E + +++  ++++R+L
Sbjct: 62  NTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVL 121
Query: 171 RDNNN-TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
            D     S+GV F R + + + ++ I  FNG   PGS EP+ VKFA
Sbjct: 122 VDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVKFA 167

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 94.4 bits (233), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 55/166 (33%), Positives = 86/166 (51%), Gaps = 8/166 (4%)
Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           +TNL +  L Q+ T  +L ++ S  G + S K I DK      GYGFV++ +   A  A+
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 118 KA-----LQDKGIHAQMARQQEQ--DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRIL 170
                  LQ K I    AR   +     NLYI+ LP    + D+E + +++  ++++R+L
Sbjct: 62  NTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVL 121
Query: 171 RDNNN-TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
            D     S+GV F R + + + ++ I  FNG   PGS EP+ V FA
Sbjct: 122 VDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVXFA 167

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 90.5 bits (223), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 57/167 (34%), Positives = 87/167 (52%), Gaps = 8/167 (4%)
Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           SKTNL +  L Q+ T ++  ++    G I S K + DK T +  GYGFV++     A  A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 117 VKA-----LQDKGIHAQMARQQEQD--PTNLYIANLPLNFKECDLESLLAKYVTVVSTRI 169
           +       LQ K I    AR         NLY++ LP    + +LE L ++Y  ++++RI
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
Query: 170 LRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
           L D     S+GVGF R + + + ++ I+  NG    G+ EP+ VKFA
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 89.7 bits (221), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 56/169 (33%), Positives = 88/169 (52%), Gaps = 8/169 (4%)
Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           SKTNL +  L Q+ T  +  ++    G I S K + DK T +  GYGFV++     A  A
Sbjct: 3   SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 117 VKA-----LQDKGIHAQMARQQEQD--PTNLYIANLPLNFKECDLESLLAKYVTVVSTRI 169
           +       LQ K I    AR         NLY++ LP    + ++E L ++Y  ++++RI
Sbjct: 63  INTLNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRI 122
Query: 170 LRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
           L D     S+GVGF R + + + ++ I+  NG    G+ EP+ VKFA++
Sbjct: 123 LLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKFANN 171

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 84.7 bits (208), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 54/167 (32%), Positives = 81/167 (48%), Gaps = 8/167 (4%)
Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           S TNL +  L QD TD++L  +    GPI + + + D  T    GY FVDF S   +  A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 117 VKAL-----QDKGIHAQMAR--QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRI 169
           +K L     ++K +    AR   +    TNLY+ NLP    +  L+++  KY ++V   I
Sbjct: 62  IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 170 LRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
           LRD      +GV F R   +++  + I   N     G  +PL V+ A
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 84.3 bits (207), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 54/168 (32%), Positives = 81/168 (48%), Gaps = 8/168 (4%)
Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           S TNL +  L QD TD++L  +    GPI + +   D  T    GY FVDF S   +  A
Sbjct: 13  SNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRA 72
Query: 117 VKAL-----QDKGIHAQMAR--QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRI 169
           +K L     ++K +    AR   +    TNLY+ NLP    +  L+++  KY ++V   I
Sbjct: 73  IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 170 LRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD 216
           LRD      +GV F R   +++  + I   N     G  +PL V+ A+
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLAE 180

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 62.4 bits (150), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 48/196 (24%), Positives = 87/196 (44%), Gaps = 15/196 (7%)
Query: 46  SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
           +P  P+ P      +LY+  L  D T+  L    S  GPI+S +   D  T +  GY +V
Sbjct: 7   NPSAPSYP----MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62
Query: 106 DFESGGYALAAVKALQDKGIHAQMAR--QQEQDPT-------NLYIANLPLNFKECDLES 156
           +F+    A  A+  +    I  +  R    ++DP+       N++I NL  +     L  
Sbjct: 63  NFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 122
Query: 157 LLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD 216
             + +  ++S +++ D N  SKG GF   E+++  ++ I+  NG  L   ++  + +F  
Sbjct: 123 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLL-NDRKVFVGRFKS 180
Query: 217 SGLKKRGAGAGGPNIY 232
              ++   GA     Y
Sbjct: 181 RKEREAELGARAKEFY 196

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 62.0 bits (149), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 39/143 (27%), Positives = 71/143 (49%), Gaps = 6/143 (4%)
Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
            ++I GL  DTT+ +L     +YG +   K + D  T + RG+GF+ FE        VK 
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 120 ---LQDKGIHAQMAR-QQEQDPT-NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN 174
              L  K I  + A  + EQD T  +++  +  + +  + E   +++ T++  +++ D +
Sbjct: 65  QHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKD 124
Query: 175 N-TSKGVGFARLESKDKCDQMIQ 196
              S+G GF   +S D  D++ Q
Sbjct: 125 TGQSRGFGFVTYDSADAVDRVCQ 147

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 62.0 bits (149), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 45/187 (24%), Positives = 82/187 (43%), Gaps = 15/187 (8%)
Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTN--KCRG 101
           NG+   P  P+ L    +++  + +  ++KDL  +  QYG +     + D++ N  + +G
Sbjct: 2   NGTLDHPDQPD-LDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG 60
Query: 102 YGFVDFESGGYALAAVKALQDK----GIH-------AQMARQQEQDPTNLYIANLPLNFK 150
             FV F +   AL A  AL +     G+H       A   +    +   L+I  +     
Sbjct: 61  CCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCT 120
Query: 151 ECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ-LFNGSTLPGSKEP 209
           E D+  + + +  +   RILR  +  S+G  F    ++      I+ +    T+ G   P
Sbjct: 121 ENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSP 180
Query: 210 LLVKFAD 216
           ++VKFAD
Sbjct: 181 MVVKFAD 187

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 40/90 (44%), Gaps = 4/90 (4%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT---SKGVGFARLES- 187
           Q + D   +++  +P  + E DL  L  +Y  V    +LRD +     SKG  F    + 
Sbjct: 10  QPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR 69
Query: 188 KDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
           K   +    L N   LPG   P+ +K ADS
Sbjct: 70  KAALEAQNALHNMKVLPGMHHPIQMKPADS 99

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 61.6 bits (148), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 50/80 (62%), Gaps = 1/80 (1%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQL 197
           NLY++ LP    + ++E L ++Y  ++++RIL D     S+GVGF R + + + ++ I+ 
Sbjct: 3   NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 198 FNGSTLPGSKEPLLVKFADS 217
            NG    G+ EP+ VKFA++
Sbjct: 63  LNGQKPLGAAEPITVKFANN 82

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 61.2 bits (147), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 45/171 (26%), Positives = 78/171 (45%), Gaps = 14/171 (8%)
Query: 46  SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
           +P  P+ P      +LY+  L  D T+  L    S  GPI+S +   D  T +  GY +V
Sbjct: 2   NPSAPSYP----MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 57
Query: 106 DFESGGYALAAVKALQDKGIHAQMAR--QQEQDPT-------NLYIANLPLNFKECDLES 156
           +F+    A  A+  +    I  +  R    ++DP+       N++I NL  +     L  
Sbjct: 58  NFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 117
Query: 157 LLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSK 207
             + +  ++S +++ D N  SKG GF   E+++  ++ I+  NG  L   K
Sbjct: 118 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRK 167

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 57.4 bits (137), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 40/170 (23%), Positives = 75/170 (44%), Gaps = 14/170 (8%)
Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTN--KCRGYGFVDFESGGYALAAVK 118
           +++  + +  ++KDL  +  QYG +     + D++ N  + +G  FV F +   AL A  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 119 ALQDK----GIH-------AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVST 167
           AL +     G+H       A   +    +   L+I  +     E D+  + + +  +   
Sbjct: 66  ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC 125
Query: 168 RILRDNNNTSKGVGFARLESKDKCDQMIQ-LFNGSTLPGSKEPLLVKFAD 216
           RILR  +  S+G  F    ++      I+ +    T+ G   P++VKFAD
Sbjct: 126 RILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 175

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 40/160 (25%), Positives = 73/160 (45%), Gaps = 15/160 (9%)
Query: 49  TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           +P  PEQL K  L+I GL+ +TTD+ L +   Q+G +     + D  T + RG+GFV + 
Sbjct: 7   SPKEPEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 64
Query: 109 SGGYALAAVKA----LQDKGIHAQMA--RQQEQDP------TNLYIANLPLNFKECDLES 156
           +     AA+ A    +  + +  + A  R+  Q P        +++  +  + +E  L  
Sbjct: 65  TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 124
Query: 157 LLAKYVTVVSTRILRDNNNTSK-GVGFARLESKDKCDQMI 195
              +Y  +    I+ D  +  K G  F   +  D  D+++
Sbjct: 125 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 54.3 bits (129), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 40/160 (25%), Positives = 73/160 (45%), Gaps = 15/160 (9%)
Query: 49  TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           +P  PEQL K  L+I GL+ +TTD+ L +   Q+G +     + D  T + RG+GFV + 
Sbjct: 6   SPKEPEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 109 SGGYALAAVKA----LQDKGIHAQMA--RQQEQDP------TNLYIANLPLNFKECDLES 156
           +     AA+ A    +  + +  + A  R+  Q P        +++  +  + +E  L  
Sbjct: 64  TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 123
Query: 157 LLAKYVTVVSTRILRDNNNTSK-GVGFARLESKDKCDQMI 195
              +Y  +    I+ D  +  K G  F   +  D  D+++
Sbjct: 124 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 54.3 bits (129), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 40/160 (25%), Positives = 73/160 (45%), Gaps = 15/160 (9%)
Query: 49  TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           +P  PEQL K  L+I GL+ +TTD+ L +   Q+G +     + D  T + RG+GFV + 
Sbjct: 6   SPKEPEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 109 SGGYALAAVKA----LQDKGIHAQMA--RQQEQDP------TNLYIANLPLNFKECDLES 156
           +     AA+ A    +  + +  + A  R+  Q P        +++  +  + +E  L  
Sbjct: 64  TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 123
Query: 157 LLAKYVTVVSTRILRDNNNTSK-GVGFARLESKDKCDQMI 195
              +Y  +    I+ D  +  K G  F   +  D  D+++
Sbjct: 124 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 40/160 (25%), Positives = 73/160 (45%), Gaps = 15/160 (9%)
Query: 49  TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           +P  PEQL K  L+I GL+ +TTD+ L +   Q+G +     + D  T + RG+GFV + 
Sbjct: 5   SPKEPEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 62
Query: 109 SGGYALAAVKA----LQDKGIHAQMA--RQQEQDP------TNLYIANLPLNFKECDLES 156
           +     AA+ A    +  + +  + A  R+  Q P        +++  +  + +E  L  
Sbjct: 63  TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 122
Query: 157 LLAKYVTVVSTRILRDNNNTSK-GVGFARLESKDKCDQMI 195
              +Y  +    I+ D  +  K G  F   +  D  D+++
Sbjct: 123 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 40/160 (25%), Positives = 73/160 (45%), Gaps = 15/160 (9%)
Query: 49  TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           +P  PEQL K  L+I GL+ +TTD+ L +   Q+G +     + D  T + RG+GFV + 
Sbjct: 4   SPKEPEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 61
Query: 109 SGGYALAAVKA----LQDKGIHAQMA--RQQEQDP------TNLYIANLPLNFKECDLES 156
           +     AA+ A    +  + +  + A  R+  Q P        +++  +  + +E  L  
Sbjct: 62  TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 121
Query: 157 LLAKYVTVVSTRILRDNNNTSK-GVGFARLESKDKCDQMI 195
              +Y  +    I+ D  +  K G  F   +  D  D+++
Sbjct: 122 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQ 196
           TNLY+ NLP    +  L+++  KY ++V   ILRD      +GV F R   +++  + I 
Sbjct: 14  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 197 LFNGSTLPGSKEPLLVKFAD 216
             N     G  +PL V+ A+
Sbjct: 74  ALNNVIPEGGSQPLSVRLAE 93

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 43/165 (26%), Positives = 73/165 (44%), Gaps = 13/165 (7%)
Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           LY+  L +  T+  L       GPI + K ++DK  NK   Y FV++     A  A++ L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTL 61
Query: 121 QDKGIHAQMAR-----QQEQ----DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILR 171
             K I   + +     Q +Q    D  NL++ +L +N  +  L +    + + +S  ++ 
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 172 D-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
           D    +S+G GF    S+D     +    G  L G   PL + +A
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG--RPLRINWA 164

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 51.6 bits (122), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 39/156 (25%), Positives = 71/156 (45%), Gaps = 15/156 (9%)
Query: 53  PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
           PEQL K  L+I GL+ +TTD+ L +   Q+G +     + D  T + RG+GFV + +   
Sbjct: 3   PEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60
Query: 113 ALAAVKA----LQDKGIHAQMA--RQQEQDP------TNLYIANLPLNFKECDLESLLAK 160
             AA+ A    +  + +  + A  R+  Q P        +++  +  + +E  L     +
Sbjct: 61  VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 120
Query: 161 YVTVVSTRILRDNNNTSK-GVGFARLESKDKCDQMI 195
           Y  +    I+ D  +  K G  F   +  D  D+++
Sbjct: 121 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 51.6 bits (122), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 40/160 (25%), Positives = 66/160 (41%), Gaps = 14/160 (8%)
Query: 71  TDKDLINMCSQYGPIISTKAILDKTTN--KCRGYGFVDFESGGYALAAVKALQDK----G 124
           ++KDL  +  QYG +     + D++ N  + +G  FV F +   AL A  AL +     G
Sbjct: 16  SEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNXKVLPG 75
Query: 125 IH-------AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTS 177
            H       A   +    +   L+I  +     E D+    + +  +   RILR  +  S
Sbjct: 76  XHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLS 135
Query: 178 KGVGFARLESKDKCDQMIQLFN-GSTLPGSKEPLLVKFAD 216
           +G  F    ++      I+  +   T  G   P +VKFAD
Sbjct: 136 RGCAFVTFTTRAXAQTAIKAXHQAQTXEGCSSPXVVKFAD 175

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 51.2 bits (121), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 37/74 (50%)
Query: 47  PGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVD 106
           P T   PE     NL +  +     +  L  +  +YGPI S K + D+ T + RGYGFV 
Sbjct: 31  PPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVK 90
Query: 107 FESGGYALAAVKAL 120
           F+SG  A  A+  L
Sbjct: 91  FQSGSSAQQAIAGL 104

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 5/84 (5%)
Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           GPE     NL+I  L Q+  D+DL+ M   +G ++S K  +DK TN  + +GFV +++  
Sbjct: 22  GPE---GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 78
Query: 112 YALAAVKALQDKGIHAQMARQQEQ 135
            A AA++++   G    M R + Q
Sbjct: 79  SAQAAIQSM--NGFQIGMKRLKVQ 100

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 30/84 (35%), Positives = 48/84 (57%), Gaps = 5/84 (5%)
Query: 43  HNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
            +GS G P    Q SKT L+++GL++DTT++ L      +   +  + + D+ T   +G+
Sbjct: 2   SSGSSG-PNARSQPSKT-LFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGF 56
Query: 103 GFVDFESGGYALAAVKALQDKGIH 126
           GFVDF S   A AA +A++D  I 
Sbjct: 57  GFVDFNSEEDAKAAKEAMEDGEID 80

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 40/69 (57%), Gaps = 3/69 (4%)
Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           GPE     NL+I  L Q+ TD DL +    +G +IS K  +DK T+  + +GFV F++  
Sbjct: 37  GPE---GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPD 93
Query: 112 YALAAVKAL 120
            A  A+KA+
Sbjct: 94  SAQVAIKAM 102

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%)
Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++ GL+ DT ++ L  + S+YG I     + D+ T + RG+GFV FE+   A  A+ A+
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 121 QDKGIHAQMAR 131
             K +  +  R
Sbjct: 75  NGKSVDGRQIR 85

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L+I GL ++T +K L  +  ++GPI     I D+T+ K RG+ F+ FE+   A  A K +
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKNAAKDM 68
Query: 121 QDKGIHAQMAR-QQEQDPT 138
             K +H +  + +Q + P+
Sbjct: 69  NGKSLHGKAIKVEQAKKPS 87

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 18/60 (30%), Positives = 37/60 (61%)
Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +Y+  +  D T++ ++++CS  GP+I+ K + D  T + +GY F++F     + +AV+ L
Sbjct: 5   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           GP ++    +Y+  +  D T++ ++++CS  GP+I+ K + D  T + +GY F++F    
Sbjct: 1   GPSRV----VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE 56
Query: 112 YALAAVKAL 120
            + +AV+ L
Sbjct: 57  SSASAVRNL 65

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 20/49 (40%), Positives = 33/49 (67%)
Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           +++ GL+ +TT +D+ +   Q+G +     + DKTTN+ RG+GFV FES
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES 50

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 1/81 (1%)
Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLE 186
           + M  + +  P  L+++N+P  F++ DL  +  ++  ++   I+  N   SKG GF   E
Sbjct: 19  SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF-NERGSKGFGFVTFE 77
Query: 187 SKDKCDQMIQLFNGSTLPGSK 207
           +    D+  +  +G+ + G K
Sbjct: 78  NSADADRAREKLHGTVVEGRK 98

>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 = 46.2 bits (108), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 18/60 (30%), Positives = 37/60 (61%)
Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +Y+  +  D T++ ++++CS  GP+I+ K + D  T + +GY F++F     + +AV+ L
Sbjct: 7   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/48 (43%), Positives = 31/48 (64%)
Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           L++ GL   TT + L +  SQYG ++    + DKTTN+ RG+GFV F+
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66

>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 = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/75 (25%), Positives = 44/75 (58%)
Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           S  ++++  +  + T++ L ++ S+ GP++S + + D+ T K +GYGF +++    AL+A
Sbjct: 7   SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66
Query: 117 VKALQDKGIHAQMAR 131
           ++ L  +    +  R
Sbjct: 67  MRNLNGREFSGRALR 81

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 31/105 (29%), Positives = 53/105 (50%), Gaps = 17/105 (16%)
Query: 56  LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           L   N++I+ L +   +K L +  S +G I+S K + D+  N  +GYGFV FE+   A  
Sbjct: 3   LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAER 60
Query: 116 AVKA-----LQDKGIH-----AQMARQQE-----QDPTNLYIANL 145
           A++      L D+ +      ++  R+ E     ++ TN+YI N 
Sbjct: 61  AIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNF 105

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 20/48 (41%), Positives = 31/48 (64%)
Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           ++I GL+ DTT KDL +  S++G ++     LD  T + RG+GFV F+
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFK 49

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 25/64 (39%), Positives = 34/64 (53%)
Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           S TNL +  L QD TD++L  +    GPI + + + D  T    GY FVDF S   +  A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 117 VKAL 120
           +K L
Sbjct: 62  IKVL 65

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 29/97 (29%), Positives = 44/97 (45%), Gaps = 5/97 (5%)
Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           +GS G  T     +K  LY+ GL ++  DK L      +G I   +  LD  T K RG+ 
Sbjct: 3   SGSSGMAT-----TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 57
Query: 104 FVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNL 140
           FV+FE    A AA+  + +  +  +  R     P  +
Sbjct: 58  FVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRI 94

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
           P  L+++N+P  F++ DL  +  ++  ++   I+  N   SKG GF   E+    D+  +
Sbjct: 15  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF-NERGSKGFGFVTFENSADADRARE 73
Query: 197 LFNGSTLPGSK 207
             +G+ + G K
Sbjct: 74  KLHGTVVEGRK 84

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           L++  L     E D+  L   +  +    ILR  +  SKG  F +  S  +    I   +
Sbjct: 18  LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 200 GS-TLPGSKEPLLVKFADS 217
           GS T+PG+   L+VKFAD+
Sbjct: 78  GSQTMPGASSSLVVKFADT 96

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
           EQ  K  L+I GL+ +TT++ L N   Q+G +     + D  + + RG+GFV F S    
Sbjct: 25  EQFRK--LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Query: 114 LAAVKA 119
            AA+ A
Sbjct: 83  DAAMAA 88

>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 = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           +GS G    P+      L + GL+  TT++DL  + S+YGPI     + D+ + + RG+ 
Sbjct: 3   SGSSGNRANPD--PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 104 FVDFES 109
           FV FE+
Sbjct: 61  FVYFEN 66

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/67 (29%), Positives = 36/67 (53%)
Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
           E  +   +Y+  + QD +D D+ ++   +G I S     D TT K +GYGF+++E    +
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS 180
Query: 114 LAAVKAL 120
             AV ++
Sbjct: 181 QDAVSSM 187

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           +GS G    P+      L + GL+  TT++DL  + S+YGPI     + D+ + + RG+ 
Sbjct: 3   SGSSGNRANPD--PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 104 FVDFES 109
           FV FE+
Sbjct: 61  FVYFEN 66

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 31/49 (63%)
Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           L + GL+  TT++DL  + S+YGPI     + D+ + + RG+ FV FE+
Sbjct: 49  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 97

>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5 Rna Binding Protein Length = 105

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 2/90 (2%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF 198
            L++  L     E D+  L   +  +    +LR  + +SKG  F +  S  +    I   
Sbjct: 17  KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 199 NGS-TLPGSKEPLLVKFADSGLKKRGAGAG 227
           +GS T+PG+   L+VKFAD+  K+ G  +G
Sbjct: 77  HGSQTMPGASSSLVVKFADTD-KESGPSSG 105

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           N+Y+  L    T + +  + SQ+G + + K I D+ T K +G+GFV+ +    +  A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVS-EAIAK 61
Query: 120 LQDKGIHAQMARQQEQDP 137
           L +     +  R  E +P
Sbjct: 62  LDNTDFMGRTIRVTEANP 79

>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide Repeat Containing 4 Variant Length = 102

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF 198
            L++  L     + D+  +   + T+    +LR  + TSKG  F + ++  +    I   
Sbjct: 14  KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 199 NGS-TLPGSKEPLLVKFADS 217
           + S TLPG+   L+VKFAD+
Sbjct: 74  HSSRTLPGASSSLVVKFADT 93

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/75 (33%), Positives = 37/75 (49%)
Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           SK  LY+ GL ++  DK L      +G I   +  LD  T K RG+ FV+FE    A AA
Sbjct: 1   SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 117 VKALQDKGIHAQMAR 131
           +  + +  +  +  R
Sbjct: 61  IDNMNESELFGRTIR 75

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/67 (29%), Positives = 36/67 (53%)
Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
           E  +   +Y+  + QD +D D+ ++   +G I S     D TT K +GYGF+++E    +
Sbjct: 106 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 165
Query: 114 LAAVKAL 120
             AV ++
Sbjct: 166 QDAVSSM 172

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           +TNL +  L Q+ T  +L ++ S  G + S K I DK      GYGFV++ +   A  A+
Sbjct: 4   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 63
Query: 118 KA-----LQDKGIHAQMAR 131
                  LQ K I    AR
Sbjct: 64  NTLNGLRLQSKTIKVSYAR 82

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 19/49 (38%), Positives = 31/49 (63%)
Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           L + GL+  TT++DL  + S+YGPI     + D+ + + RG+ FV FE+
Sbjct: 15  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/80 (31%), Positives = 38/80 (47%)
Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           G    +K  LY+ GL ++  DK L      +G I   +  LD  T K RG+ FV+FE   
Sbjct: 1   GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 112 YALAAVKALQDKGIHAQMAR 131
            A AA+  + +  +  +  R
Sbjct: 61  DAAAAIDNMNESELFGRTIR 80

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 37/136 (27%), Positives = 63/136 (46%), Gaps = 11/136 (8%)
Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           ++  + IRGL  D T++++ ++ S Y      K       +K +G  FV   +G  A AA
Sbjct: 21  NRRKILIRGLPGDVTNQEVHDLLSDY----ELKYCF---VDKYKGTAFVTLLNGEQAEAA 73
Query: 117 VKALQDKGIHAQMARQQEQDPTN--LYIANLPLNFKECDLESLLAKYVTVVSTRIL-RDN 173
           + A     +  +    Q Q PT+  L +ANLP +  +   E L+  + ++    ++  + 
Sbjct: 74  INAFHQSRLRERELSVQLQ-PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER 132
Query: 174 NNTSKGVGFARLESKD 189
              SKG GFA    KD
Sbjct: 133 TGQSKGYGFAEYMKKD 148

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 35/66 (53%)
Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
           E  +   +Y+  + QD +D D+ ++   +G I S     D TT K +GYGF+++E    +
Sbjct: 105 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 164
Query: 114 LAAVKA 119
             AV +
Sbjct: 165 QDAVSS 170

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 37/136 (27%), Positives = 63/136 (46%), Gaps = 11/136 (8%)
Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           ++  + IRGL  D T++++ ++ S Y      K       +K +G  FV   +G  A AA
Sbjct: 19  NRRKILIRGLPGDVTNQEVHDLLSDY----ELKYCF---VDKYKGTAFVTLLNGEQAEAA 71
Query: 117 VKALQDKGIHAQMARQQEQDPTN--LYIANLPLNFKECDLESLLAKYVTVVSTRIL-RDN 173
           + A     +  +    Q Q PT+  L +ANLP +  +   E L+  + ++    ++  + 
Sbjct: 72  INAFHQSRLRERELSVQLQ-PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER 130
Query: 174 NNTSKGVGFARLESKD 189
              SKG GFA    KD
Sbjct: 131 TGQSKGYGFAEYMKKD 146

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 24/75 (32%), Positives = 37/75 (49%)
Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           +K  LY+ GL ++  DK L      +G I   +  LD  T K RG+ FV+FE    A AA
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63
Query: 117 VKALQDKGIHAQMAR 131
           +  + +  +  +  R
Sbjct: 64  IDNMNESELFGRTIR 78

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 37/136 (27%), Positives = 63/136 (46%), Gaps = 11/136 (8%)
Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           ++  + IRGL  D T++++ ++ S Y      K       +K +G  FV   +G  A AA
Sbjct: 21  NRRKILIRGLPGDVTNQEVHDLLSDY----ELKYCF---VDKYKGTAFVTLLNGEQAEAA 73
Query: 117 VKALQDKGIHAQMARQQEQDPTN--LYIANLPLNFKECDLESLLAKYVTVVSTRIL-RDN 173
           + A     +  +    Q Q PT+  L +ANLP +  +   E L+  + ++    ++  + 
Sbjct: 74  INAFHQSRLRERELSVQLQ-PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER 132
Query: 174 NNTSKGVGFARLESKD 189
              SKG GFA    KD
Sbjct: 133 TGQSKGYGFAEYMKKD 148

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN-TSKGVGFARLESKDKCDQMIQ 196
           + +Y++NLP +    DL  + +KY  VV   I++D +   SKGV F     KD      +
Sbjct: 17  STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 197 LFNGSTLPG 205
             N   L G
Sbjct: 77  AINNKQLFG 85

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 40/68 (58%)
Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++ G+ ++ T++D+ +  ++YG I +    LD+ T   +GY  V++E+   A AA++ L
Sbjct: 26  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 121 QDKGIHAQ 128
             + +  Q
Sbjct: 86  NGQDLMGQ 93

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/67 (31%), Positives = 37/67 (55%)
Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
           E+     +Y+ GL +  ++  L  +  Q GP+++T    D+ T + +GYGFV+F S   A
Sbjct: 11  ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70
Query: 114 LAAVKAL 120
             A+K +
Sbjct: 71  DYAIKIM 77

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 37/75 (49%)
Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           +K  LY+ GL ++  DK L      +G I   +  LD  T K RG+ FV+FE    A AA
Sbjct: 62  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121
Query: 117 VKALQDKGIHAQMAR 131
           +  + +  +  +  R
Sbjct: 122 IDNMNESELFGRTIR 136

>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna Length = 88

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 4/86 (4%)
Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT---SKGVGFARLES-KDKC 191
           D   +++  +P  + E DL  L  +Y  V    +LRD +     SKG  F    + K   
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADS 217
           +    L N   LPG   P+ +K ADS
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADS 87

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 2/61 (3%)
Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           N++I+ L +   +K L +  S +G I+S K + D+  N  +GYGFV FE+   A  A++ 
Sbjct: 13  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 70
Query: 120 L 120
           +
Sbjct: 71  M 71

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           SKTNL +  L Q+ T  +  ++    G I S K + DK T +  GYGFV++     A  A
Sbjct: 3   SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 117 VKA-----LQDKGIHAQMAR 131
           +       LQ K I    AR
Sbjct: 63  INTLNGLKLQTKTIKVSYAR 82

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 40/68 (58%)
Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++ G+ ++ T++D+ +  ++YG I +    LD+ T   +GY  V++E+   A AA++ L
Sbjct: 25  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 121 QDKGIHAQ 128
             + +  Q
Sbjct: 85  NGQDLMGQ 92

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 40/68 (58%)
Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++ G+ ++ T++D+ +  ++YG I +    LD+ T   +GY  V++E+   A AA++ L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 121 QDKGIHAQ 128
             + +  Q
Sbjct: 70  NGQDLMGQ 77

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	305
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-57
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-15
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	9e-57
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-15
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-52
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-13
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-34
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	6e-34
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-30
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-12
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-06
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-33
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-30
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-29
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-07
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-29
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	8e-12
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-28
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-28
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-27
1x4e_A	85	RNA binding motif, single-stranded interacting pro	9e-13
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	6e-27
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-16
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-27
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-13
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-24
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-24
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-08
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-23
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-12
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-21
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-21
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-10
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-20
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	7e-12
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-20
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-11
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-19
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-11
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	7e-18
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-17
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-17
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	8e-11
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-17
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-10
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	4e-17
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-07
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-17
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-06
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	9e-17
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-08
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-16
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	4e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-16
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	8e-12
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-16
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-07
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-16
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-11
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-16
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	9e-08
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-16
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-07
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	7e-16
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-09
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	8e-16
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	6e-06
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	1e-15
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-15
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-06
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-15
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-15
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-07
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-15
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-10
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-15
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-10
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-15
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-07
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-15
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-10
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-15
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	8e-07
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-15
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-09
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-15
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	7e-06
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-15
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-13
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	7e-15
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-11
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	7e-15
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-04
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	7e-15
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	4e-08
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	9e-15
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-09
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	9e-15
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-07
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	9e-15
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	1e-07
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-14
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	9e-06
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-14
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-14
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-14
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-07
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-14
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-09
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-14
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	6e-09
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-14
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-14
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-14
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	5e-14
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-14
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-08
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	5e-14
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-09
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-14
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-06
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	6e-14
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-05
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	7e-14
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	6e-08
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-13
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-13
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-13
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-07
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-13
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	8e-09
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-13
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	5e-12
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-13
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-11
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-13
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-08
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-13
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-12
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-13
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-07
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-13
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-05
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-13
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	5e-10
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-13
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-13
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-10
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	5e-13
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-07
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-13
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	3e-07
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	5e-13
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	5e-13
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-10
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	7e-13
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-12
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-13
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-10
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	9e-13
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-11
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-12
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-12
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-12
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-12
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-12
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-12
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	8e-05
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-12
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-08
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-04
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-04
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-12
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	7e-06
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-12
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-06
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-12
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-06
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	4e-12
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-07
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-12
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-07
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-12
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	5e-10
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	5e-12
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-06
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-12
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-05
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-11
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-06
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-11
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-06
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-11
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-06
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	6e-07
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-11
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-09
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-11
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-11
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-07
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-11
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-06
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	4e-07
2div_A	99	TRNA selenocysteine associated protein; structural	4e-11
2div_A	99	TRNA selenocysteine associated protein; structural	2e-06
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	4e-11
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-04
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-08
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	6e-11
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-07
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	8e-11
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	8e-05
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-10
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-08
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-10
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	5e-10
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-10
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-06
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	5e-10
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-05
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-10
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-08
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	6e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	4e-05
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	9e-10
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-09
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	9e-10
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-09
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-04
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-07
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-09
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-06
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	5e-09
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	3e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	7e-09
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-06
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-08
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-08
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	7e-05
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-08
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-07
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-08
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-08
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-04
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-08
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-08
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	9e-07
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	6e-08
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-04
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	7e-08
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	9e-08
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-07
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-07
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	6e-05
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-07
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	3e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-07
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	7e-07
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-05
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	8e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	8e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	9e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	5e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	5e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	6e-06
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	7e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	8e-06
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-05
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	7e-05
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	9e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-04
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	3e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	4e-04
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	4e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-04

>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 =  181 bits (462), Expect = 2e-57
 Identities = 53/167 (31%), Positives = 86/167 (51%), Gaps = 8/167 (4%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           SKTNL +  L Q+ T ++  ++    G I S K + DK T +  GYGFV++     A  A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 117 VKALQDKGIHAQMARQQEQDP-------TNLYIANLPLNFKECDLESLLAKYVTVVSTRI 169
           +  L    +  +  +     P        NLY++ LP    + +LE L ++Y  ++++RI
Sbjct: 61  INTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120

Query: 170 LRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
           L D     S+GVGF R + + + ++ I+  NG    G+ EP+ VKFA
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 72.2 bits (178), Expect = 1e-15
 Identities = 25/67 (37%), Positives = 39/67 (58%)

Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
             +   NLY+ GL +  T K+L  + SQYG II+++ ++D+ T   RG GF+ F+    A
Sbjct: 84  ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 143

Query: 114 LAAVKAL 120
             A+K L
Sbjct: 144 EEAIKGL 150

>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 =  179 bits (457), Expect = 9e-57
 Identities = 52/167 (31%), Positives = 78/167 (46%), Gaps = 8/167 (4%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           S TNL +  L QD TD++L  +    GPI + + + D  T    GY FVDF S   +  A
Sbjct: 2   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61

Query: 117 VKALQDKGIHAQMARQQEQDP-------TNLYIANLPLNFKECDLESLLAKYVTVVSTRI 169
           +K L    +  +  +     P       TNLY+ NLP    +  L+++  KY ++V   I
Sbjct: 62  IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121

Query: 170 LRDNNN-TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
           LRD      +GV F R   +++  + I   N     G  +PL V+ A
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 71.1 bits (175), Expect = 3e-15
 Identities = 23/67 (34%), Positives = 33/67 (49%)

Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
           E +  TNLY+  L +  TD  L  +  +YG I+    + DK T + RG  FV +     A
Sbjct: 85  ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144

Query: 114 LAAVKAL 120
             A+ AL
Sbjct: 145 QEAISAL 151

>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 =  168 bits (428), Expect = 3e-52
 Identities = 38/172 (22%), Positives = 74/172 (43%), Gaps = 14/172 (8%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTN--KCRGYGFVDFESGGYALAA 116
             +++  + +  ++KDL  +  QYG +     + D++ N  + +G  FV F +   AL A
Sbjct: 4   IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63

Query: 117 VKALQDKGIHAQMA-----------RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVV 165
             AL +  +   M            +    +   L+I  +     E D+  + + +  + 
Sbjct: 64  QNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIE 123

Query: 166 STRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGS-TLPGSKEPLLVKFAD 216
             RILR  +  S+G  F    ++      I+  + + T+ G   P++VKFAD
Sbjct: 124 ECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 175

>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 = 65.7 bits (161), Expect = 3e-13
 Identities = 24/101 (23%), Positives = 39/101 (38%), Gaps = 7/101 (6%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD---NNNTSKGVGFARLESKDKCD 192
           D   +++  +P  + E DL  L  +Y  V    +LRD   N   SKG  F    ++    
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 193 QMIQLFNGS-TLPGSKEPLLVKFADSGLKKRGAGAGGPNIY 232
           +     +    LPG   P+ +K ADS             ++
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDR---KLF 99

>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 =  120 bits (304), Expect = 1e-34
 Identities = 55/111 (49%), Positives = 75/111 (67%), Gaps = 6/111 (5%)

Query: 113 ALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD 172
             +    L+  G+ AQMA+QQEQDPTNLYI+NLPL+  E +LE++L  +  V+STRILRD
Sbjct: 1   GSSGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD 60

Query: 173 NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPG------SKEPLLVKFADS 217
           ++ TS+GVGFAR+ES +KC+ +I  FNG  +          EPLL KF+  
Sbjct: 61  SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGP 111

>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 = 70.7 bits (174), Expect = 1e-15
 Identities = 24/88 (27%), Positives = 35/88 (39%), Gaps = 1/88 (1%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           TNLYI  L     +++L NM   +G +IST+ + D  +   RG GF   ES     A + 
Sbjct: 26  TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIG 84

Query: 119 ALQDKGIHAQMARQQEQDPTNLYIANLP 146
               K I          +P     +   
Sbjct: 85  HFNGKFIKTPPGVSAPTEPLLCKFSGPS 112

>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 =  124 bits (313), Expect = 6e-34
 Identities = 31/170 (18%), Positives = 57/170 (33%), Gaps = 13/170 (7%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           +   L +  L    T +    +   +G +     +  + T + +GYGF ++     A  A
Sbjct: 94  TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153

Query: 117 VKALQDKGIH--------AQM--ARQQEQDPTNLYIANLPLNFKECD-LESLLAKYVTVV 165
              L  K +                        L +  LP  F + D L   L+   +  
Sbjct: 154 KSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPT 213

Query: 166 STRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
             ++    +   KG      E+ +  ++  Q  +G +L GS   L V F 
Sbjct: 214 FCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGS--HLRVSFC 261

>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 =  113 bits (286), Expect = 5e-30
 Identities = 41/178 (23%), Positives = 71/178 (39%), Gaps = 12/178 (6%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           ++  + IRGL  D T++++ ++ S Y        +     +K +G  FV   +G  A AA
Sbjct: 21  NRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAA 73

Query: 117 VKALQDKGIHAQMARQQEQDP-TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NN 174
           + A     +  +    Q Q     L +ANLP +  +   E L+  + ++    ++     
Sbjct: 74  INAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERT 133

Query: 175 NTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIY 232
             SKG GFA    KD   +      G  L      L V + D+G +   A      + 
Sbjct: 134 GQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR--TLYVHWTDAG-QLTPALLHSRCLC 188

>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 = 66.2 bits (162), Expect = 1e-12
 Identities = 12/77 (15%), Positives = 24/77 (31%), Gaps = 2/77 (2%)

Query: 53  PEQLSKTNLYIRGLTQDTTDKD-LINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           P  L    L +  L     D D L    S        +    +   + +G+  +++E+  
Sbjct: 179 PALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAE 237

Query: 112 YALAAVKALQDKGIHAQ 128
            A  A +      +   
Sbjct: 238 MAEEAQQQADGLSLGGS 254

>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 = 46.1 bits (110), Expect = 5e-06
 Identities = 19/101 (18%), Positives = 38/101 (37%), Gaps = 10/101 (9%)

Query: 120 LQDKGIHAQMARQQEQ--DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTS 177
           L  + I  ++   + Q  +   + I  LP +    ++  LL+ Y       +     +  
Sbjct: 3   LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDY------ELKYCFVDKY 56

Query: 178 KGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSG 218
           KG  F  L + ++ +  I  F+ S L      L V+   + 
Sbjct: 57  KGTAFVTLLNGEQAEAAINAFHQSRLRER--ELSVQLQPTD 95

>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 =  122 bits (309), Expect = 1e-33
 Identities = 37/211 (17%), Positives = 72/211 (34%), Gaps = 9/211 (4%)

Query: 50  PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           P       +  L++  L  D T++D   +  +YG         D      RG+GF+  ES
Sbjct: 14  PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLES 67

Query: 110 GGYALAAVKALQDKGIHAQMARQQEQDPT-NLYIANLPLNFKECDLESLLAKYVTVVSTR 168
              A  A   L    + ++  R +       L + NL        LE   +++  V    
Sbjct: 68  RTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAV 127

Query: 169 ILRDNNNTSKGVGFARLESKDKCDQMIQLFNGST--LPGSKEPLLVKFADSGLKKRGAGA 226
           ++ D+   + G GF    +K    + ++        L  +  P++V+  +    + G   
Sbjct: 128 VVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPE 187

Query: 227 GGPNIYRGPGAEVRLWGRDSADSQLAYEHPM 257
                 +    E     R +      +E+  
Sbjct: 188 KLMQKTQQYHKEREQPPRFAQPGTFEFEYAS 218

>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 =  114 bits (287), Expect = 5e-30
 Identities = 35/182 (19%), Positives = 64/182 (35%), Gaps = 17/182 (9%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           T + ++ L +      +       GPII           K   +  ++F     ALAA+ 
Sbjct: 42  TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAIT 99

Query: 119 ALQ----DKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKY-VTVVSTRILRDN 173
                     I      +       L++ N P ++ + ++  LL    V  +S R+    
Sbjct: 100 KTHKVVGQNEIIVSHLTE-----CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR 154

Query: 174 NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKK---RGAGAGGPN 230
            NTS+   +  + SK+     ++  NG  + G    L+ K ++   K      A   G  
Sbjct: 155 FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG--YTLVTKVSNPLEKSKRTDSATLEGRE 212

Query: 231 IY 232
           I 
Sbjct: 213 IM 214

>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 =  112 bits (283), Expect = 2e-29
 Identities = 28/181 (15%), Positives = 59/181 (32%), Gaps = 20/181 (11%)

Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
             L++  L++       T +++ ++      +  +  +     N  R + ++D  S   A
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 172

Query: 114 LAAVKALQDKGIH--------AQMARQQEQDP------TNLYIANLPLNF-KECDLESLL 158
              V+ L    I         +    + ++          + I NL      E  L    
Sbjct: 173 RYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESF 232

Query: 159 AKYVTVVSTRILRDNNNT--SKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD 216
             + ++    I         +    F   E+KD  ++ +Q+ N S L      + V  AD
Sbjct: 233 EGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQM-NRSLLGNR--EISVSLAD 289

Query: 217 S 217
            
Sbjct: 290 K 290

>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 = 48.8 bits (117), Expect = 6e-07
 Identities = 12/105 (11%), Positives = 26/105 (24%), Gaps = 7/105 (6%)

Query: 100 RGYGFVDFESGGYALAAVKALQD----KGIHAQMARQQEQDPTNLYIANLPLNFKECDLE 155
             YG          L            K  +  + R +E   T + + NLP ++ +  + 
Sbjct: 2   MEYGHHARPDSKRPLDEGSPAAAGLTSKKANEALTRNREL--TTVLVKNLPKSYNQNKVY 59

Query: 156 SLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNG 200
                   ++   +       +           D     I   + 
Sbjct: 60  KYFKHCGPIIHVDVADSLKK-NFRFARIEFARYDGALAAITKTHK 103

>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 =  108 bits (272), Expect = 5e-29
 Identities = 32/187 (17%), Positives = 70/187 (37%), Gaps = 20/187 (10%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           GS          +  NL+I  L  + +  +L    S+         ++D  T   R +G+
Sbjct: 1   GSHMVEGSEST-TPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGY 58

Query: 105 VDFESGGYALAAVKA----LQDKGIHAQMARQQEQ----DPTNLYIANLPLNFKECDLES 156
           VDFES      A++     +    I  +  + ++         L   NL  N  E +L+ 
Sbjct: 59  VDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKE 118

Query: 157 LLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD 216
           +    + +         +  SKG+ +   +S+   ++ ++   G+ + G    + + +  
Sbjct: 119 VFEDALEIRL----VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGR--SVSLYYT- 171

Query: 217 SGLKKRG 223
               ++G
Sbjct: 172 ---GEKG 175

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 61.5 bits (150), Expect = 8e-12
 Identities = 15/102 (14%), Positives = 39/102 (38%), Gaps = 5/102 (4%)

Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
             +   P NL+I NL  N    +L+  +++        ++     T++  G+   ES + 
Sbjct: 7   GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED 66

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIY 232
            ++ ++L  G  + G+   + ++      +          + 
Sbjct: 67  LEKALEL-TGLKVFGN--EIKLEKPKG--RDSKKVRAARTLL 103

>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 =  106 bits (268), Expect = 4e-28
 Identities = 41/179 (22%), Positives = 75/179 (41%), Gaps = 13/179 (7%)

Query: 46  SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
               P+ P      +LY+  L  D T+  L    S  GPI+S +   D  T +  GY +V
Sbjct: 4   GSMNPSAPSY-PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62

Query: 106 DFESGGYALAAVKA-----LQDKGIHAQMARQQEQ----DPTNLYIANLPLNFKECDLES 156
           +F+    A  A+       ++ K +    +++          N++I NL  +     L  
Sbjct: 63  NFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 122

Query: 157 LLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
             + +  ++S +++ D  N SKG GF   E+++  ++ I+  NG  L      + V   
Sbjct: 123 TFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAIEKMNGMLLND--RKVFVGRF 178

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  106 bits (267), Expect = 6e-28
 Identities = 38/225 (16%), Positives = 72/225 (32%), Gaps = 28/225 (12%)

Query: 31  GGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKA 90
           G      T   Q                + +Y+  +  +  +  +    + +GPI S   
Sbjct: 1   GSHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDM 60

Query: 91  ILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH------------------AQMARQ 132
             D  T K +G+ FV++E    A  A++ +    +                        +
Sbjct: 61  SWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAE 120

Query: 133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKC 191
           + +    +Y+A++  +  + D++S+   +  + S  + RD      KG GF   E     
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS 180

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPG 236
              +   N   L G  + L V  A             P     PG
Sbjct: 181 QDAVSSMNLFDLGG--QYLRVGKA----VTPPMPLLTPA---TPG 216

>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 =  101 bits (255), Expect = 1e-27
 Identities = 47/74 (63%), Positives = 57/74 (77%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           + LYIRGL   TTD+DL+ +C  YG I+STKAILDKTTNKC+GYGFVDF+S   A  AV 
Sbjct: 6   SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65

Query: 119 ALQDKGIHAQMARQ 132
           AL+  G+ AQMA+Q
Sbjct: 66  ALKASGVQAQMAKQ 79

>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 = 61.8 bits (151), Expect = 9e-13
 Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 1/71 (1%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDKCDQM 194
             + LYI  L     + DL  L   Y  +VST+ + D   N  KG GF   +S     + 
Sbjct: 4   GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63

Query: 195 IQLFNGSTLPG 205
           +     S +  
Sbjct: 64  VTALKASGVQA 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 =  100 bits (251), Expect = 6e-27
 Identities = 27/102 (26%), Positives = 47/102 (46%), Gaps = 2/102 (1%)

Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLE 186
           +  +  +      L++  L     E D+  L   +  +    +LR  + +SKG  F +  
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFS 64

Query: 187 SKDKCDQMIQLFNGS-TLPGSKEPLLVKFADSGLKKRGAGAG 227
           S  +    I   +GS T+PG+   L+VKFAD+  K+ G  +G
Sbjct: 65  SHTEAQAAIHALHGSQTMPGASSSLVVKFADTD-KESGPSSG 105

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 72.3 bits (178), Expect = 3e-16
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 45  GSPGTPTGPEQLSK-TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           GS G+     +  +   L++  L +  +++D++ +   +G I     +L       +G  
Sbjct: 1   GSSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECT-VLRGPDGSSKGCA 59

Query: 104 FVDFESGGYALAAVKALQDK 123
           FV F S   A AA+ AL   
Sbjct: 60  FVKFSSHTEAQAAIHALHGS 79

>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 =  102 bits (257), Expect = 6e-27
 Identities = 39/170 (22%), Positives = 77/170 (45%), Gaps = 11/170 (6%)

Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
           ++  K  ++I GL  DTT+ +L     +YG +   K + D  T + RG+GF+ FE     
Sbjct: 1   KESCK--MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSV 58

Query: 114 LAAVKA---LQDKGIHAQMA--RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTR 168
              VK    L  K I  + A  R ++     +++  +  + +  + E   +++ T++  +
Sbjct: 59  DEVVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 118

Query: 169 ILRD-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
           ++ D +   S+G GF   +S D  D++ Q             + +K A+ 
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDR--KIEIKRAEP 165

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 66.0 bits (162), Expect = 2e-13
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 53  PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
            EQ     +++ G+  D   K+     SQ+G II  + +LDK T + RG+GFV ++S   
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS--- 138

Query: 113 ALAAVKALQDKGI 125
           A A  +  Q+K I
Sbjct: 139 ADAVDRVCQNKFI 151

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 97.4 bits (243), Expect = 1e-24
 Identities = 48/198 (24%), Positives = 85/198 (42%), Gaps = 20/198 (10%)

Query: 49  TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           +P  PEQL K  L+I GL+ +TTD+ L +   Q+G +     + D  T + RG+GFV + 
Sbjct: 6   SPKEPEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63

Query: 109 SGGYALAAVKA----LQDKGIHAQMA--RQQEQDPTN------LYIANLPLNFKECDLES 156
           +     AA+ A    +  + +  + A  R+  Q P        +++  +  + +E  L  
Sbjct: 64  TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 123

Query: 157 LLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
              +Y  +    I+ D  +   +G  F   +  D  D+++      T+ G      V+ A
Sbjct: 124 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHN--CEVRKA 180

Query: 216 DSGLKKRGAGAGGPNIYR 233
            S  K+  A A      R
Sbjct: 181 LS--KQEMASASSSQRGR 196

>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 = 95.3 bits (238), Expect = 3e-24
 Identities = 44/165 (26%), Positives = 73/165 (44%), Gaps = 13/165 (7%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           LY+  L +  T+  L       GPI + K ++DK  NK   Y FV++     A  A++ L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 121 QDKGIH--------AQMARQQEQDPT-NLYIANLPLNFKECDLESLLAKYVTVVSTRILR 171
             K I         A  ++Q   D T NL++ +L +N  +  L +    + + +S  ++ 
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121

Query: 172 D-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
           D    +S+G GF    S+D     +    G  L G   PL + +A
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG--RPLRINWA 164

>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 = 58.7 bits (143), Expect = 7e-11
 Identities = 20/62 (32%), Positives = 30/62 (48%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           NL++  L  +  D+ L N    +   +S   + D  T   RGYGFV F S   A  A+ +
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148

Query: 120 LQ 121
           +Q
Sbjct: 149 MQ 150

>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 = 51.0 bits (123), Expect = 5e-08
 Identities = 16/93 (17%), Positives = 33/93 (35%), Gaps = 4/93 (4%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           LY+ NL     E  L+        + + +I+ D NN +    F         +  +Q  N
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 200 GSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIY 232
           G  +  +   + + +A    +         N++
Sbjct: 63  GKQIENN--IVKINWAFQSQQSSSDDTF--NLF 91

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 93.4 bits (233), Expect = 2e-23
 Identities = 35/171 (20%), Positives = 66/171 (38%), Gaps = 14/171 (8%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKA-----ILDKTTNKCRGYGFVDFESGG 111
           S   LY+  +    T++ +++  +    +          +L    N+ + + F++F S  
Sbjct: 3   SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 112 YALAAVKA----LQDKGIHAQMA--RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVV 165
               A+       Q + +  +     Q       L+I  LP    +  ++ LL  +  + 
Sbjct: 63  ETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLK 122

Query: 166 STRILRD-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
           +  +++D     SKG  F      +  DQ I   NG  L G K  LLV+ A
Sbjct: 123 AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL-GDK-KLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 63.0 bits (154), Expect = 3e-12
 Identities = 14/68 (20%), Positives = 26/68 (38%)

Query: 53  PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
                   L+I GL     D  +  + + +GP+ +   + D  T   +GY F ++     
Sbjct: 89  QPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV 148

Query: 113 ALAAVKAL 120
              A+  L
Sbjct: 149 TDQAIAGL 156

>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 = 88.9 bits (221), Expect = 2e-21
 Identities = 35/192 (18%), Positives = 67/192 (34%), Gaps = 34/192 (17%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIIS-----TKAILDKTTNKCRGYGFVDFESGGYALA 115
           LY+  +    T++ +++  +    +          +L    N+ + + F++F S      
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 116 AVKA----LQDKGIHAQMARQQEQ----------------------DPTNLYIANLPLNF 149
           A+       Q + +  +     +                           L+I  LP   
Sbjct: 67  AMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYL 126

Query: 150 KECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKE 208
            +  ++ LL  +  + +  +++D     SKG  F      +  DQ I   NG  L G K 
Sbjct: 127 NDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL-GDK- 184

Query: 209 PLLVKFADSGLK 220
            LLV+ A  G K
Sbjct: 185 KLLVQRASVGAK 196

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 64.3 bits (157), Expect = 1e-12
 Identities = 17/75 (22%), Positives = 30/75 (40%)

Query: 46  SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
            PG  +     S   L+I GL     D  +  + + +GP+ +   + D  T   +GY F 
Sbjct: 102 VPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 161

Query: 106 DFESGGYALAAVKAL 120
           ++        A+  L
Sbjct: 162 EYVDINVTDQAIAGL 176

>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 = 86.1 bits (214), Expect = 3e-21
 Identities = 30/115 (26%), Positives = 50/115 (43%), Gaps = 19/115 (16%)

Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           GP      N++I+ L +   +K L +  S +G I+S K + D   N  +GYGFV FE+  
Sbjct: 1   GPL--GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQE 56

Query: 112 YALAAVKA-----LQDKGIHAQMAR----------QQEQDPTNLYIANLPLNFKE 151
            A  A++      L D+ +     +           + ++ TN+YI N       
Sbjct: 57  AAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTR 111

>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 = 55.3 bits (134), Expect = 4e-10
 Identities = 21/103 (20%), Positives = 41/103 (39%), Gaps = 7/103 (6%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
              N++I NL  +     L    + +  ++S +++ D  N SKG GF   E+++  ++ I
Sbjct: 4   GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAI 62

Query: 196 QLFNGSTLPGSKEPLLVKFA----DSGLKKRGAGAGGPNIYRG 234
           +  NG  L      + V       +   +         N+Y  
Sbjct: 63  EKMNGMLLNDR--KVFVGRFKSRKEREAELGARAKEFTNVYIK 103

>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 = 83.1 bits (206), Expect = 3e-20
 Identities = 26/109 (23%), Positives = 51/109 (46%), Gaps = 5/109 (4%)

Query: 37  TTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTT 96
            ++ +         +  E     NL+I  L Q+  D+DL+ M   +G ++S K  +DK T
Sbjct: 4   GSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT 63

Query: 97  NKCRGYGFVDFESGGYALAAVKAL-----QDKGIHAQMARQQEQDPTNL 140
           N  + +GFV +++   A AA++++       K +  Q+ R +    +  
Sbjct: 64  NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGP 112

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 60.4 bits (147), Expect = 7e-12
 Identities = 30/111 (27%), Positives = 49/111 (44%), Gaps = 3/111 (2%)

Query: 119 ALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTS 177
            L  + I A  ++++  +  NL+I +LP  F + DL  +   +  VVS ++  D   N S
Sbjct: 7   GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS 66

Query: 178 KGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
           K  GF   ++       IQ  NG  + G K  L V+   S    +   + G
Sbjct: 67  KCFGFVSYDNPVSAQAAIQSMNGFQI-GMK-RLKVQLKRSKNDSKSGPSSG 115

>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 = 83.3 bits (206), Expect = 6e-20
 Identities = 34/119 (28%), Positives = 48/119 (40%), Gaps = 13/119 (10%)

Query: 37  TTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTT 96
                Q    P T   PE     NL +  +     +  L  +  +YGPI S K + D+ T
Sbjct: 21  QLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRET 80

Query: 97  NKCRGYGFVDFESGGYALAAVKAL-----QDKGIHAQMARQQEQDP--------TNLYI 142
            + RGYGFV F+SG  A  A+  L      +K +   +A    Q P         N Y+
Sbjct: 81  RQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 59.4 bits (144), Expect = 3e-11
 Identities = 30/123 (24%), Positives = 47/123 (38%), Gaps = 5/123 (4%)

Query: 113 ALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD 172
            L  ++  Q + I       +     NL +  +P    E  L  L  +Y  + S +I+ D
Sbjct: 18  QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77

Query: 173 -NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKK--RGAGAGGP 229
                S+G GF + +S     Q I   NG  +    + L V  A SG ++       G  
Sbjct: 78  RETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN--KRLKVALAASGHQRPGIAGAVGDG 135

Query: 230 NIY 232
           N Y
Sbjct: 136 NGY 138

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 81.6 bits (202), Expect = 1e-19
 Identities = 27/94 (28%), Positives = 45/94 (47%)

Query: 27  GSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPII 86
            +    T P+ +  +    +       E     NL+I  L Q+ TD DL +    +G +I
Sbjct: 9   SASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVI 68

Query: 87  STKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           S K  +DK T+  + +GFV F++   A  A+KA+
Sbjct: 69  SAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 59.3 bits (144), Expect = 2e-11
 Identities = 27/99 (27%), Positives = 44/99 (44%), Gaps = 3/99 (3%)

Query: 118 KALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNT 176
            AL      A   + +  +  NL+I +LP  F + DL S    +  V+S ++  D   + 
Sbjct: 21  VALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSL 80

Query: 177 SKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
           SK  GF   ++ D     I+  NG  + G+K  L V+  
Sbjct: 81  SKCFGFVSFDNPDSAQVAIKAMNGFQV-GTK-RLKVQLK 117

>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 = 76.6 bits (189), Expect = 7e-18
 Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 1/88 (1%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           GS G+    +      L+I  + ++  +KDL  +  ++G I     + D+ T   +G  F
Sbjct: 1   GSSGSSGMKDH-DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAF 59

Query: 105 VDFESGGYALAAVKALQDKGIHAQMARQ 132
           + +     AL A  AL ++     M R 
Sbjct: 60  LTYCERESALKAQSALHEQKTLPGMNRP 87

>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 = 75.4 bits (186), Expect = 2e-17
 Identities = 25/99 (25%), Positives = 42/99 (42%), Gaps = 2/99 (2%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDK 190
            ++ D   L+I  +P N  E DL+ L  ++  +    +L+D      KG  F     ++ 
Sbjct: 8   MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERES 67

Query: 191 CDQMIQLFNGS-TLPGSKEPLLVKFADSGLKKRGAGAGG 228
             +     +   TLPG   P+ VK ADS  +     + G
Sbjct: 68  ALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSGPSSG 106

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 76.3 bits (188), Expect = 1e-17
 Identities = 17/71 (23%), Positives = 26/71 (36%)

Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
              +    L  +  +  L +MC +YG +   + +L   T K  G   V F S   A   V
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 118 KALQDKGIHAQ 128
           K L    +   
Sbjct: 66  KNLHLTSVMGN 76

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 57.4 bits (139), Expect = 8e-11
 Identities = 14/87 (16%), Positives = 31/87 (35%), Gaps = 3/87 (3%)

Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMI 195
              +  A L  N +E  L+ +  KY  V    IL         G+      S     + +
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65

Query: 196 QLFNGSTLPGSKEPLLVKFADSGLKKR 222
           +  + +++ G+   +  +    G ++ 
Sbjct: 66  KNLHLTSVMGN--IIHAQLDIKGQQRM 90

>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 = 74.2 bits (183), Expect = 4e-17
 Identities = 21/80 (26%), Positives = 37/80 (46%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           +      +G    SK+ +Y+  L    T+ DL  + S+YG ++    + DK T K +G  
Sbjct: 2   SSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVA 61

Query: 104 FVDFESGGYALAAVKALQDK 123
           F+ F     A    +A+ +K
Sbjct: 62  FILFLDKDSAQNCTRAINNK 81

>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 = 56.1 bits (136), Expect = 1e-10
 Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 129 MARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLES 187
           M+       + +Y++NLP +    DL  + +KY  VV   I++D +   SKGV F     
Sbjct: 8   MSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLD 67

Query: 188 KDKCDQMIQLFNGSTLPG 205
           KD      +  N   L G
Sbjct: 68  KDSAQNCTRAINNKQLFG 85

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 74.7 bits (184), Expect = 4e-17
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 2/79 (2%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           GS G P+   +     ++IR L+ D+ ++ L  +  Q+G +   + +L   T   +G  F
Sbjct: 4   GSSGLPSDVTEGKT--VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61

Query: 105 VDFESGGYALAAVKALQDK 123
             F +   A   + A   +
Sbjct: 62  AQFMTQEAAQKCLAAASLE 80

>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 = 48.1 bits (115), Expect = 2e-07
 Identities = 20/103 (19%), Positives = 41/103 (39%), Gaps = 9/103 (8%)

Query: 133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDKC 191
              +   ++I NL  + +E  L  +L ++  +   R++   +   SKG  FA+  +++  
Sbjct: 11  DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70

Query: 192 DQMIQLFNGSTLPGSKE----PLLVKFADSGLKKRGAGAGGPN 230
            + +   +     G  +     L V  A      R   A GP+
Sbjct: 71  QKCLAAASLEAEGGGLKLDGRQLKVDLA----VTRDEAASGPS 109

>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 = 76.0 bits (187), Expect = 6e-17
 Identities = 18/82 (21%), Positives = 35/82 (42%)

Query: 42  QHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRG 101
             +     P     +    L++  + ++  + ++      YG I +    LD+ T   +G
Sbjct: 56  NEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG 115

Query: 102 YGFVDFESGGYALAAVKALQDK 123
           Y  V++E+   ALAA +AL   
Sbjct: 116 YALVEYETHKQALAAKEALNGA 137

>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 = 46.7 bits (111), Expect = 1e-06
 Identities = 17/117 (14%), Positives = 44/117 (37%), Gaps = 4/117 (3%)

Query: 100 RGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLA 159
           RG+G  D  +     +  +   +     +   Q+  +   L++ ++    +E +++    
Sbjct: 36  RGFG-SDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFC 94

Query: 160 KYVTVVSTRILRDNN-NTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
            Y  + +  +  D     SKG      E+  +     +  NG+ + G  + + V + 
Sbjct: 95  DYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG--QTIQVDWC 149

>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 = 73.4 bits (181), Expect = 9e-17
 Identities = 25/98 (25%), Positives = 38/98 (38%), Gaps = 6/98 (6%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           GS G+  GP+      L +  LT  T+   L  +  +YG +       +  T   RG+ F
Sbjct: 1   GSSGSS-GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAF 59

Query: 105 VDFESGGYALAAVKALQDKG-----IHAQMARQQEQDP 137
           V F     A  A  A+         +  Q+AR   +D 
Sbjct: 60  VRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDL 97

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 20/97 (20%), Positives = 31/97 (31%), Gaps = 3/97 (3%)

Query: 133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKC 191
                  L + NL        L  +  KY  V    I R+ +    +G  F R   +   
Sbjct: 9   DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
                  +G+ L G    L V+ A  G +     + G
Sbjct: 69  QDAEAAMDGAELDG--RELRVQVARYGRRDLSGPSSG 103

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 73.0 bits (180), Expect = 1e-16
 Identities = 21/99 (21%), Positives = 40/99 (40%), Gaps = 7/99 (7%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           +GS G     +      + +  L++DT + DL  +   +G I       DKTT + +G+ 
Sbjct: 3   SGSSGPNRRAD--DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60

Query: 104 FVDFESGGYALAAVKALQDKG-----IHAQMARQQEQDP 137
           F+ F     A  A+  +   G     ++ + A+      
Sbjct: 61  FISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSG 99

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 52.2 bits (126), Expect = 4e-09
 Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 1/80 (1%)

Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARL 185
           +    ++  D   + + NL  + +E DL+ L   + ++    + +D     SKG  F   
Sbjct: 5   SSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64

Query: 186 ESKDKCDQMIQLFNGSTLPG 205
             ++   + I   +G     
Sbjct: 65  HRREDAARAIAGVSGFGYDH 84

>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 = 75.5 bits (185), Expect = 2e-16
 Identities = 30/205 (14%), Positives = 55/205 (26%), Gaps = 53/205 (25%)

Query: 59  TNLYIRGLTQDTTDKD-LINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
             L + GL Q   + D + N+   YG +   K +  K      G   V+   G     A+
Sbjct: 5   PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAI 59

Query: 118 KALQDKGIHAQ-----MARQQEQDP----------------------------------- 137
             L +  +  Q     +++Q    P                                   
Sbjct: 60  THLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRI 119

Query: 138 ----TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDKCD 192
                 L+  N PL   E +   +  +      T +   +  +     G    +SK    
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179

Query: 193 QMIQLFNGSTLPGS--KEPLLVKFA 215
           + +   N   +       P  +K  
Sbjct: 180 ETLGFLNHYQMKNPNGPYPYTLKLC 204

>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 = 62.4 bits (151), Expect = 8e-12
 Identities = 16/119 (13%), Positives = 36/119 (30%)

Query: 8   RVSNATSPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLT 67
            V  +  PA     S               + N + +          Q     L+     
Sbjct: 73  NVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAP 132

Query: 68  QDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
            + T+++   +C + G    T   +    ++    G ++++S   AL  +  L    + 
Sbjct: 133 LEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMK 191

>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 = 72.8 bits (179), Expect = 3e-16
 Identities = 27/111 (24%), Positives = 45/111 (40%)

Query: 16  ANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDL 75
           ++ H   SS    +      +T       GS              L + GL+  TT++DL
Sbjct: 4   SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDL 63

Query: 76  INMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
             + S+YGPI     + D+ + + RG+ FV FE+   A  A +      + 
Sbjct: 64  REVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD 114

>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 = 49.0 bits (117), Expect = 1e-07
 Identities = 21/86 (24%), Positives = 31/86 (36%), Gaps = 1/86 (1%)

Query: 121 QDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKG 179
             +G      R        L +  L L   E DL  + +KY  +    I+ D     S+G
Sbjct: 30  MGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG 89

Query: 180 VGFARLESKDKCDQMIQLFNGSTLPG 205
             F   E+ D   +  +  NG  L G
Sbjct: 90  FAFVYFENVDDAKEAKERANGMELDG 115

>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 = 74.5 bits (183), Expect = 3e-16
 Identities = 32/207 (15%), Positives = 65/207 (31%), Gaps = 52/207 (25%)

Query: 56  LSKTNLYIRGLTQDT-TDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYAL 114
           +  + L +  L  +  T + L  +   YG +   K + +K     +    V    G  A 
Sbjct: 1   MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQ 55

Query: 115 AAVKALQ-----DKGIHAQMARQQEQDP-------------------------------- 137
            A+  L       K I   +++ Q                                    
Sbjct: 56  LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 115

Query: 138 -----TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCD 192
                  L+++N+P +  E DL+ L +    VV        +   + +   ++ S ++  
Sbjct: 116 IFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD---RKMALIQMGSVEEAV 172

Query: 193 QMIQLFNGSTLPGSKEPLLVKFADSGL 219
           Q +   +   L  +   L V F+ S +
Sbjct: 173 QALIDLHNHDLGENH-HLRVSFSKSTI 198

>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 = 59.9 bits (145), Expect = 5e-11
 Identities = 16/115 (13%), Positives = 39/115 (33%), Gaps = 6/115 (5%)

Query: 14  SPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTN--LYIRGLTQDTT 71
           + +   +      G ++ G      N+  H          + +   +  L++  +    +
Sbjct: 74  TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVS 133

Query: 72  DKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
           ++DL  + S  G ++       K   K R    +   S   A+ A+  L +  + 
Sbjct: 134 EEDLKVLFSSNGGVVKGF----KFFQKDRKMALIQMGSVEEAVQALIDLHNHDLG 184

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 71.6 bits (176), Expect = 6e-16
 Identities = 19/100 (19%), Positives = 40/100 (40%), Gaps = 7/100 (7%)

Query: 27  GSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPII 86
           GS       I    +  + +PG P          LY++ L+   T++DL+++ +++    
Sbjct: 1   GSSGSSGEEIRKIPMFSSYNPGEPN-------KVLYLKNLSPRVTERDLVSLFARFQEKK 53

Query: 87  STKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
                    T + RG  F+ F +   A  A+  +    ++
Sbjct: 54  GPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLY 93

>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 = 48.8 bits (117), Expect = 9e-08
 Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 4/89 (4%)

Query: 129 MARQQEQDPT-NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLE 186
            +     +P   LY+ NL     E DL SL A++       I         +G  F    
Sbjct: 16  FSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFP 75

Query: 187 SKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
           +K+   Q + L NG  L G  + L+++F 
Sbjct: 76  NKEIAWQALHLVNGYKLYG--KILVIEFG 102

>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 = 71.1 bits (175), Expect = 7e-16
 Identities = 22/92 (23%), Positives = 44/92 (47%), Gaps = 6/92 (6%)

Query: 52  GPEQLSKTN-LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESG 110
           G    S +  L++R L+  ++++DL  + S YGP+      +D  T K +G+ FV F   
Sbjct: 1   GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60

Query: 111 GYALAAVKAL-----QDKGIHAQMARQQEQDP 137
            +A+ A   +     Q + +H   +  +++  
Sbjct: 61  EHAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>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 = 46.1 bits (110), Expect = 6e-07
 Identities = 15/75 (20%), Positives = 23/75 (30%), Gaps = 1/75 (1%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDK 190
                   L++ NL     E DLE L + Y  +       D+     KG  F      + 
Sbjct: 3   SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62

Query: 191 CDQMIQLFNGSTLPG 205
             +     +G    G
Sbjct: 63  AVKAYAEVDGQVFQG 77

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 70.8 bits (174), Expect = 7e-16
 Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 3/73 (4%)

Query: 53  PEQLSKTNLYIRGLTQDTTDKDLINMCSQYG--PIISTKAILDKTTNKCRGYGFVDFESG 110
                 T + +R +   T    ++   S Y    + + + I DK T + RG+ FV   S 
Sbjct: 5   HHHHMDT-IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSA 63

Query: 111 GYALAAVKALQDK 123
             A   ++ LQ  
Sbjct: 64  MDASQLLQILQSL 76

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 18/95 (18%), Positives = 38/95 (40%), Gaps = 5/95 (5%)

Query: 129 MARQQEQDPTNLYIANLPLNFKECDLESLLAKY--VTVVSTRILRD-NNNTSKGVGFARL 185
           M          + + N+  +     + + L+ Y  + V + R+++D     ++G  F +L
Sbjct: 1   MGHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQL 60

Query: 186 ESKDKCDQMIQLFNGSTLPGSKE--PLLVKFADSG 218
            S     Q++Q+      P   +   + V FA S 
Sbjct: 61  SSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKSA 95

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 72.1 bits (177), Expect = 8e-16
 Identities = 24/77 (31%), Positives = 35/77 (45%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
                  +G    +K  LY+ GL ++  DK L      +G I   +  LD  T K RG+ 
Sbjct: 49  GSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 108

Query: 104 FVDFESGGYALAAVKAL 120
           FV+FE    A AA+  +
Sbjct: 109 FVEFELAEDAAAAIDNM 125

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 44.4 bits (105), Expect = 6e-06
 Identities = 14/77 (18%), Positives = 23/77 (29%), Gaps = 1/77 (1%)

Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESK 188
           +         LY+  L     +  L +    +  +   +I  D      +G  F   E  
Sbjct: 56  SGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 115

Query: 189 DKCDQMIQLFNGSTLPG 205
           +     I   N S L G
Sbjct: 116 EDAAAAIDNMNESELFG 132

>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 = 70.3 bits (173), Expect = 1e-15
 Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 5/80 (6%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           +GS G     ++ S   L + GL   TT++DL    S +G ++  +   D  T   +G+G
Sbjct: 3   SGSSGVKRAVQKTSD--LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60

Query: 104 FVDFESGGYALAAVKALQDK 123
           FV F         VK +  +
Sbjct: 61  FVRFTE---YETQVKVMSQR 77

>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 = 69.5 bits (171), Expect = 2e-15
 Identities = 24/72 (33%), Positives = 35/72 (48%)

Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           G    +K  LY+ GL ++  DK L      +G I   +  LD  T K RG+ FV+FE   
Sbjct: 1   GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60

Query: 112 YALAAVKALQDK 123
            A AA+  + + 
Sbjct: 61  DAAAAIDNMNES 72

>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 = 43.3 bits (103), Expect = 4e-06
 Identities = 16/78 (20%), Positives = 25/78 (32%), Gaps = 5/78 (6%)

Query: 129 MARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLES 187
           MA  +      LY+  L     +  L +    +  +   +I  D      +G  F   E 
Sbjct: 3   MATTK----RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 58

Query: 188 KDKCDQMIQLFNGSTLPG 205
            +     I   N S L G
Sbjct: 59  AEDAAAAIDNMNESELFG 76

>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 = 70.4 bits (173), Expect = 2e-15
 Identities = 25/77 (32%), Positives = 33/77 (42%)

Query: 43  HNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
            +GS G     +  + T +++ GL   TTD  L      +G I     I D+ T K RGY
Sbjct: 2   SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGY 61

Query: 103 GFVDFESGGYALAAVKA 119
           GFV       A  A K 
Sbjct: 62  GFVTMADRAAAERACKD 78

>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 = 69.9 bits (172), Expect = 2e-15
 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 50  PTGPEQLS--KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
            +G   ++  K  LY+ GL ++  DK L      +G I   +  LD  T K RG+ FV+F
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61

Query: 108 ESGGYALAAVKALQDK 123
           E    A AA+  + + 
Sbjct: 62  ELAEDAAAAIDNMNES 77

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 46.8 bits (112), Expect = 3e-07
 Identities = 19/99 (19%), Positives = 28/99 (28%), Gaps = 7/99 (7%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDK 190
                   LY+  L     +  L +    +  +   +I  D      +G  F   E  + 
Sbjct: 7   GMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 66

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGP 229
               I   N S L G    + V  A    K       GP
Sbjct: 67  AAAAIDNMNESELFG--RTIRVNLA----KPMRIKESGP 99

>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 = 69.6 bits (171), Expect = 2e-15
 Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 46  SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT-TNKCRGYGF 104
           S  +   P++ + + + +R +      +++  + S +G + + +     T T   RG+GF
Sbjct: 3   SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62

Query: 105 VDFESGGYALAAVKALQD 122
           VDF +   A  A  AL  
Sbjct: 63  VDFITKQDAKKAFNALCH 80

>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 = 56.2 bits (136), Expect = 2e-10
 Identities = 18/101 (17%), Positives = 45/101 (44%), Gaps = 5/101 (4%)

Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT--SKGVGFARLESK 188
             ++Q  + + + N+P    + ++  L + +  + + R+ +    T   +G GF    +K
Sbjct: 9   VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITK 68

Query: 189 DKCDQMIQ-LFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
               +    L + + L G    L++++ADS +  +   + G
Sbjct: 69  QDAKKAFNALCHSTHLYGR--RLVLEWADSEVTVQSGPSSG 107

>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 = 69.2 bits (170), Expect = 3e-15
 Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 7/88 (7%)

Query: 45  GSPGTPTGPEQLS-KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           GS G+  G +  + ++ L++  L  D T++++  +  +YG         DK      G+G
Sbjct: 1   GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFG 54

Query: 104 FVDFESGGYALAAVKALQDKGIHAQMAR 131
           F+  E+   A  A   L +  +  +  R
Sbjct: 55  FIRLETRTLAEIAKVELDNMPLRGKQLR 82

>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 = 54.6 bits (132), Expect = 5e-10
 Identities = 24/98 (24%), Positives = 38/98 (38%), Gaps = 7/98 (7%)

Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
            +     + L++ NLP +  E ++  L  KY       I +D     KG GF RLE++  
Sbjct: 9   EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTL 63

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
            +      +   L G    L V+FA          + G
Sbjct: 64  AEIAKVELDNMPLRGK--QLRVRFACHSASLTSGPSSG 99

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 70.5 bits (173), Expect = 3e-15
 Identities = 29/138 (21%), Positives = 48/138 (34%), Gaps = 17/138 (12%)

Query: 7   HRVSNATSPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGL 66
           H  S+   P  +H +S +       G                    P+    T+L +  L
Sbjct: 8   HHHSSGLVPRGSHMASMTGGQQMGRG------------SMSYGRPPPDVEGMTSLKVDNL 55

Query: 67  TQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG-- 124
           T  T+   L  +  +YG +       D+ T + RG+ FV F     A  A+ A+      
Sbjct: 56  TYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLD 115

Query: 125 ---IHAQMARQQEQDPTN 139
              +  QMAR      ++
Sbjct: 116 GRELRVQMARYGRPPDSH 133

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 47.4 bits (113), Expect = 4e-07
 Identities = 19/80 (23%), Positives = 28/80 (35%), Gaps = 1/80 (1%)

Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARL 185
                   +  T+L + NL        L  +  KY  V    I RD     S+G  F R 
Sbjct: 37  YGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRF 96

Query: 186 ESKDKCDQMIQLFNGSTLPG 205
             K   +  +   +G+ L G
Sbjct: 97  HDKRDAEDAMDAMDGAVLDG 116

>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 = 69.2 bits (170), Expect = 3e-15
 Identities = 18/67 (26%), Positives = 42/67 (62%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           S  ++++  +  + T++ L ++ S+ GP++S + + D+ T K +GYGF +++    AL+A
Sbjct: 7   SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66

Query: 117 VKALQDK 123
           ++ L  +
Sbjct: 67  MRNLNGR 73

>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 = 55.3 bits (134), Expect = 3e-10
 Identities = 25/103 (24%), Positives = 44/103 (42%), Gaps = 6/103 (5%)

Query: 133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKC 191
            ++   ++++ N+P    E  L+ + ++   VVS R++ D      KG GF   + ++  
Sbjct: 4   VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKK---RGAGAGGPNI 231
              ++  NG    G    L V  A S   K   +  G G P I
Sbjct: 64  LSAMRNLNGREFSG--RALRVDNAASEKNKEELKSLGTGAPVI 104

>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 = 69.2 bits (170), Expect = 3e-15
 Identities = 29/100 (29%), Positives = 48/100 (48%), Gaps = 8/100 (8%)

Query: 45  GSPGTPTGP--EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
           GS G  +GP  E+     +Y+ GL +  ++  L  +  Q GP+++T    D+ T + +GY
Sbjct: 1   GSSG-SSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGY 59

Query: 103 GFVDFESGGYALAAVKALQD-----KGIHAQMARQQEQDP 137
           GFV+F S   A  A+K +       K I    A    ++ 
Sbjct: 60  GFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNL 99

>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 = 45.7 bits (109), Expect = 8e-07
 Identities = 26/103 (25%), Positives = 44/103 (42%), Gaps = 5/103 (4%)

Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARL 185
           +    ++ QD T +Y+  L     E  L  L  +   VV+T + +D      +G GF   
Sbjct: 6   SGPISERNQDAT-VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64

Query: 186 ESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
            S++  D  I++ +   L G  +P+ V  A S   K  +G   
Sbjct: 65  LSEEDADYAIKIMDMIKLYG--KPIRVNKA-SAHNKNLSGPSS 104

>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 = 68.4 bits (168), Expect = 5e-15
 Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 2/80 (2%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           +GS G    P+      L + GL+  TT++DL  + S+YGPI     + D+ + + RG+ 
Sbjct: 3   SGSSGNRANPD--PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60

Query: 104 FVDFESGGYALAAVKALQDK 123
           FV FE+   A  A +     
Sbjct: 61  FVYFENVDDAKEAKERANGM 80

>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 = 51.8 bits (125), Expect = 5e-09
 Identities = 23/93 (24%), Positives = 35/93 (37%), Gaps = 3/93 (3%)

Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARL 185
           +   R        L +  L L   E DL  + +KY  +    I+ D  +  S+G  F   
Sbjct: 5   SSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 64

Query: 186 ESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSG 218
           E+ D   +  +  NG  L G    + V    SG
Sbjct: 65  ENVDDAKEAKERANGMELDG--RRIRVSGPSSG 95

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 68.4 bits (168), Expect = 6e-15
 Identities = 21/80 (26%), Positives = 44/80 (55%), Gaps = 1/80 (1%)

Query: 45  GSPGTPTGPEQ-LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
              G   GP++ +    L++ G+ ++ T++D+ +  ++YG I +    LD+ T   +GY 
Sbjct: 9   EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 68

Query: 104 FVDFESGGYALAAVKALQDK 123
            V++E+   A AA++ L  +
Sbjct: 69  LVEYETYKEAQAAMEGLNGQ 88

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 3/85 (3%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDK 190
           Q+  +   L++  +     E D+    A+Y  + +  +  D      KG      E+  +
Sbjct: 18  QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 77

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFA 215
               ++  NG  L G  +P+ V + 
Sbjct: 78  AQAAMEGLNGQDLMG--QPISVDWC 100

>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 = 68.0 bits (167), Expect = 6e-15
 Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 3/84 (3%)

Query: 45  GSPGTPTGP--EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
           GS G+      ++ +   +++  L     ++ L  +  Q GP+       D+   K + +
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSF 59

Query: 103 GFVDFESGGYALAAVKALQDKGIH 126
           GFV F+       A+  L    ++
Sbjct: 60  GFVCFKHPESVSYAIALLNGIRLY 83

>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 = 63.4 bits (155), Expect = 4e-13
 Identities = 23/92 (25%), Positives = 35/92 (38%), Gaps = 2/92 (2%)

Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLE 186
           + M   QE+    +++ NL    +E  L  L  +   +    I +D     K  GF   +
Sbjct: 6   SGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFK 65

Query: 187 SKDKCDQMIQLFNGSTLPGSKEPLLVKFADSG 218
             +     I L NG  L G   P+ V    SG
Sbjct: 66  HPESVSYAIALLNGIRLYGR--PINVSGPSSG 95

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 68.5 bits (168), Expect = 7e-15
 Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           +GS G       L K  L+I GL    T ++L  +C  +G +   + + ++   K +G  
Sbjct: 3   SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLA 61

Query: 104 FVDFESGGYALAAVKAL 120
           +V++E+   A  AV  +
Sbjct: 62  YVEYENESQASQAVMKM 78

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 20/101 (19%), Positives = 42/101 (41%), Gaps = 3/101 (2%)

Query: 123 KGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGF 182
            G           +   L+I+ LP +  + +LE +   + TV   R++ +     KG+ +
Sbjct: 3   SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAY 62

Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRG 223
              E++ +  Q +   +G T+      + V  ++SG    G
Sbjct: 63  VEYENESQASQAVMKMDGMTIKE--NIIKVAISNSG-PSSG 100

>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 = 71.6 bits (175), Expect = 7e-15
 Identities = 34/233 (14%), Positives = 70/233 (30%), Gaps = 56/233 (24%)

Query: 30  NGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDT-TDKDLINMCSQYGPIIST 88
           +        +++     PG          + L +  L  +  T + L  +   YG +   
Sbjct: 10  HSSGLVPRGSHMGRIAIPGLAGAG----NSVLLVSNLNPERVTPQSLFILFGVYGDVQRV 65

Query: 89  KAILDKTTNKCRGYGFVDFESGGYALAAVKALQ-----DKGIHAQMARQQEQDP------ 137
           K + +K     +    V    G  A  A+  L       K I   +++ Q          
Sbjct: 66  KILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQE 120

Query: 138 -------------------------------TNLYIANLPLNFKECDLESLLAKYVTVVS 166
                                            L+++N+P +  E DL+ L +    VV 
Sbjct: 121 DQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK 180

Query: 167 TRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGL 219
                  +   + +   ++ S ++  Q +   +   L  +   L V F+ S +
Sbjct: 181 GFKFFQKD---RKMALIQMGSVEEAVQALIDLHNHDLGENH-HLRVSFSKSTI 229

>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 = 56.5 bits (136), Expect = 1e-09
 Identities = 16/115 (13%), Positives = 39/115 (33%), Gaps = 6/115 (5%)

Query: 14  SPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTN--LYIRGLTQDTT 71
           + +   +      G ++ G      N+  H          + +   +  L++  +    +
Sbjct: 105 TLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVS 164

Query: 72  DKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
           ++DL  + S  G ++       K   K R    +   S   A+ A+  L +  + 
Sbjct: 165 EEDLKVLFSSNGGVVKGF----KFFQKDRKMALIQMGSVEEAVQALIDLHNHDLG 215

>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 = 40.4 bits (94), Expect = 3e-04
 Identities = 17/136 (12%), Positives = 38/136 (27%), Gaps = 5/136 (3%)

Query: 126 HAQMARQQEQDPTNLYIANL-PLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFAR 184
              +        + L ++NL P       L  L   Y  V   +IL +     K     +
Sbjct: 23  RIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQ 78

Query: 185 LESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGR 244
           +   ++    +   NG  L G    + +    +    R              + +  + +
Sbjct: 79  MADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKK 138

Query: 245 DSADSQLAYEHPMTPI 260
             + +      P   +
Sbjct: 139 PGSKNFQNIFPPSATL 154

>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 = 68.1 bits (167), Expect = 7e-15
 Identities = 24/104 (23%), Positives = 42/104 (40%), Gaps = 15/104 (14%)

Query: 45  GSPGTPTGPEQLSK-TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           GS G+    + +S    LY+R L   T+++ +    +   P    +        K R Y 
Sbjct: 1   GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVER------VKKIRDYA 54

Query: 104 FVDFESGGYALAAVKALQDKGIH--------AQMARQQEQDPTN 139
           FV F +   A+ A+KAL  K +         A+   +    P++
Sbjct: 55  FVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPSS 98

>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 = 49.6 bits (119), Expect = 4e-08
 Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 7/91 (7%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
             LY+ NL L+  E  +E            R+ +      +   F    +++   + ++ 
Sbjct: 16  KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKA 70

Query: 198 FNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
            NG  L GS  P+ V  A    K     + G
Sbjct: 71  LNGKVLDGS--PIEVTLAKPVDKDSSGPSSG 99

>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 = 68.0 bits (167), Expect = 9e-15
 Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           GS G+        K  L++ GL+ DT ++ L  + S+YG I     + D+ T + RG+GF
Sbjct: 1   GSSGSSGMASDEGK--LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGF 58

Query: 105 VDFESGGYALAAVKALQDK 123
           V FE+   A  A+ A+  K
Sbjct: 59  VTFENIDDAKDAMMAMNGK 77

>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 = 53.0 bits (128), Expect = 2e-09
 Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 7/101 (6%)

Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKD 189
                D   L++  L  +  E  LE + +KY  +    +++D     S+G GF   E+ D
Sbjct: 6   SGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENID 65

Query: 190 KCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPN 230
                +   NG ++ G    + V  A     K      GP+
Sbjct: 66  DAKDAMMAMNGKSVDG--RQIRVDQA----GKSSDNRSGPS 100

>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 = 68.6 bits (168), Expect = 9e-15
 Identities = 19/80 (23%), Positives = 40/80 (50%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
                 P     +    L++ G+ ++ T++D+ +  ++YG I +    LD+ T   +GY 
Sbjct: 8   EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 67

Query: 104 FVDFESGGYALAAVKALQDK 123
            V++E+   A AA++ L  +
Sbjct: 68  LVEYETYKEAQAAMEGLNGQ 87

>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 = 48.9 bits (117), Expect = 1e-07
 Identities = 21/106 (19%), Positives = 39/106 (36%), Gaps = 3/106 (2%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDK 190
           Q+  +   L++  +     E D+    A+Y  + +  +  D      KG      E+  +
Sbjct: 17  QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 76

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPG 236
               ++  NG  L G  +P+ V +       +G   GG    R P 
Sbjct: 77  AQAAMEGLNGQDLMG--QPISVDWCFVRGPPKGKRRGGRRRSRSPD 120

>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 = 67.6 bits (166), Expect = 9e-15
 Identities = 18/62 (29%), Positives = 37/62 (59%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
             +Y+  +  D T++ ++++CS  GP+I+ K + D  T + +GY F++F     + +AV+
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 119 AL 120
            L
Sbjct: 63  NL 64

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 13/69 (18%), Positives = 28/69 (40%), Gaps = 1/69 (1%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQ 196
             +Y+ ++P +  E  +  L +    V++ +++ D     SKG  F      +     ++
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 197 LFNGSTLPG 205
             NG  L  
Sbjct: 63  NLNGYQLGS 71

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 67.3 bits (165), Expect = 2e-14
 Identities = 18/82 (21%), Positives = 35/82 (42%)

Query: 42  QHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRG 101
             +     P     +    L++  + ++  + ++      YG I +    LD+ T   +G
Sbjct: 10  NEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG 69

Query: 102 YGFVDFESGGYALAAVKALQDK 123
           Y  V++E+   ALAA +AL   
Sbjct: 70  YALVEYETHKQALAAKEALNGA 91

>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 = 43.0 bits (102), Expect = 9e-06
 Identities = 13/99 (13%), Positives = 37/99 (37%), Gaps = 3/99 (3%)

Query: 118 KALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNT 176
           +   +     +   Q+  +   L++ ++    +E +++     Y  + +  +  D     
Sbjct: 7   RVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGF 66

Query: 177 SKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
           SKG      E+  +     +  NG+ + G  + + V + 
Sbjct: 67  SKGYALVEYETHKQALAAKEALNGAEIMG--QTIQVDWC 103

>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 = 67.3 bits (165), Expect = 2e-14
 Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 5/81 (6%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
             S    +G +++ K  L++ GL   TT + L +  SQYG ++    + DKTTN+ RG+G
Sbjct: 4   GSSGMNNSGADEIGK--LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61

Query: 104 FVDFESGGYALAAVKALQDKG 124
           FV F+           L  + 
Sbjct: 62  FVKFKD---PNCVGTVLASRP 79

>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 = 66.4 bits (163), Expect = 2e-14
 Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 50  PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
               E   K  +++ GL+ DT+ KDL +  +++G ++     +D  T + RG+GF+ F+ 
Sbjct: 5   SKNEEDAGK--MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKD 62

Query: 110 GGYALAAVKA 119
                  +  
Sbjct: 63  AASVEKVLDQ 72

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 68.4 bits (167), Expect = 3e-14
 Identities = 20/123 (16%), Positives = 42/123 (34%), Gaps = 7/123 (5%)

Query: 16  ANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLS-----KTNLYIRGLTQDT 70
           ++     + N   Q+    P          +  TP      S     +  +Y+   +  T
Sbjct: 8   SSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWT 67

Query: 71  TDKDLINMCSQYGP--IISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ 128
           TD+ LI +    G   ++  K   ++   + +GY  V   S       ++ L  K ++ +
Sbjct: 68  TDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGE 127

Query: 129 MAR 131
              
Sbjct: 128 KVD 130

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 48.0 bits (114), Expect = 3e-07
 Identities = 21/114 (18%), Positives = 39/114 (34%), Gaps = 6/114 (5%)

Query: 126 HAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKY--VTVVSTRILRD-NNNTSKGVGF 182
                         +Y+ +      +  L  ++       VV  +   +  N  SKG   
Sbjct: 44  ILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAE 103

Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS-GLKKRGAGAGGPNIYRGP 235
             + S++   ++++L  G  L G  E + V+ A    L +  A A      R P
Sbjct: 104 VVVASENSVHKLLELLPGKVLNG--EKVDVRPATRQNLSQFEAQARKRECVRVP 155

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 66.6 bits (163), Expect = 3e-14
 Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 8/84 (9%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           GS        +LS T L++R    D  + +L  +   +GP+   K +         G+ F
Sbjct: 18  GSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAF 69

Query: 105 VDFESGGYALAAVKALQDKGIHAQ 128
           V+FE    A  A++ +  K    Q
Sbjct: 70  VEFEEAESAAKAIEEVHGKSFANQ 93

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 53.5 bits (129), Expect = 2e-09
 Identities = 20/100 (20%), Positives = 41/100 (41%), Gaps = 9/100 (9%)

Query: 123 KGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGF 182
           +G H    ++ E   T L++   PL+ +E +L  +   +  +   +IL        G  F
Sbjct: 17  RGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAF 69

Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKR 222
              E  +   + I+  +G +     +PL V ++    K+ 
Sbjct: 70  VEFEEAESAAKAIEEVHGKSFAN--QPLEVVYSKLPAKRY 107

>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 = 66.1 bits (162), Expect = 3e-14
 Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 7/87 (8%)

Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGP--IISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           +  LYI  LT  TTD+DL       G   I+  K   ++   + +G+  V   S   +  
Sbjct: 1   RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60

Query: 116 AVKALQDKGIHAQ-----MARQQEQDP 137
            +  L  + +H Q      + + E   
Sbjct: 61  LMDLLPKRELHGQNPVVTPSNKLEHHH 87

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 51.4 bits (124), Expect = 6e-09
 Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 5/80 (6%)

Query: 139 NLYIANLPLNFKECDLESLLAKY--VTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMI 195
            LYI NL     + DL   +       ++  +   +  N  SKG     + S+    +++
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 196 QLFNGSTLPGSKEPLLVKFA 215
            L     L G  +  +V  +
Sbjct: 63  DLLPKRELHG--QNPVVTPS 80

>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 = 66.4 bits (163), Expect = 3e-14
 Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           GS    +   + +K  +++ G+  +  + +L     ++G +     I D    + RG+GF
Sbjct: 1   GSS--GSSGSKSNK--IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGF 56

Query: 105 VDFESGGYALAAVKALQDKG 124
           + FE      +  +A+    
Sbjct: 57  ITFEDEQ---SVDQAVNMHF 73

>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 = 66.6 bits (163), Expect = 4e-14
 Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
             L+I GL ++T +K L  +  ++GPI     I D+ T+K RG+ F+ FE+   A  A K
Sbjct: 8   GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAK 66

Query: 119 ALQDK 123
            +  K
Sbjct: 67  DMNGK 71

>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 = 53.9 bits (130), Expect = 2e-09
 Identities = 21/101 (20%), Positives = 39/101 (38%), Gaps = 2/101 (1%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
            P  L+I  L     E  L+++  K+  +    +++D  + S+G  F   E+        
Sbjct: 6   HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65

Query: 196 QLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPG 236
           +  NG +L G  + + V+ A     + G     P   R   
Sbjct: 66  KDMNGKSLHG--KAIKVEQAKKPSFQSGGRRRPPASSRNRS 104

>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 = 66.6 bits (163), Expect = 4e-14
 Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 8/84 (9%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
             LYIR L    T +++ ++  +YGPI     I    T + RG  +V +E    A  AV 
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNAVD 65

Query: 119 ALQ-----DKGIHAQMARQQEQDP 137
            L      ++ +            
Sbjct: 66  HLSGFNVSNRYLVVLYYNANRAFQ 89

>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 = 48.1 bits (115), Expect = 2e-07
 Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 4/78 (5%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
             LYI NLP      ++  +  KY  +   R+       ++G  +   E        +  
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNAVDH 66

Query: 198 FNGSTLPGSKEPLLVKFA 215
            +G  +      L+V + 
Sbjct: 67  LSGFNVSN--RYLVVLYY 82

>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 = 65.7 bits (161), Expect = 5e-14
 Identities = 17/65 (26%), Positives = 30/65 (46%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           + LY+  L  + T+  L  +   +G I +   + D  T + +GYGF+ F     A  A++
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65

Query: 119 ALQDK 123
            L   
Sbjct: 66  QLNGF 70

>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 = 52.6 bits (127), Expect = 2e-09
 Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 7/96 (7%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQM 194
             + LY+ +L  N  E  L  +   +  + +  +++D +   SKG GF      +   + 
Sbjct: 4   GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63

Query: 195 IQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPN 230
           ++  NG  L G   P+ V        +R  G  GP+
Sbjct: 64  LEQLNGFELAG--RPMRVGHV----TERLDGGSGPS 93

>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 = 65.2 bits (160), Expect = 5e-14
 Identities = 20/65 (30%), Positives = 31/65 (47%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
            NL++  L  +  D+ L N    +   +S   + D  T   RGYGFV F S   A  A+ 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 119 ALQDK 123
           ++Q +
Sbjct: 62  SMQGQ 66

>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 = 48.6 bits (117), Expect = 5e-08
 Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQ 196
            NL++ +L +N  +  L +    + + +S  ++ D    +S+G GF    S+D     + 
Sbjct: 2   FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61

Query: 197 LFNGSTLPG 205
              G  L G
Sbjct: 62  SMQGQDLNG 70

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 66.2 bits (162), Expect = 5e-14
 Identities = 19/88 (21%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 38  TNNVQHNGSPGTPTGPEQLSK--TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT 95
            ++   + +       ++ S     LY+  L  + T+  L  +   +G I S + ++D  
Sbjct: 4   HHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSE 63

Query: 96  TNKCRGYGFVDFESGGYALAAVKALQDK 123
           T + +GYGF+ F     A  A++ L   
Sbjct: 64  TGRSKGYGFITFSDSECAKKALEQLNGF 91

>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 = 52.3 bits (126), Expect = 4e-09
 Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 1/80 (1%)

Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARL 185
           A   ++    P  LY+ +L  N  E  L  +   +  + S +++ D     SKG GF   
Sbjct: 16  ANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITF 75

Query: 186 ESKDKCDQMIQLFNGSTLPG 205
              +   + ++  NG  L G
Sbjct: 76  SDSECAKKALEQLNGFELAG 95

>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 = 65.7 bits (161), Expect = 5e-14
 Identities = 29/104 (27%), Positives = 47/104 (45%), Gaps = 11/104 (10%)

Query: 45  GSPGTPT-GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           GS G+     +      LY+  L++D T+  ++ + SQ GP  S K I + T+N    Y 
Sbjct: 1   GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYC 58

Query: 104 FVDFESGGYALAAVKALQDKGIH--------AQMARQQEQDPTN 139
           FV+F     A AA+ A+  + I         A     Q+  P++
Sbjct: 59  FVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSGPSS 102

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 17/98 (17%), Positives = 37/98 (37%), Gaps = 4/98 (4%)

Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
            + +  P  LY+ NL  +  E  +  L ++     S +++ + + ++    F        
Sbjct: 9   MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE-HTSNDPYCFVEFYEHRD 67

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFA-DSGLKKRGAGAG 227
               +   NG  + G    + V +A     +K G  +G
Sbjct: 68  AAAALAAMNGRKILGK--EVKVNWATTPSSQKSGPSSG 103

>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 = 67.1 bits (164), Expect = 6e-14
 Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 1/84 (1%)

Query: 42  QHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRG 101
              G         + S T LY+  L+  TT++ +  + S+ G I      LDK      G
Sbjct: 24  HFRGDNEEQEKLLKKSCT-LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82

Query: 102 YGFVDFESGGYALAAVKALQDKGI 125
           + FV++ S   A  A++ +    +
Sbjct: 83  FCFVEYYSRADAENAMRYINGTRL 106

>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 = 43.3 bits (102), Expect = 2e-05
 Identities = 24/137 (17%), Positives = 48/137 (35%), Gaps = 11/137 (8%)

Query: 121 QDKGIHAQMARQQEQDP--TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTS 177
           +D+        Q++       LY+ NL     E  +  L +K   +    +  D    T+
Sbjct: 21  RDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTA 80

Query: 178 KGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA--DSGLKKRGAGAGGPNI---Y 232
            G  F    S+   +  ++  NG+ L      +   +       ++ G G  G  +   Y
Sbjct: 81  CGFCFVEYYSRADAENAMRYINGTRLDD--RIIRTDWDAGFKEGRQYGRGRSGGQVRDEY 138

Query: 233 RGPGAEVRL-WGRDSAD 248
           R      R  +G+ + +
Sbjct: 139 RQDYDAGRGGYGKLAQN 155

>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 = 64.9 bits (159), Expect = 7e-14
 Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDK-TTNKCRGYGFVDFESGGYALA 115
             T ++I  LT++ T   ++ + S YG I      +++   +  +GY +V+FE+   A  
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 116 AVKAL 120
           A+K +
Sbjct: 63  ALKHM 67

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 48.3 bits (116), Expect = 6e-08
 Identities = 13/81 (16%), Positives = 33/81 (40%), Gaps = 4/81 (4%)

Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT--SKGVGFARLESKDKCDQM 194
           PT ++I  L  N  +  +  + + Y  +    +  +  +   SKG  +   E+ D+ ++ 
Sbjct: 4   PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63

Query: 195 IQLFNGSTLPGSKEPLLVKFA 215
           ++  +G  + G    +     
Sbjct: 64  LKHMDGGQIDGQ--EITATAV 82

>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 = 65.4 bits (160), Expect = 1e-13
 Identities = 21/81 (25%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 40  NVQHNGSPGTPTGPEQLSKTN-LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNK 98
           +  H+ S   P G    S    ++I GL+  TT + L     Q+G +     + D  T +
Sbjct: 6   HHHHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKR 65

Query: 99  CRGYGFVDFESGGYALAAVKA 119
            RG+GFV F         +  
Sbjct: 66  SRGFGFVTFMDQAGVDKVLAQ 86

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 64.0 bits (157), Expect = 1e-13
 Identities = 20/59 (33%), Positives = 34/59 (57%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           +++ GL+ +TT +D+ +   Q+G +     + DKTTN+ RG+GFV FES        + 
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

>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 = 67.8 bits (165), Expect = 1e-13
 Identities = 22/113 (19%), Positives = 41/113 (36%), Gaps = 2/113 (1%)

Query: 16  ANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDL 75
           + + ++  +        T P T  +    G+           +  LYI  LT  TTD+DL
Sbjct: 26  SPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDL 85

Query: 76  INMCSQYGP--IISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
                  G   I+  K   ++   + +G+  V   S   +   +  L  + +H
Sbjct: 86  TEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELH 138

>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 = 50.1 bits (119), Expect = 2e-07
 Identities = 26/189 (13%), Positives = 43/189 (22%), Gaps = 11/189 (5%)

Query: 115 AAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKY--VTVVSTRILRD 172
             V     KG    +          LYI NL     + DL   +       ++  +   +
Sbjct: 46  PTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFEN 105

Query: 173 -NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNI 231
             N  SKG     + S+    +++ L     L G  +  +V   +     +         
Sbjct: 106 RANGQSKGFALVGVGSEASSKKLMDLLPKRELHG--QNPVVTPVNKQFLSQFEMQSRKTT 163

Query: 232 YRGPGAEVRLWGRDSADSQLAYEHPMTPIPATIQYQRFTAGPGGTGHIPAGYTPWVPTQY 291
             G          +                      RF     G    P    P  P   
Sbjct: 164 QSGQM------SGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPPP 217

Query: 292 VMPAPHMSQ 300
                    
Sbjct: 218 FPAGQTHHH 226

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 66.4 bits (162), Expect = 1e-13
 Identities = 24/101 (23%), Positives = 39/101 (38%), Gaps = 5/101 (4%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
            GS       +    T+L +  LT  T+   L  +  +YG +       D+ T + RG+ 
Sbjct: 56  EGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFA 115

Query: 104 FVDFESGGYALAAVKALQDK-----GIHAQMARQQEQDPTN 139
           FV F     A  A+ A+         +  QMAR      ++
Sbjct: 116 FVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH 156

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 52.9 bits (127), Expect = 8e-09
 Identities = 22/92 (23%), Positives = 32/92 (34%), Gaps = 1/92 (1%)

Query: 115 AAVKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN 174
           A       +G H        +  T+L + NL        L  +  KY  V    I RD  
Sbjct: 48  ATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY 107

Query: 175 -NTSKGVGFARLESKDKCDQMIQLFNGSTLPG 205
              S+G  F R   K   +  +   +G+ L G
Sbjct: 108 TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG 139

>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 = 64.6 bits (158), Expect = 1e-13
 Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 4/77 (5%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           +GS G            L++  +     D DL  M  Q+G I+  + I ++  +  +G+G
Sbjct: 3   SGSSGNSESKST--PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFG 58

Query: 104 FVDFESGGYALAAVKAL 120
           FV FE+   A  A + L
Sbjct: 59  FVTFENSADADRAREKL 75

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 60.4 bits (147), Expect = 5e-12
 Identities = 20/98 (20%), Positives = 45/98 (45%), Gaps = 3/98 (3%)

Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
            + +  P  L+++N+P  F++ DL  +  ++  ++   I+ +    SKG GF   E+   
Sbjct: 9   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKGFGFVTFENSAD 67

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
            D+  +  +G+ + G    + V  A + +      + G
Sbjct: 68  ADRAREKLHGTVVEG--RKIEVNNATARVMTNSGPSSG 103

>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 = 64.2 bits (157), Expect = 2e-13
 Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKC---RGYGFVDFESGGYALA 115
           + L+I+ L   TT++ L  + S+ G I S      K         G+GFV+++    A  
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 116 AVKALQDK 123
           A+K LQ  
Sbjct: 66  ALKQLQGH 73

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 21/97 (21%), Positives = 40/97 (41%), Gaps = 6/97 (6%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN----NTSKGVGFARLESKDKC 191
             + L+I NL  +  E  L+ + +K   + S  I +  N      S G GF   +  ++ 
Sbjct: 4   GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
            + ++   G T+ G    L V+ ++   K     + G
Sbjct: 64  QKALKQLQGHTVDGH--KLEVRISERATKPASGPSSG 98

>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 = 64.2 bits (157), Expect = 2e-13
 Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 51  TGPE-QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           + PE ++    +++ G+     + ++ +  ++YG +   K I D+ T   +GYGFV F +
Sbjct: 1   SLPEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYN 59

Query: 110 GGYALAAVKALQD 122
                  V++  +
Sbjct: 60  DVDVQKIVESQIN 72

>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 = 49.9 bits (120), Expect = 3e-08
 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
           P  +++  + +   E ++ S  A+Y +V   +I+ D    SKG GF    +     ++++
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68

Query: 197 LFNGSTLPGSKEPLLVKFA 215
             +     G K  L +  A
Sbjct: 69  --SQINFHGKK--LKLGPA 83

>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 = 64.3 bits (157), Expect = 3e-13
 Identities = 23/102 (22%), Positives = 39/102 (38%), Gaps = 7/102 (6%)

Query: 45  GSPGTPTGPEQLSK-TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           GS G+    +     + +++  L      K L  + S  G ++    + DK   K RG G
Sbjct: 1   GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIG 59

Query: 104 FVDFESGGYALAAVKA-----LQDKGIHAQMARQQEQDPTNL 140
            V FE    A+ A+       L D+ +H +M  +        
Sbjct: 60  TVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFF 101

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 62.3 bits (152), Expect = 1e-12
 Identities = 28/108 (25%), Positives = 44/108 (40%), Gaps = 2/108 (1%)

Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKD 189
           A Q  +  + +++ANL        L+ + +    VV   IL D +  S+G+G    E   
Sbjct: 8   ALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSI 67

Query: 190 KCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPGA 237
           +  Q I +FNG  L     P+ VK  +  L K            GP +
Sbjct: 68  EAVQAISMFNGQLLFD--RPMHVKMDERALPKGDFFPPERPQQSGPSS 113

>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 = 63.3 bits (155), Expect = 3e-13
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           N+Y+  L    T + +  + SQ+G + + K I D+ T K +G+GFV+ +       A+  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK 61

Query: 120 LQDK 123
           L + 
Sbjct: 62  LDNT 65

>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 = 47.2 bits (113), Expect = 2e-07
 Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQL 197
           N+Y+ NL  +     ++ L +++  V + +++ D      KG GF  ++ +    + I  
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK 61

Query: 198 FNGSTLPGSKEPLLVKFA 215
            + +   G    + V  A
Sbjct: 62  LDNTDFMGR--TIRVTEA 77

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 63.3 bits (155), Expect = 3e-13
 Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 4/74 (5%)

Query: 50  PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           P G       ++++  L+ + T   +    + +G I   + + D  T K +GYGFV F +
Sbjct: 2   PLGSH----FHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 57

Query: 110 GGYALAAVKALQDK 123
              A  A++ +  +
Sbjct: 58  KWDAENAIQQMGGQ 71

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 41.4 bits (98), Expect = 2e-05
 Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDKCDQMIQL 197
           ++++ +L        + +  A +  +   R+++D     SKG GF    +K   +  IQ 
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 198 FNGSTLPG 205
             G  L G
Sbjct: 68  MGGQWLGG 75

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 63.6 bits (155), Expect = 3e-13
 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 3/75 (4%)

Query: 46  SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
           S  + + P++     L IR +      + L ++  QYG + S + +   +         V
Sbjct: 3   SGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNV 59

Query: 106 DFESGGYALAAVKAL 120
            + S   A  A+  L
Sbjct: 60  TYSSKDQARQALDKL 74

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 54.8 bits (132), Expect = 5e-10
 Identities = 19/93 (20%), Positives = 36/93 (38%), Gaps = 6/93 (6%)

Query: 126 HAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT-SKGVGFAR 184
            +  +  + Q    L I N+P + +   L+SLL +Y  V S   +  ++ T    V ++ 
Sbjct: 4   GSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSS 63

Query: 185 LESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
            +   +    +   NG  L      L V +   
Sbjct: 64  KDQARQA---LDKLNGFQLENF--TLKVAYIPD 91

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 62.9 bits (154), Expect = 4e-13
 Identities = 16/59 (27%), Positives = 26/59 (44%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           ++I GL+  TT + L     Q+G +     + D  T + RG+GFV F         +  
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

>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 = 64.3 bits (157), Expect = 4e-13
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 42  QHNGSPGTPTGPEQLSK-TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCR 100
           QH+       G E +     L +  L    +D D+  + +++G +       D+ + +  
Sbjct: 18  QHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSL 76

Query: 101 GYGFVDFESGGYALAAVKAL 120
           G   V FE    AL A+K  
Sbjct: 77  GTADVHFERRADALKAMKQY 96

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 57.0 bits (138), Expect = 1e-10
 Identities = 18/100 (18%), Positives = 38/100 (38%), Gaps = 2/100 (2%)

Query: 118 KALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTS 177
           K   D         +  +    L ++NL     + D++ L A++ T+    +  D +  S
Sbjct: 16  KWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS 75

Query: 178 KGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
            G      E +    + ++ + G  L G   P+ ++   S
Sbjct: 76  LGTADVHFERRADALKAMKQYKGVPLDG--RPMDIQLVAS 113

>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 = 63.1 bits (154), Expect = 5e-13
 Identities = 13/75 (17%), Positives = 30/75 (40%), Gaps = 6/75 (8%)

Query: 49  TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
             +   + ++T L  + L+ + T+ +L  +      I      L     K +G  +++F+
Sbjct: 8   CTSKKVRAART-LLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFK 61

Query: 109 SGGYALAAVKALQDK 123
           S   A   ++  Q  
Sbjct: 62  SEADAEKNLEEKQGA 76

>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 = 45.7 bits (109), Expect = 6e-07
 Identities = 14/92 (15%), Positives = 36/92 (39%), Gaps = 6/92 (6%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKC 191
           ++ +    L   NL  N  E +L+ +    + +         +  SKG+ +   +S+   
Sbjct: 11  KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEADA 66

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKRG 223
           ++ ++   G+ + G    + + +       RG
Sbjct: 67  EKNLEEKQGAEIDGR--SVSLYYTGEKGGTRG 96

>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 = 63.1 bits (154), Expect = 5e-13
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 7/80 (8%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
             S  +    E  SKT L +  L+   T++ L  +  +   I     +      K +GY 
Sbjct: 4   GSSGNSTWSGE--SKT-LVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYA 56

Query: 104 FVDFESGGYALAAVKALQDK 123
           F++F S   A  A+ +   +
Sbjct: 57  FIEFASFEDAKEALNSCNKR 76

>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 = 46.9 bits (112), Expect = 3e-07
 Identities = 18/99 (18%), Positives = 37/99 (37%), Gaps = 9/99 (9%)

Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
                +   L ++NL  +  E  L+ +  K   +   ++ ++ N  SKG  F    S + 
Sbjct: 9   STWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFED 65

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGP 229
             + +   N   + G    + ++        RG+   GP
Sbjct: 66  AKEALNSCNKREIEG--RAIRLELQ----GPRGSPNSGP 98

>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 = 63.5 bits (155), Expect = 5e-13
 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 49  TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
                EQ  K  L+I GL+ +TT++ L N   Q+G +     + D  + + RG+GFV F 
Sbjct: 20  KKREKEQFRK--LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFS 77

Query: 109 SGGYALAAVKA 119
           S     AA+ A
Sbjct: 78  SMAEVDAAMAA 88

>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 = 63.0 bits (154), Expect = 5e-13
 Identities = 26/101 (25%), Positives = 50/101 (49%), Gaps = 15/101 (14%)

Query: 43  HNGSPGTPTGPEQLSK---TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKC 99
            +GS G     +++++    NLY++ L     D+ L    S +G I S K +++    + 
Sbjct: 2   SSGSSG-----DRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRS 54

Query: 100 RGYGFVDFESGGYALAAVKALQD-----KGIHAQMARQQEQ 135
           +G+GFV F S   A  AV  +       K ++  +A+++E+
Sbjct: 55  KGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEE 95

>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 = 56.8 bits (138), Expect = 1e-10
 Identities = 23/106 (21%), Positives = 44/106 (41%), Gaps = 4/106 (3%)

Query: 124 GIHAQMARQQEQDP-TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGF 182
           G       +  +    NLY+ NL     +  L    + + T+ S +++ +    SKG GF
Sbjct: 1   GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGR-SKGFGF 59

Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
               S ++  + +   NG  +  +K PL V  A    +++   + G
Sbjct: 60  VCFSSPEEATKAVTEMNGRIV-ATK-PLYVALAQRKEERQSGPSSG 103

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.1 bits (154), Expect = 7e-13
 Identities = 20/89 (22%), Positives = 43/89 (48%), Gaps = 3/89 (3%)

Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLE 186
           + M  + +  P  L+++N+P  F++ DL  +  ++  ++   I+ +    SKG GF   E
Sbjct: 19  SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGSKGFGFVTFE 77

Query: 187 SKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
           +    D+  +  +G+ + G    + V  A
Sbjct: 78  NSADADRAREKLHGTVVEG--RKIEVNNA 104

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 61.6 bits (150), Expect = 2e-12
 Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
             L++  +     D DL  M  Q+G I+  + I ++     +G+GFV FE+   A  A +
Sbjct: 30  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRARE 87

Query: 119 AL 120
            L
Sbjct: 88  KL 89

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 62.2 bits (152), Expect = 8e-13
 Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 13/95 (13%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           GS G+           +++R L  D T K L +  ++ G ++     ++    K +G G 
Sbjct: 1   GSSGSSGA------CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGV 52

Query: 105 VDFESGGYALAAVKA-----LQDKGIHAQMARQQE 134
           V FES   A  A +      L  + I  ++ R   
Sbjct: 53  VKFESPEVAERACRMMNGMKLSGREIDVRIDRNAS 87

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 56.4 bits (137), Expect = 1e-10
 Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 7/92 (7%)

Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
              +++ NLP +F    L+    +   V+   I  +N   SKG G  + ES +  ++  +
Sbjct: 8   ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGK-SKGCGVVKFESPEVAERACR 66

Query: 197 LFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
           + NG  L G    + V+      +     + G
Sbjct: 67  MMNGMKLSG--REIDVRID----RNASGPSSG 92

>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 = 62.7 bits (153), Expect = 9e-13
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 3/78 (3%)

Query: 43  HNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
            +   G   G E      L +  L    +D D+  + +++G +       D+ + +  G 
Sbjct: 16  FDSGFGGGAGVET--GGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGT 72

Query: 103 GFVDFESGGYALAAVKAL 120
             V FE    AL A+K  
Sbjct: 73  ADVHFERKADALKAMKQY 90

>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 = 59.6 bits (145), Expect = 1e-11
 Identities = 19/97 (19%), Positives = 37/97 (38%), Gaps = 2/97 (2%)

Query: 121 QDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGV 180
            D            +    L ++NL     + D++ L A++ T+    +  D +  S G 
Sbjct: 13  HDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGT 72

Query: 181 GFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
                E K    + ++ +NG  L G   P+ ++   S
Sbjct: 73  ADVHFERKADALKAMKQYNGVPLDG--RPMNIQLVTS 107

>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 = 61.4 bits (150), Expect = 1e-12
 Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 3/63 (4%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           +++ GL+ DT ++ +      +G + S +  +D  TNK RG+ F+ F+         K +
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE---PVKKIM 58

Query: 121 QDK 123
           + K
Sbjct: 59  EKK 61

>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 = 62.3 bits (152), Expect = 1e-12
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 8/70 (11%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
             L++R L    T++ L    SQ+G +   K +        + Y F+ F+    A+ A++
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAME 63

Query: 119 ALQDKGIHAQ 128
            +  K +  +
Sbjct: 64  EMNGKDLEGE 73

>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 = 46.1 bits (110), Expect = 6e-07
 Identities = 20/98 (20%), Positives = 36/98 (36%), Gaps = 9/98 (9%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
             L++ NL     E  LE   +++  +   + L+D         F   + +D   + ++ 
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEE 64

Query: 198 FNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGP 235
            NG  L G    + + FA    +KR           GP
Sbjct: 65  MNGKDLEGE--NIEIVFAKPPDQKRKERKAQRQAASGP 100

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 61.9 bits (151), Expect = 1e-12
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 1/83 (1%)

Query: 45  GSPGTP-TGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           GS G+  +   +   T + ++ +    +  ++++    Y  I  +  +         G  
Sbjct: 1   GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 104 FVDFESGGYALAAVKALQDKGIH 126
            V FES   A AAV  L D+ I 
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIG 83

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 12/69 (17%), Positives = 23/69 (33%), Gaps = 1/69 (1%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKY-VTVVSTRILRDNNNTSKGVGFARLESKDKCDQM 194
            PT + + N+P      ++      Y V   S  +  +      G      ES+D+    
Sbjct: 14  GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73

Query: 195 IQLFNGSTL 203
           +   N   +
Sbjct: 74  VIDLNDRPI 82

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 62.1 bits (151), Expect = 1e-12
 Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 4/72 (5%)

Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
             +   ++YI+G   D T  D+       G +++ + +        +G  FV F+S    
Sbjct: 7   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDS---I 62

Query: 114 LAAVKALQDKGI 125
            +A K ++  G 
Sbjct: 63  ESAKKFVETPGQ 74

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 61.7 bits (150), Expect = 2e-12
 Identities = 15/91 (16%), Positives = 34/91 (37%), Gaps = 1/91 (1%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKC 191
           + +    ++YI   P +    D++  L     V++ ++ R  +   KG  F   +S +  
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 65

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKR 222
            + ++   G     +   +L K      K  
Sbjct: 66  KKFVET-PGQKYKETDLLILFKDDYFAKKNE 95

>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 = 66.4 bits (161), Expect = 2e-12
 Identities = 20/66 (30%), Positives = 30/66 (45%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++  +  DTT+  L      YGPI     +  K + K RGY F+++E      +A K  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 121 QDKGIH 126
             K I 
Sbjct: 165 DGKKID 170

>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 = 42.9 bits (100), Expect = 8e-05
 Identities = 11/74 (14%), Positives = 25/74 (33%), Gaps = 2/74 (2%)

Query: 136 DPTN-LYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQ 193
           D    L++A +  +  E  L      Y  +    ++    +   +G  F   E +     
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159

Query: 194 MIQLFNGSTLPGSK 207
             +  +G  + G +
Sbjct: 160 AYKHADGKKIDGRR 173

>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 = 62.4 bits (152), Expect = 2e-12
 Identities = 19/91 (20%), Positives = 37/91 (40%), Gaps = 4/91 (4%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
             P +    +++ K ++Y+  +   +T +DL    S  G I     + DK +   +GY +
Sbjct: 23  PQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAY 82

Query: 105 VDFESGGYALAAV----KALQDKGIHAQMAR 131
           ++F       AAV       + + I     R
Sbjct: 83  IEFAERNSVDAAVAMDETVFRGRTIKVLPKR 113

>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 = 51.6 bits (124), Expect = 1e-08
 Identities = 14/86 (16%), Positives = 33/86 (38%), Gaps = 2/86 (2%)

Query: 121 QDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKG 179
           +          ++E D  ++Y+ N+       DLE+  +   ++    IL D  +   KG
Sbjct: 20  EGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKG 79

Query: 180 VGFARLESKDKCDQMIQLFNGSTLPG 205
             +     ++  D  + + + +   G
Sbjct: 80  YAYIEFAERNSVDAAVAM-DETVFRG 104

>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 = 61.5 bits (150), Expect = 2e-12
 Identities = 24/97 (24%), Positives = 33/97 (34%), Gaps = 15/97 (15%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           +GS G    P +     LY+ G   D T   L    S +G II       +         
Sbjct: 3   SGSSGERRAPRK--GNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR------NCA 52

Query: 104 FVDFESGGYALAAVKALQDKGIHAQM-----ARQQEQ 135
           FV +E    A  AV  L    + +       AR+Q  
Sbjct: 53  FVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM 89

>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 = 38.0 bits (89), Expect = 4e-04
 Identities = 14/98 (14%), Positives = 29/98 (29%), Gaps = 9/98 (9%)

Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
           R+  +    LY+     +     L    + +  ++   +        +   F   E  + 
Sbjct: 9   RRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMES 61

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
            DQ +   NG+ +      L V  A          + G
Sbjct: 62  ADQAVAELNGTQVESV--QLKVNIARKQPMLDSGPSSG 97

>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 = 61.6 bits (150), Expect = 3e-12
 Identities = 21/106 (19%), Positives = 40/106 (37%), Gaps = 15/106 (14%)

Query: 26  TGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPI 85
           +   +G T  +   +V +  SP             +Y  G+    TD+ +    S +G I
Sbjct: 2   SSGSSGNTKQLRFEDVVNQSSP---------KNCTVYCGGIASGLTDQLMRQTFSPFGQI 52

Query: 86  ISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR 131
           +  +   +K      GY FV F +   A  A+ ++    I   + +
Sbjct: 53  MEIRVFPEK------GYSFVRFSTHESAAHAIVSVNGTTIEGHVVK 92

>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 = 43.1 bits (102), Expect = 7e-06
 Identities = 13/101 (12%), Positives = 31/101 (30%), Gaps = 7/101 (6%)

Query: 128 QMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLES 187
            +  Q       +Y   +     +  +    + +  ++  R+  +     KG  F R  +
Sbjct: 16  DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFST 70

Query: 188 KDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
            +     I   NG+T+ G    +   +           + G
Sbjct: 71  HESAAHAIVSVNGTTIEGH--VVKCYWGKESPDMTSGPSSG 109

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 61.2 bits (149), Expect = 3e-12
 Identities = 23/109 (21%), Positives = 41/109 (37%), Gaps = 19/109 (17%)

Query: 27  GSQNGGT----HPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQY 82
           GSQ  G     +P   +++  +  P           T  YI  +    T+ DLI +   +
Sbjct: 1   GSQTIGLPPQVNPQAVDHIIRSAPP---------RVTTAYIGNIPHFATEADLIPLFQNF 51

Query: 83  GPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR 131
           G I+  K   +K      G  F+ +++   A   + AL +     +  R
Sbjct: 52  GFILDFKHYPEK------GCCFIKYDTHEQAAVCIVALANFPFQGRNLR 94

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 5/80 (6%)

Query: 128 QMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLES 187
            + R      T  YI N+P    E DL  L   +  ++  +   +     KG  F + ++
Sbjct: 18  HIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDT 72

Query: 188 KDKCDQMIQLFNGSTLPGSK 207
            ++    I         G  
Sbjct: 73  HEQAAVCIVALANFPFQGRN 92

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 60.8 bits (148), Expect = 3e-12
 Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 1/83 (1%)

Query: 45  GSPGTP-TGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           GS G+      +   T + ++ +    +  ++++    Y  I  +  +         G  
Sbjct: 1   GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60

Query: 104 FVDFESGGYALAAVKALQDKGIH 126
            V FES   A AAV  L D+ I 
Sbjct: 61  MVAFESRDEATAAVIDLNDRPIG 83

>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 = 45.4 bits (108), Expect = 1e-06
 Identities = 13/75 (17%), Positives = 25/75 (33%), Gaps = 1/75 (1%)

Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKY-VTVVSTRILRDNNNTSKGVGFARLESK 188
           A   +  PT + + N+P      ++      Y V   S  +  +      G      ES+
Sbjct: 8   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 67

Query: 189 DKCDQMIQLFNGSTL 203
           D+    +   N   +
Sbjct: 68  DEATAAVIDLNDRPI 82

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 60.7 bits (148), Expect = 4e-12
 Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 3/80 (3%)

Query: 46  SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
           S  +           L+++GL++DTT++ L      +   +  + + D+ T   +G+GFV
Sbjct: 3   SGSSGPNARSQPSKTLFVKGLSEDTTEETLKES---FDGSVRARIVTDRETGSSKGFGFV 59

Query: 106 DFESGGYALAAVKALQDKGI 125
           DF S   A AA +A++D  I
Sbjct: 60  DFNSEEDAKAAKEAMEDGEI 79

>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 = 47.3 bits (113), Expect = 2e-07
 Identities = 23/108 (21%), Positives = 39/108 (36%), Gaps = 11/108 (10%)

Query: 124 GIHAQMARQQEQDPT-NLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVG 181
           G            P+  L++  L  +  E  L+         V  RI+ D    +SKG G
Sbjct: 1   GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFG 57

Query: 182 FARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGP 229
           F    S++      +      + G+   + + +A    K +G G  GP
Sbjct: 58  FVDFNSEEDAKAAKEAMEDGEIDGN--KVTLDWA----KPKGEGGSGP 99

>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 = 61.0 bits (148), Expect = 4e-12
 Identities = 14/72 (19%), Positives = 29/72 (40%), Gaps = 2/72 (2%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAIL--DKTTNKCRGYGFVDFESGGYAL 114
               L+I G+ +    ++++   ++    +    +        K RG+ FV++ES   A 
Sbjct: 7   GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 115 AAVKALQDKGIH 126
            A + L    I 
Sbjct: 67  MARRKLMPGRIQ 78

>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 = 47.5 bits (113), Expect = 3e-07
 Identities = 14/85 (16%), Positives = 28/85 (32%), Gaps = 3/85 (3%)

Query: 135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRIL---RDNNNTSKGVGFARLESKDKC 191
                L+I  +P   K  ++   +AK    V   I+     +   ++G  F   ES    
Sbjct: 6   SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFAD 216
               +      +      + V +A+
Sbjct: 66  AMARRKLMPGRIQLWGHQIAVDWAE 90

>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 = 60.8 bits (148), Expect = 5e-12
 Identities = 14/73 (19%), Positives = 28/73 (38%)

Query: 46  SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
            P     PE+     ++   L      +DL +  S  G +   + I D+ + + +G  +V
Sbjct: 13  EPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYV 72

Query: 106 DFESGGYALAAVK 118
           +F        A+ 
Sbjct: 73  EFCEIQSVPLAIG 85

>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 = 55.0 bits (133), Expect = 5e-10
 Identities = 24/98 (24%), Positives = 39/98 (39%), Gaps = 5/98 (5%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDK 190
            +E+D   ++   L    +  DLE   +    V   RI+ D N   SKG+ +        
Sbjct: 20  PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
               I L  G  L G   P++V+ + +  K R +G   
Sbjct: 80  VPLAIGL-TGQRLLGV--PIIVQASQAE-KNRLSGPSS 113

>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 = 60.8 bits (148), Expect = 5e-12
 Identities = 17/78 (21%), Positives = 38/78 (48%)

Query: 46  SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
           S  +    +  +  ++++  L+ + T +D+    + +G I   + + D  T K +GYGFV
Sbjct: 3   SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62

Query: 106 DFESGGYALAAVKALQDK 123
            F +   A  A++ +  +
Sbjct: 63  SFFNKWDAENAIQQMGGQ 80

>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 = 45.0 bits (107), Expect = 2e-06
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKD 189
           ++   +  ++++ +L       D+++  A +  +   R+++D     SKG GF    +K 
Sbjct: 9   KKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKW 68

Query: 190 KCDQMIQLFNGSTLPG 205
             +  IQ   G  L G
Sbjct: 69  DAENAIQQMGGQWLGG 84

>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 = 59.6 bits (145), Expect = 7e-12
 Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 9/88 (10%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           GS G+    E  + T LY+ GL    T+ DL N   Q+G I +   +  +         F
Sbjct: 1   GSSGSS--GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAF 52

Query: 105 VDFESGGYA-LAAVKALQDKGIHAQMAR 131
           + F +   A +AA K+     ++ +   
Sbjct: 53  IQFATRQAAEVAAEKSFNKLIVNGRRLN 80

>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 = 41.9 bits (99), Expect = 1e-05
 Identities = 15/87 (17%), Positives = 33/87 (37%), Gaps = 10/87 (11%)

Query: 132 QQEQDPTN--LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKD 189
              +D T   LY+  L     E DL +   ++  + +  +++      +   F +  ++ 
Sbjct: 5   SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQ 59

Query: 190 KCDQ-MIQLFNGSTLPGSKEPLLVKFA 215
             +    + FN   + G    L VK+ 
Sbjct: 60  AAEVAAEKSFNKLIVNG--RRLNVKWG 84

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 6/73 (8%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           T L++ GL  +T+   L     ++G I +   +          + ++ +ES   A AA  
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACA 71

Query: 119 ALQDKGIHAQMAR 131
            ++   +     R
Sbjct: 72  KMRGFPLGGPDRR 84

>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 = 47.6 bits (114), Expect = 2e-07
 Identities = 18/83 (21%), Positives = 29/83 (34%), Gaps = 6/83 (7%)

Query: 137 PTN-LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
           PT  L++  L  N     L     ++ ++ +   ++          + + ES D      
Sbjct: 16  PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAAC 70

Query: 196 QLFNGSTLPGSKEPLLVKFADSG 218
               G  L G    L V FA SG
Sbjct: 71  AKMRGFPLGGPDRRLRVDFAKSG 93

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 59.2 bits (144), Expect = 1e-11
 Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 8/82 (9%)

Query: 50  PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIIST--------KAILDKTTNKCRG 101
                      ++++GL ++ T + + +   Q G I +             D+ T K +G
Sbjct: 5   HHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKG 64

Query: 102 YGFVDFESGGYALAAVKALQDK 123
              V F+    A AA+     K
Sbjct: 65  EATVSFDDPPSAKAAIDWFDGK 86

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 43.4 bits (103), Expect = 5e-06
 Identities = 14/98 (14%), Positives = 26/98 (26%), Gaps = 11/98 (11%)

Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVST--------RILRD-NNNTS 177
                    D   +++  L  N     +     +   + +          +  D      
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 178 KGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
           KG      +        I  F+G    G+  P+ V FA
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKEFSGN--PIKVSFA 98

>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 = 59.5 bits (144), Expect = 2e-11
 Identities = 21/128 (16%), Positives = 47/128 (36%), Gaps = 28/128 (21%)

Query: 14  SPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDK 73
             ++ H   SS    +         +++  + S G P      S+  ++IR L  D T+ 
Sbjct: 2   GSSHHHHHHSSGLVPRG--------SHMGDSRSAGVP------SRV-IHIRKLPIDVTEG 46

Query: 74  DLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG-------IH 126
           ++I++   +G + +   +      K +   F++  +   A   V              I+
Sbjct: 47  EVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY 100

Query: 127 AQMARQQE 134
            Q +  +E
Sbjct: 101 IQFSNHKE 108

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 44.9 bits (106), Expect = 2e-06
 Identities = 17/95 (17%), Positives = 42/95 (44%), Gaps = 5/95 (5%)

Query: 123 KGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGF 182
           +G H   +R        ++I  LP++  E ++ SL   +  V +  +L+      K   F
Sbjct: 17  RGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAF 71

Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
             + +++  + M+  +   T     +P+ ++F++ 
Sbjct: 72  IEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 59.0 bits (143), Expect = 2e-11
 Identities = 18/92 (19%), Positives = 33/92 (35%), Gaps = 13/92 (14%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPI--------ISTKAILDKTTNKCRGYGFVDFESG 110
             ++++GL ++ T + + +   Q G I               D+ T K +G   V F+  
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 111 GYALAAVKALQDK-----GIHAQMARQQEQDP 137
             A AA+     K      I    A ++    
Sbjct: 68  PSAKAAIDWFDGKEFSGNPIKVSFATRRADFN 99

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 17/114 (14%), Positives = 29/114 (25%), Gaps = 11/114 (9%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVST--------RILRD-NNNTSKGVGF 182
           Q   D   +++  L  N     +     +   + +          +  D      KG   
Sbjct: 2   QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61

Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPG 236
              +        I  F+G    G+  P+ V FA         G  G        
Sbjct: 62  VSFDDPPSAKAAIDWFDGKEFSGN--PIKVSFATRRADFNRGGGNGRGGLEHHH 113

>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 = 59.8 bits (145), Expect = 2e-11
 Identities = 20/102 (19%), Positives = 34/102 (33%), Gaps = 17/102 (16%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKA-----ILDKTTNK 98
           +  PG P          +Y++ L +   +KDL  +  +Y    S        I      +
Sbjct: 38  SYEPGEPN-------CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGR 90

Query: 99  CRGYGFVDFESGGYALAAVKALQ-----DKGIHAQMARQQEQ 135
            +G  F+   +   A  A+K         K +  Q AR    
Sbjct: 91  MKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARP 132

>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 = 47.1 bits (112), Expect = 6e-07
 Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 8/84 (9%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTR------ILRDNNNTSKGVGFARLESKDKC 191
             +Y+ NL  + +E DL+ +  +YV   S        I        KG  F  L ++   
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFA 215
            + ++  NG  L G  +P++V+FA
Sbjct: 106 AKALKEANGYVLFG--KPMVVQFA 127

>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 = 58.3 bits (142), Expect = 2e-11
 Identities = 10/67 (14%), Positives = 28/67 (41%), Gaps = 1/67 (1%)

Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           G E  +++ +Y+  +    T ++L       G +     + DK +   +G+ +++F    
Sbjct: 1   GMEADARS-IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 59

Query: 112 YALAAVK 118
               ++ 
Sbjct: 60  SVRTSLA 66

>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 = 51.4 bits (124), Expect = 6e-09
 Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCD 192
           E D  ++Y+ N+       +LE+      +V    IL D  +   KG  +     K+   
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 193 QMIQLFNGSTLPG 205
             + L + S   G
Sbjct: 63  TSLAL-DESLFRG 74

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 58.4 bits (142), Expect = 2e-11
 Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 12/91 (13%)

Query: 53  PEQLSKTNLYIRGLTQDTTDKDL----INMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           PE      +YI  L +     +L      + S++G I+         + K RG  FV F+
Sbjct: 3   PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFK 59

Query: 109 SGGYALAAVKALQ-----DKGIHAQMARQQE 134
               A  A++++Q     DK +  Q A+   
Sbjct: 60  EVSSATNALRSMQGFPFYDKPMRIQYAKTDS 90

>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 = 58.6 bits (142), Expect = 3e-11
 Identities = 28/104 (26%), Positives = 44/104 (42%), Gaps = 14/104 (13%)

Query: 45  GSPGTPTGPEQLSK-TNLYIRGLTQDTTDKDLINMCSQYGPIIST--------KAILDKT 95
           GS G+   P++ S  + +Y++GL    T  DL +   Q G +              LDK 
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 96  TNKCRGYGFVDFESGGYALAAVKALQDK-----GIHAQMARQQE 134
           T K +G   V +E    A AAV+    K      +   +AR++ 
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 104

>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 = 48.6 bits (116), Expect = 1e-07
 Identities = 20/106 (18%), Positives = 31/106 (29%), Gaps = 11/106 (10%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVST--------RILRD-NNNTSKGVGF 182
            ++ D + +Y+  L  +    DL     +   V            I  D      KG   
Sbjct: 10  DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 69

Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
              E        ++ F+G    GSK  L V  A          + G
Sbjct: 70  VSYEDPPTAKAAVEWFDGKDFQGSK--LKVSLARKKPPMNSGPSSG 113

>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 = 3e-11
 Identities = 19/74 (25%), Positives = 29/74 (39%), Gaps = 8/74 (10%)

Query: 50  PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
            +G   ++K  LYI  L+   T  DL  +             L        GY FVD+  
Sbjct: 2   SSGSSGMNK--LYIGNLSPAVTADDLRQLFGDRKLP------LAGQVLLKSGYAFVDYPD 53

Query: 110 GGYALAAVKALQDK 123
             +A+ A++ L  K
Sbjct: 54  QNWAIRAIETLSGK 67

>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 = 44.2 bits (105), Expect = 3e-06
 Identities = 18/93 (19%), Positives = 33/93 (35%), Gaps = 8/93 (8%)

Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
              LYI NL       DL  L       ++ ++L        G  F     ++   + I+
Sbjct: 8   MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIE 62

Query: 197 LFNGST-LPGSKEPLLVKFADSGLKKRGAGAGG 228
             +G   L G  + + V ++ S   +    + G
Sbjct: 63  TLSGKVELHG--KIMEVDYSVSKKLRSSGPSSG 93

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 57.9 bits (140), Expect = 4e-11
 Identities = 18/106 (16%), Positives = 41/106 (38%), Gaps = 20/106 (18%)

Query: 36  ITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT 95
           +  ++  H+   G P      S+  ++IR L  D T+ ++I++   +G + +   +    
Sbjct: 1   MRGSHHHHHHGSGVP------SRV-IHIRKLPIDVTEGEVISLGLPFGKVTNLLML---- 49

Query: 96  TNKCRGYGFVDFESGGYALAAVKALQDKG-------IHAQMARQQE 134
             K +   F++  +   A   V              I+ Q +  +E
Sbjct: 50  --KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE 93

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 46.8 bits (111), Expect = 4e-07
 Identities = 16/95 (16%), Positives = 40/95 (42%), Gaps = 5/95 (5%)

Query: 123 KGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGF 182
           +G H             ++I  LP++  E ++ SL   +  V +  +L+      K   F
Sbjct: 2   RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAF 56

Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
             + +++  + M+  +   T     +P+ ++F++ 
Sbjct: 57  IEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 91

>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 = 57.7 bits (140), Expect = 4e-11
 Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 1/71 (1%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYG-PIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
              +L++  L     +  +    +  G  ++S K I ++ T    GY FV+F     A  
Sbjct: 8   MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEK 67

Query: 116 AVKALQDKGIH 126
            +  +  K + 
Sbjct: 68  CLHKINGKPLP 78

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 2/80 (2%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKY-VTVVSTRILRD-NNNTSKGVGFARLESKD 189
                  +L++ +L     E  +    A    TV+S +I+R+       G  F       
Sbjct: 4   GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLA 63

Query: 190 KCDQMIQLFNGSTLPGSKEP 209
             ++ +   NG  LPG+   
Sbjct: 64  TAEKCLHKINGKPLPGATPA 83

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 58.8 bits (142), Expect = 4e-11
 Identities = 18/103 (17%), Positives = 36/103 (34%), Gaps = 13/103 (12%)

Query: 42  QHNGSPGTPTGPEQLSKTN-LYIRGLTQDTTDKDL----INMCSQYGPIISTKAILDKTT 96
           QH  SP   + P     +  + I  +  +   + L      + S  G I+    I+   +
Sbjct: 12  QHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD---IVVDLS 68

Query: 97  NKCRGYGFVDFESGGYALAAVKALQ-----DKGIHAQMARQQE 134
           +   G  ++ F +   A A V+A Q        +    +   +
Sbjct: 69  DDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ 111

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 17/113 (15%), Positives = 44/113 (38%), Gaps = 13/113 (11%)

Query: 114 LAAVKALQDKGIHAQMARQQEQDP-----TNLYIANLPLNFKECDLESLL----AKYVTV 164
           +    A + +  H          P       + I N+     +  L++LL    +    +
Sbjct: 1   MKETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDI 60

Query: 165 VSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
           +   I+ D ++ + G  +    +++     ++ F G    G+  PL++ F+++
Sbjct: 61  LD--IVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGN--PLVITFSET 109

>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 = 57.6 bits (140), Expect = 4e-11
 Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 14/79 (17%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           GS G+           L+I  L ++ T++++ ++  QYG ++    I        + YGF
Sbjct: 1   GSSGSS------GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGF 46

Query: 105 VDFESGGYALAAVKALQDK 123
           V  E    A  A++ L   
Sbjct: 47  VHIEDKTAAEDAIRNLHHY 65

>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 = 49.1 bits (118), Expect = 5e-08
 Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 9/91 (9%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
             L+I NLP    E ++ SL  +Y  V+   I+       K  GF  +E K   +  I+ 
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRN 61

Query: 198 FNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
            +   L G    + V+ + +  K     + G
Sbjct: 62  LHHYKLHG--VNINVEASKNKSKASSGPSSG 90

>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 = 57.2 bits (139), Expect = 6e-11
 Identities = 19/92 (20%), Positives = 41/92 (44%), Gaps = 13/92 (14%)

Query: 51  TGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESG 110
           +G    + T L++  ++   T+++L     +YGP+I    +        + Y FV  E  
Sbjct: 3   SGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERA 54

Query: 111 GYALAAVKALQDK---G--IHAQMARQQEQDP 137
             A+ A++ L +    G  +H Q++  + +  
Sbjct: 55  EDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTA 86

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 15/98 (15%), Positives = 37/98 (37%), Gaps = 9/98 (9%)

Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
               +  T L++ N+       +L +   +Y  V+   I++          F  +E  + 
Sbjct: 4   GSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-------DYAFVHMERAED 56

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
             + I+  + +   G  + + V+ + S L+     + G
Sbjct: 57  AVEAIRGLDNTEFQG--KRMHVQLSTSRLRTASGPSSG 92

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 60.7 bits (146), Expect = 7e-11
 Identities = 25/92 (27%), Positives = 39/92 (42%), Gaps = 12/92 (13%)

Query: 53  PEQLSKTNLYIRGLTQDTTDKDL----INMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
           PE      +YI  L +     +L      + SQ+G I+    IL   + K RG  FV F+
Sbjct: 4   PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFK 60

Query: 109 SGGYALAAVKALQ-----DKGIHAQMARQQEQ 135
               A  A++++Q     DK +  Q A+    
Sbjct: 61  EVSSATNALRSMQGFPFYDKPMRIQYAKTDSD 92

>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 = 54.1 bits (129), Expect = 1e-08
 Identities = 21/174 (12%), Positives = 53/174 (30%), Gaps = 8/174 (4%)

Query: 129 MARQQEQDPTNLYIANLPLNFKECDLESLL----AKYVTVVSTRILRDNNNTSKGVGFAR 184
           MA  + +    +YI NL    K+ +L+  L    +++  ++   + R      +G  F  
Sbjct: 1   MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK--MRGQAFVI 58

Query: 185 LESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPGAEVRLWGR 244
            +        ++   G        P+ +++A +         G          + +   +
Sbjct: 59  FKEVSSATNALRSMQGFPFYDK--PMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQ 116

Query: 245 DSADSQLAYEHPMTPIPATIQYQRFTAGPGGTGHIPAGYTPWVPTQYVMPAPHM 298
           ++  ++ A +                  P  T      +       Y+ P   +
Sbjct: 117 ETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMI 170

>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 = 50.6 bits (120), Expect = 2e-07
 Identities = 18/138 (13%), Positives = 40/138 (28%), Gaps = 11/138 (7%)

Query: 1   MTMQLYHRVSNATSPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTN 60
               ++H                            +    +     P      E      
Sbjct: 150 APRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHI 209

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++  L ++T +  L  + +Q+      + +  +         FV+F++   A AA  AL
Sbjct: 210 LFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDAL 264

Query: 121 Q------DKGIHAQMARQ 132
           Q      +  +    A++
Sbjct: 265 QGFKITQNNAMKISFAKK 282

>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 = 56.8 bits (138), Expect = 8e-11
 Identities = 21/85 (24%), Positives = 42/85 (49%), Gaps = 6/85 (7%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIIST-KAILDKTTNKCRGYGFVDFESGGYALAAVK 118
            ++I  L  +  +K L +  S +G I+ T K + D  T   +GY F++F S   + AA++
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 119 ALQ-----DKGIHAQMARQQEQDPT 138
           A+      ++ I    A +++   +
Sbjct: 67  AMNGQYLCNRPITVSYAFKKDSKGS 91

>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 = 39.9 bits (94), Expect = 8e-05
 Identities = 27/97 (27%), Positives = 42/97 (43%), Gaps = 7/97 (7%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVST-RILRD-NNNTSKGVGFARLESKDKCDQ 193
             + ++I NL     E  L    + +  ++ T +I+RD +   SKG  F    S D  D 
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 194 MIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPN 230
            I+  NG  L     P+ V +A    KK   G+G  +
Sbjct: 64  AIEAMNGQYLCNR--PITVSYA---FKKDSKGSGPSS 95

>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 = 56.6 bits (137), Expect = 1e-10
 Identities = 19/69 (27%), Positives = 28/69 (40%), Gaps = 3/69 (4%)

Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           GP   +   +Y+  L  D   KD+ ++  +YG I     I  K       + FV+FE   
Sbjct: 16  GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRD---IDLKNRRGGPPFAFVEFEDPR 72

Query: 112 YALAAVKAL 120
            A  AV   
Sbjct: 73  DAEDAVYGR 81

>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 = 50.8 bits (122), Expect = 1e-08
 Identities = 18/93 (19%), Positives = 33/93 (35%), Gaps = 4/93 (4%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
           +   +Y+ NLP + +  D+E +  KY  +    +            F   E     +  +
Sbjct: 21  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG--GPPFAFVEFEDPRDAEDAV 78

Query: 196 QLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
              +G    G +  L V+F  SG       + G
Sbjct: 79  YGRDGYDYDGYR--LRVEFPRSGRGTGSGPSSG 109

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 58.3 bits (141), Expect = 2e-10
 Identities = 20/109 (18%), Positives = 36/109 (33%), Gaps = 3/109 (2%)

Query: 13  TSPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTD 72
             PA      +           P    +   +   G   G E      L +  L    +D
Sbjct: 45  NRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVET--GAKLLVSNLDFGVSD 102

Query: 73  KDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ 121
            D+  + +++G +       D+ + +  G   V FE    AL A+K  +
Sbjct: 103 ADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYK 150

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 56.8 bits (137), Expect = 5e-10
 Identities = 18/100 (18%), Positives = 38/100 (38%), Gaps = 2/100 (2%)

Query: 118 KALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTS 177
           K   D         +  +    L ++NL     + D++ L A++ T+    +  D +  S
Sbjct: 69  KWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS 128

Query: 178 KGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
            G      E +    + ++ + G  L G   P+ ++   S
Sbjct: 129 LGTADVHFERRADALKAMKQYKGVPLDGR--PMDIQLVAS 166

>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 = 55.6 bits (134), Expect = 3e-10
 Identities = 18/99 (18%), Positives = 37/99 (37%), Gaps = 16/99 (16%)

Query: 45  GSPGTPTGPEQL--SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
           GS G+         S+  L+IR L  + T+ ++I +   +G + +          K +  
Sbjct: 1   GSSGSSGDKMDGAPSRV-LHIRKLPGEVTETEVIALGLPFGKVTNIL------MLKGKNQ 53

Query: 103 GFVDFESGGYALAAVKALQDKG-------IHAQMARQQE 134
            F++  +   A+  V              I+ Q +  +E
Sbjct: 54  AFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE 92

>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 = 44.0 bits (104), Expect = 4e-06
 Identities = 16/93 (17%), Positives = 39/93 (41%), Gaps = 6/93 (6%)

Query: 124 GIHAQMARQQEQDPTN-LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGF 182
           G       + +  P+  L+I  LP    E ++ +L   +  V +  +L+      K   F
Sbjct: 1   GSSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAF 55

Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
             L +++    M+  ++  T     +P+ ++++
Sbjct: 56  LELATEEAAITMVNYYSAVTPHLRNQPIYIQYS 88

>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 = 55.2 bits (133), Expect = 5e-10
 Identities = 17/99 (17%), Positives = 33/99 (33%), Gaps = 16/99 (16%)

Query: 45  GSPGTPTGPEQL--SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
           GS G+     ++  S   +++RGL +   + DL+    ++G I              +  
Sbjct: 1   GSSGSSGSHHKVSVSPV-VHVRGLCESVVEADLVEALEKFGTICYVM------MMPFKRQ 53

Query: 103 GFVDFESGGYALAAVKALQDKG-------IHAQMARQQE 134
             V+FE+   A   V    D              +  + 
Sbjct: 54  ALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKR 92

>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 = 41.3 bits (97), Expect = 3e-05
 Identities = 11/87 (12%), Positives = 29/87 (33%), Gaps = 6/87 (6%)

Query: 132 QQEQDPTN-LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
             +   +  +++  L  +  E DL   L K+ T+    ++       K       E+ D 
Sbjct: 9   HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDS 63

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADS 217
             + +       +  + +     ++ S
Sbjct: 64  AKECVTFAADVPVYIAGQQAFFNYSTS 90

>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 = 54.5 bits (132), Expect = 5e-10
 Identities = 18/98 (18%), Positives = 40/98 (40%), Gaps = 18/98 (18%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           GS G+           +++  ++   T ++L ++  + G +I    +        + Y F
Sbjct: 1   GSSGSSGNT-----WKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAF 47

Query: 105 VDFESGGYALAAVKALQDK---G--IHAQMARQQEQDP 137
           V  E    A AA+  L  K   G  I+ +++ + ++  
Sbjct: 48  VHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKKS 85

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 50.3 bits (121), Expect = 1e-08
 Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 9/97 (9%)

Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
                +   +++ N+       +L SL  +   V+   ++       K   F  +E +  
Sbjct: 3   SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEAD 55

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAG 227
               I   NG  + G  + + V+ +  G KK G  +G
Sbjct: 56  AKAAIAQLNGKEVKG--KRINVELSTKGQKKSGPSSG 90

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 54.4 bits (131), Expect = 6e-10
 Identities = 18/85 (21%), Positives = 29/85 (34%), Gaps = 14/85 (16%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           S   ++IRGL     + DL+    ++GPI     +        +    V+FE    A  A
Sbjct: 21  SPV-VHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNA 73

Query: 117 VKALQDKG-------IHAQMARQQE 134
           V    D              +  Q+
Sbjct: 74  VNYAADNQIYIAGHPAFVNYSTSQK 98

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 40.9 bits (96), Expect = 4e-05
 Identities = 15/100 (15%), Positives = 29/100 (29%), Gaps = 11/100 (11%)

Query: 124 GIHAQMARQQEQDPTN------LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTS 177
           G H     +   DP        ++I  L     E DL   L ++  +    ++       
Sbjct: 2   GHHHHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----K 56

Query: 178 KGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
           K       E        +     + +  +  P  V ++ S
Sbjct: 57  KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTS 96

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 54.2 bits (131), Expect = 9e-10
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           NL+I  L  + +  +L    S+         ++D  T   R +G+VDFES      A++
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFESAEDLEKALE 76

>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 = 53.4 bits (129), Expect = 2e-09
 Identities = 17/93 (18%), Positives = 39/93 (41%), Gaps = 3/93 (3%)

Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
             +   P NL+I NL  N    +L+  +++        ++     T++  G+   ES + 
Sbjct: 11  GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED 70

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRG 223
            ++ ++L  G  + G+   + ++        RG
Sbjct: 71  LEKALEL-TGLKVFGN--EIKLEKPKGRDGTRG 100

>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 = 53.8 bits (130), Expect = 9e-10
 Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 7/71 (9%)

Query: 48  GTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
           G+       SK  +++   T+D T ++L     QYG +      + K     R + FV F
Sbjct: 3   GSHHHHHHGSK--VFVGRCTEDMTAEELQQFFCQYGEV--VDVFIPK---PFRAFAFVTF 55

Query: 108 ESGGYALAAVK 118
                A +   
Sbjct: 56  ADDKVAQSLCG 66

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 53.2 bits (128), Expect = 2e-09
 Identities = 14/59 (23%), Positives = 28/59 (47%)

Query: 62  YIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
            I         K L ++ S+ G +++ +  +D+ T K +G+ FV+  S   A   +K+ 
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSF 74

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 1/77 (1%)

Query: 141 YIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLFN 199
            I +  +   +  L SL +K   VV+     D     +KG  F    S +   ++I+ F+
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 200 GSTLPGSKEPLLVKFAD 216
           G  L       L    D
Sbjct: 76  GKRLDLKHRLFLYTMKD 92

>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 = 54.5 bits (131), Expect = 2e-09
 Identities = 23/105 (21%), Positives = 37/105 (35%), Gaps = 8/105 (7%)

Query: 16  ANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDL 75
           AN +      T      T  +T  +  H+      + P       +Y+  L  +    +L
Sbjct: 34  ANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCP---LDCKVYVGNLGNNGNKTEL 90

Query: 76  INMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
                 YGP+ S     +       G+ FV+FE    A  AV+ L
Sbjct: 91  ERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVREL 130

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 48.0 bits (114), Expect = 4e-07
 Identities = 20/90 (22%), Positives = 33/90 (36%), Gaps = 6/90 (6%)

Query: 126 HAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARL 185
           H  M R        +Y+ NL  N  + +LE     Y  + S  + R+      G  F   
Sbjct: 62  HHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEF 117

Query: 186 ESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
           E        ++  +G TL G    + V+ +
Sbjct: 118 EDPRDAADAVRELDGRTLCG--CRVRVELS 145

>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 = 52.4 bits (126), Expect = 2e-09
 Identities = 9/70 (12%), Positives = 26/70 (37%), Gaps = 7/70 (10%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
             + + ++ L QD+  +++ ++   Y        +     ++ +   FV   +G  A  A
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNA 56

Query: 117 VKALQDKGIH 126
           ++        
Sbjct: 57  IQMFHQYSFR 66

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 47.0 bits (112), Expect = 2e-07
 Identities = 17/91 (18%), Positives = 36/91 (39%), Gaps = 8/91 (8%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
           + + + NLP +    ++  LL  Y  +    + R     +K   F  L + ++    IQ+
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDR-----NKRTAFVTLLNGEQAQNAIQM 59

Query: 198 FNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
           F+  +  G    L+V+   +        + G
Sbjct: 60  FHQYSFRGK--DLIVQLQPTDALLCSGPSSG 88

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 52.1 bits (125), Expect = 5e-09
 Identities = 23/94 (24%), Positives = 34/94 (36%), Gaps = 10/94 (10%)

Query: 46  SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
            PG+P G       ++Y+  L +D    DL     + G +      L  T    R   F+
Sbjct: 7   GPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-----LRLTWQGPRRRAFL 61

Query: 106 DFESGGYALAAVKALQD-----KGIHAQMARQQE 134
            +     A  AV  LQ        +   +ARQQ 
Sbjct: 62  HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQR 95

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 20/96 (20%), Positives = 31/96 (32%), Gaps = 8/96 (8%)

Query: 122 DKGIHAQMARQQEQDP--TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKG 179
             G     +   E  P   ++Y+ NLP + +  DL+  L +  +V     LR      + 
Sbjct: 2   SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP----LRLTWQGPRR 57

Query: 180 VGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
             F          Q +    G  L      L V  A
Sbjct: 58  RAFLHYPDSAAAQQAVSCLQGLRLGTD--TLRVALA 91

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 52.3 bits (126), Expect = 5e-09
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 3/76 (3%)

Query: 43  HNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
            +GS G    P +   T  Y+  L  +T   D+  +      I S + + DK T+K +G+
Sbjct: 2   SSGSSGKEL-PTEPPYT-AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGF 58

Query: 103 GFVDFESGGYALAAVK 118
            +V+F+       A+ 
Sbjct: 59  CYVEFDEVDSLKEALT 74

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 20/95 (21%), Positives = 43/95 (45%), Gaps = 5/95 (5%)

Query: 135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQ 193
           + P   Y+ NLP N  + D++++     ++ S R++RD + +  KG  +   +  D   +
Sbjct: 13  EPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKE 71

Query: 194 MIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
            +   +G+ L      L V  A+   + +   + G
Sbjct: 72  ALTY-DGALLGDR--SLRVDIAEGRKQDKSGPSSG 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 = 52.0 bits (125), Expect = 7e-09
 Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 19/99 (19%)

Query: 44  NGSPGTPTGPEQLSKTN----------LYIRGL-TQDTTDKDLINMCSQYGPIISTKAIL 92
           +GS G     +  + TN          ++I  L T      D+  + S+YG +       
Sbjct: 3   SGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH- 61

Query: 93  DKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR 131
                  +GY FV + +  +A AAV     + +  Q   
Sbjct: 62  -------KGYAFVQYSNERHARAAVLGENGRVLAGQTLD 93

>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 = 45.4 bits (108), Expect = 1e-06
 Identities = 22/109 (20%), Positives = 40/109 (36%), Gaps = 12/109 (11%)

Query: 123 KGIHAQMARQQEQDPTN--LYIANLPLNF-KECDLESLLAKYVTVVSTRILRDNNNTSKG 179
           K   + +  + +    N  ++I NL     K+ D+E++ +KY  V    +        KG
Sbjct: 11  KLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKG 63

Query: 180 VGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
             F +  ++      +   NG  L G    L +  A      R   + G
Sbjct: 64  YAFVQYSNERHARAAVLGENGRVLAGQT--LDINMAGEPKPDRSGPSSG 110

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 19/92 (20%), Positives = 38/92 (41%), Gaps = 2/92 (2%)

Query: 139 NLYIANLPLNFKECDLESLLAK-YVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
           +L++ +L  +  +  L     K Y +    +++ D    SKG GF +   + +  + +  
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70

Query: 198 FNGSTLPGSKEPLLVKFADSGLKKRGAGAGGP 229
             G+   GSK P+ +  A     +      GP
Sbjct: 71  CQGAVGLGSK-PVRLSVAIPKASRVKPVESGP 101

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 2/63 (3%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIIST-KAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           +L++  LT D  D  L     +  P     K +LD+T    +GYGFV F        A+ 
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQT-GVSKGYGFVKFTDELEQKRALT 69

Query: 119 ALQ 121
             Q
Sbjct: 70  ECQ 72

>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 = 51.4 bits (123), Expect = 1e-08
 Identities = 13/70 (18%), Positives = 23/70 (32%), Gaps = 6/70 (8%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           SKT +  + L   T   ++    S++G +            +      V+F     A  A
Sbjct: 9   SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVL------LPEGGITAIVEFLEPLEARKA 62

Query: 117 VKALQDKGIH 126
            + L     H
Sbjct: 63  FRHLAYSKFH 72

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 11/86 (12%)

Query: 42  QHNGSPGTPTGPEQLSKTNLYIRGL-TQDTTDKDLINMCSQYGPIISTKAILDKTTNKCR 100
            H+ S   P G     K+ L+I  L  ++ + +DL  + S YG I+              
Sbjct: 8   HHHSSGLVPRGS--HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------N 57

Query: 101 GYGFVDFESGGYALAAVKALQDKGIH 126
            +GF+ F++      A++    +   
Sbjct: 58  AFGFIQFDNPQSVRDAIEXESQEMNF 83

>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 = 40.0 bits (94), Expect = 7e-05
 Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 10/86 (11%)

Query: 136 DPTNLYIANLPL-NFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQM 194
             + L+I NLPL N  + DL  + + Y  ++   I           GF + ++       
Sbjct: 21  MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDA 73

Query: 195 IQLFNGSTLPGSKEPLLVKFADSGLK 220
           I+  +     G K  L+++ + S  +
Sbjct: 74  IEXESQEMNFGKK--LILEVSSSNAR 97

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 50.7 bits (122), Expect = 2e-08
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 4/75 (5%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDK-TTNKCRGYG 103
           GS G+   P+    T  ++  L  D T++ +         I + +   +     + +G+G
Sbjct: 4   GSSGSRL-PKSPPYT-AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFG 60

Query: 104 FVDFESGGYALAAVK 118
           + +FE     L+A+ 
Sbjct: 61  YAEFEDLDSLLSALS 75

>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 = 48.0 bits (115), Expect = 1e-07
 Identities = 22/97 (22%), Positives = 38/97 (39%), Gaps = 6/97 (6%)

Query: 134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT--SKGVGFARLESKDKC 191
           +  P   ++ NLP +  E  ++        + + R+ R+ +N    KG G+A  E  D  
Sbjct: 12  KSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSL 70

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
              + L N  +L      + V  AD    K    + G
Sbjct: 71  LSALSL-NEESLGNK--RIRVDVADQAQDKDSGPSSG 104

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 5/64 (7%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
            +Y+  L       +L    S YGP+ +     +       G+ FV+FE    A  AV+ 
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56

Query: 120 LQDK 123
           L  K
Sbjct: 57  LDGK 60

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 47.3 bits (113), Expect = 3e-07
 Identities = 17/103 (16%), Positives = 38/103 (36%), Gaps = 12/103 (11%)

Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF 198
            +Y+ NL     + +LE   + Y  + +  I R+      G  F   E     +  ++  
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 199 NGSTLPGSKEPLLVKFADSGLKKRGAGAGGPN------IYRGP 235
           +G  + GS+  + V+ +    ++               ++ GP
Sbjct: 58  DGKVICGSR--VRVELSTGMPRRSRFDRPPARRKLLEVLFNGP 98

>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 = 50.1 bits (120), Expect = 3e-08
 Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 4/78 (5%)

Query: 45  GSPG-TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           GS G +  G    +K   +I  +    T  D++          +   +L     +  G  
Sbjct: 1   GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60

Query: 104 FVDFESGGYALAAVKALQ 121
            V F++      A K+ +
Sbjct: 61  LVQFKN---EDDARKSER 75

>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 = 38.6 bits (90), Expect = 4e-04
 Identities = 16/108 (14%), Positives = 35/108 (32%), Gaps = 4/108 (3%)

Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVST-RILRDNNNTSKGVGFARLESK 188
                      +I N+P +  + D+   L       +   +L DNN    G    + +++
Sbjct: 8   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 67

Query: 189 DKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPG 236
           D   +  +L +   L   +E  +       +++            GP 
Sbjct: 68  DDARKSERL-HRKKL-NGREAFVHVVTLEDMREIEKNPPAQG-KSGPS 112

>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 = 49.7 bits (119), Expect = 3e-08
 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 4/78 (5%)

Query: 45  GSPGTPTGPEQLSKTN-LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           GS G+       +    + +RGL    + ++++   S    + +   +      +  G  
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 104 FVDFESGGYALAAVKALQ 121
           FV F S      A KAL+
Sbjct: 61  FVQFAS---QEIAEKALK 75

>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 = 49.2 bits (118), Expect = 4e-08
 Identities = 12/67 (17%), Positives = 28/67 (41%), Gaps = 3/67 (4%)

Query: 53  PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDK-TTNKCRGYGFVDFESGG 111
           P+    T  ++  L  D T++ +         I + +   +     + +G+G+ +FE   
Sbjct: 15  PKSPPYT-AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLD 72

Query: 112 YALAAVK 118
             L+A+ 
Sbjct: 73  SLLSALS 79

>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 = 45.7 bits (109), Expect = 9e-07
 Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 6/86 (6%)

Query: 134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT--SKGVGFARLESKDKC 191
           +  P   ++ NLP +  E  ++        + + R+ R+ +N    KG G+A  E  D  
Sbjct: 16  KSPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSL 74

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADS 217
              + L N  +L      + V  AD 
Sbjct: 75  LSALSL-NEESLGNR--RIRVDVADQ 97

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 49.0 bits (117), Expect = 6e-08
 Identities = 14/73 (19%), Positives = 32/73 (43%), Gaps = 8/73 (10%)

Query: 59  TNLYIRGLTQDTTDK------DLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
           + + +  + Q   D+       +  + S++G I +      +   K +GY F+++ S  +
Sbjct: 16  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEEDGKTKGYIFLEYASPAH 73

Query: 113 ALAAVKALQDKGI 125
           A+ AVK      +
Sbjct: 74  AVDAVKNADGYKL 86

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 12/86 (13%), Positives = 30/86 (34%), Gaps = 9/86 (10%)

Query: 138 TNLYIANLPLNFKE------CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKC 191
           + + + N+P    +        +  + +K+  + +     ++   +KG  F    S    
Sbjct: 16  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGK-TKGYIFLEYASPAHA 74

Query: 192 DQMIQLFNGSTLPGSKEPLLV-KFAD 216
              ++  +G  L   +    V  F D
Sbjct: 75  VDAVKNADGYKLDK-QHTFRVNLFTD 99

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 48.4 bits (116), Expect = 7e-08
 Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 13/72 (18%)

Query: 58  KTNLYIRGL-TQDTTDKDLINMCSQYGPI--ISTKAILDKTTNKCRGYGFVDFESGGYAL 114
           K+ L+I  L  ++ + +DL  + S YG I  I+ K            +GF+ F++     
Sbjct: 10  KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK----------NAFGFIQFDNPQSVR 59

Query: 115 AAVKALQDKGIH 126
            A++    +   
Sbjct: 60  DAIECESQEMNF 71

>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 = 49.1 bits (117), Expect = 9e-08
 Identities = 17/84 (20%), Positives = 29/84 (34%), Gaps = 7/84 (8%)

Query: 42  QHNGSPGTPTGPEQLSKTN----LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTN 97
               SP         S       +Y++GL  +  +K +I+   +   +  +  I      
Sbjct: 5   SSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNG 64

Query: 98  KCRGYGFVDFESGGYALAAVKALQ 121
           K  G GFV+F +         AL 
Sbjct: 65  KATGEGFVEFRN---EADYKAALC 85

>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 = 48.3 bits (115), Expect = 1e-07
 Identities = 11/82 (13%), Positives = 32/82 (39%), Gaps = 6/82 (7%)

Query: 56  LSKTNLYIRGLTQDTTDKDLI---NMCSQYGPIISTKAILDKTTNKCR---GYGFVDFES 109
           + K  +++ GL+Q   D +++       ++G I         +    +      +V +  
Sbjct: 13  VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIR 72

Query: 110 GGYALAAVKALQDKGIHAQMAR 131
              AL A++ + +  +  +  +
Sbjct: 73  SEDALRAIQCVNNVVVDGRTLK 94

>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 = 47.9 bits (114), Expect = 2e-07
 Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 7/79 (8%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
            S  +   P + S+  + + GL    + +DL +   + G +       D       G G 
Sbjct: 2   SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGV 54

Query: 105 VDFESGGYALAAVKALQDK 123
           V+F        AV+ L + 
Sbjct: 55  VEFVRKEDMTYAVRKLDNT 73

>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 = 40.6 bits (95), Expect = 6e-05
 Identities = 13/97 (13%), Positives = 32/97 (32%), Gaps = 8/97 (8%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           + ++ LP +    DL+  + +   V    + RD      G G      K+     ++  +
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD 71

Query: 200 GSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPG 236
            +     +      +    +    + + G +   GP 
Sbjct: 72  NTKFRSHE--GETAYIRVKVDGPRSPSYGRSRSSGPS 106

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 10/67 (14%), Positives = 21/67 (31%), Gaps = 8/67 (11%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           ++++ G  +      L      +GP+     ++DK       +  V+    G   A    
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPV--ASVVMDKDKGV---FAIVEMGDVG---AREAV 61

Query: 120 LQDKGIH 126
           L      
Sbjct: 62  LSQSQHS 68

>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 = 46.4 bits (111), Expect = 3e-07
 Identities = 17/91 (18%), Positives = 31/91 (34%), Gaps = 10/91 (10%)

Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           G    S   +++   T D T+ +L    SQYG +      +       R + FV F    
Sbjct: 1   GSSGSSG--VFVGRCTGDMTEDELREFFSQYGDV--MDVFI---PKPFRAFAFVTFADDQ 53

Query: 112 YALAAVKA---LQDKGIHAQMARQQEQDPTN 139
            A +       ++   +H   A  +    + 
Sbjct: 54  IAQSLCGEDLIIKGISVHISNAEPKHNSNSG 84

>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 = 47.2 bits (112), Expect = 4e-07
 Identities = 17/87 (19%), Positives = 29/87 (33%), Gaps = 2/87 (2%)

Query: 32  GTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI 91
           G+H  +    Q  G               + +RGL    T ++++   S    + +   +
Sbjct: 18  GSHMASMTGGQQMGRGSNSADSANDGF--VRLRGLPFGCTKEEIVQFFSGLEIVPNGITL 75

Query: 92  LDKTTNKCRGYGFVDFESGGYALAAVK 118
                 K  G  FV F S   A  A+ 
Sbjct: 76  PVDPEGKITGEAFVQFASQELAEKALG 102

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 46.4 bits (110), Expect = 7e-07
 Identities = 14/97 (14%), Positives = 35/97 (36%), Gaps = 8/97 (8%)

Query: 27  GSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPII 86
           GS +   H  +    + +     P       +  + ++ L +  + +DL ++  +     
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMSKLPA-----KRYRITMKNLPEGCSWQDLKDLARENSLET 56

Query: 87  STKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDK 123
           +        T    G G ++F S    + A++ L + 
Sbjct: 57  T---FSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 16/85 (18%), Positives = 30/85 (35%), Gaps = 4/85 (4%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           + + NLP      DL+ L  +     +      N     G G     S++   + ++  N
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETT--FSSVNTRDFDGTGALEFPSEEILVEALERLN 88

Query: 200 GSTLPGSKEPLLVKFADSGLKKRGA 224
                GS   + V+  D+    R +
Sbjct: 89  NIEFRGSV--ITVERDDNPPPIRRS 111

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 45.1 bits (107), Expect = 8e-07
 Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 8/66 (12%)

Query: 61  LYIRGLTQDTTDK------DLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYAL 114
           + +  + Q   D+       +  + S++G I +      +   K +GY F+++ S  +A+
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEEDGKTKGYIFLEYASPAHAV 61

Query: 115 AAVKAL 120
            AVK  
Sbjct: 62  DAVKNA 67

>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 = 46.0 bits (109), Expect = 8e-07
 Identities = 20/99 (20%), Positives = 32/99 (32%), Gaps = 13/99 (13%)

Query: 45  GSPGTPTGPEQLSKTN-LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           G+P    GP      N + + GL    + +DL +   + G +       D       G G
Sbjct: 2   GAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTG 54

Query: 104 FVDFESGGYALAAVKALQDK-----GIHAQMARQQEQDP 137
            V+F        AV+ L +             R +   P
Sbjct: 55  VVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGP 93

>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 = 43.3 bits (102), Expect = 9e-06
 Identities = 11/97 (11%), Positives = 28/97 (28%), Gaps = 6/97 (6%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           + ++ LP +    DL+  + +   V    + RD      G G      K+     ++  +
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLD 72

Query: 200 GSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRGPG 236
            +     +             +  +     +  R   
Sbjct: 73  NTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRS 109

>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 = 45.2 bits (106), Expect = 5e-06
 Identities = 17/97 (17%), Positives = 36/97 (37%), Gaps = 3/97 (3%)

Query: 126 HAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARL 185
                 + +    ++YI   P +    D++  L     V++ ++ R  +   KG  F   
Sbjct: 98  EVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVF 157

Query: 186 ESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKR 222
           +S +   + ++   G         LL+ F D    K+
Sbjct: 158 DSIESAKKFVETP-GQKYKE--TDLLILFKDDYFAKK 191

>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 = 45.2 bits (106), Expect = 5e-06
 Identities = 17/101 (16%), Positives = 32/101 (31%), Gaps = 1/101 (0%)

Query: 23  SSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQY 82
           S     +          +        T      +   ++YI+G   D T  D+       
Sbjct: 74  SKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDK 133

Query: 83  GPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDK 123
           G +++ + +        +G  FV F+S   A   V+    K
Sbjct: 134 GQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKFVETPGQK 173

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 43.7 bits (103), Expect = 6e-06
 Identities = 24/88 (27%), Positives = 35/88 (39%), Gaps = 12/88 (13%)

Query: 43  HNGSPGTPTGPE---QLSKTN---LYIRGLTQDTTDKDLINMCSQYGPIISTKA---ILD 93
            +GS G  T  E    LSK N   + +RGL    T ++++    Q+ PI   K     + 
Sbjct: 2   SSGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVT 61

Query: 94  KTTNKCRGYGFVDFESGGYALAAVKALQ 121
               +  G  FV F        A  AL+
Sbjct: 62  YPDGRPTGDAFVLFAC---EEYAQNALR 86

>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 = 43.4 bits (102), Expect = 7e-06
 Identities = 14/93 (15%), Positives = 33/93 (35%), Gaps = 7/93 (7%)

Query: 35  PITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQD-TTDKDLINMCSQYGPIISTKAILD 93
              ++  +  G P      +Q     +++  L     +D  ++ +   YG I +      
Sbjct: 2   SSGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYI---- 57

Query: 94  KTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
               + +   F++ E+   A+A V     K + 
Sbjct: 58  --LMRMKSQAFIEMETREDAMAMVDHCLKKALW 88

>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 = 42.8 bits (101), Expect = 8e-06
 Identities = 12/72 (16%), Positives = 28/72 (38%), Gaps = 6/72 (8%)

Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLIN-----MCSQYGPIISTKAILDKTTNKCRGYGFVD 106
           GP   ++  LY+  +    T++ +++     M            +L    N+ + + F++
Sbjct: 1   GPLGSARR-LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 59

Query: 107 FESGGYALAAVK 118
           F S      A+ 
Sbjct: 60  FRSVDETTQAMA 71

>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 = 43.3 bits (102), Expect = 1e-05
 Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 5/78 (6%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
            GS  +    +  +   +++RGL    T+ D+ N  S   P+     I      +  G  
Sbjct: 32  RGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV--RVHIEIGPDGRVTGEA 89

Query: 104 FVDFESGGYALAAVKALQ 121
            V+F +      AV A+ 
Sbjct: 90  DVEFAT---HEEAVAAMS 104

>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 = 42.4 bits (100), Expect = 1e-05
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 45  GSPGTPTGPEQLSKTN--LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
           GS G+ +G    S T   +++RGL    T+ D+ N  S   P+     I      +  G 
Sbjct: 1   GSSGS-SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM--RVHIEIGPDGRVTGE 57

Query: 103 GFVDFESGGYALAAVK 118
             V+F +   A+AA+ 
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 = 42.6 bits (100), Expect = 1e-05
 Identities = 10/61 (16%), Positives = 21/61 (34%), Gaps = 6/61 (9%)

Query: 65  GLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG 124
           GL    +   L+ +  + G + +     +K       Y F  + +   +  A   L  K 
Sbjct: 34  GLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTLNGKE 87

Query: 125 I 125
           +
Sbjct: 88  V 88

>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 = 42.0 bits (99), Expect = 2e-05
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 4/76 (5%)

Query: 45  GSPGTPTGPEQLSKTN--LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
           GS G+   P  ++  +  + + G+     + D+ +        +    +L     +  G 
Sbjct: 1   GSSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR--VDAVHLLKDHVGRNNGN 58

Query: 103 GFVDFESGGYALAAVK 118
           G V F S      A+K
Sbjct: 59  GLVKFLSPQDTFEALK 74

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 40.7 bits (95), Expect = 7e-05
 Identities = 15/80 (18%), Positives = 36/80 (45%), Gaps = 8/80 (10%)

Query: 51  TGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKC--RGYGFVDFE 108
           +G     K  +++ GL  D  + ++     ++GP++       ++ +    +GY F+ F+
Sbjct: 3   SGSSGSRK--VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60

Query: 109 SGGYALAAVKALQDKGIHAQ 128
                 ++V+AL D  +   
Sbjct: 61  EE----SSVQALIDACLEED 76

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 40.3 bits (94), Expect = 9e-05
 Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 6/99 (6%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI--LDKTTNKCRG 101
           +GS G   GPE      + +RGL    + +D+ N  S          +  +     +  G
Sbjct: 3   SGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSG 62

Query: 102 YGFVDFESGGYALAAV----KALQDKGIHAQMARQQEQD 136
             FV+ ES      A+    +++  + I    + + E D
Sbjct: 63  EAFVELESEDDVKLALKKDRESMGHRYIEVFKSHRTEMD 101

>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 = 39.2 bits (92), Expect = 1e-04
 Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 5/72 (6%)

Query: 50  PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
            +G    +   + +RG   + T+K+++   +   P+     I+        GY FVDF +
Sbjct: 2   SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV--AIRIVRNAHGNKTGYIFVDFSN 59

Query: 110 GGYALAAVKALQ 121
                   +AL+
Sbjct: 60  ---EEEVKQALK 68

>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 = 39.5 bits (92), Expect = 2e-04
 Identities = 16/73 (21%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 48  GTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI--LDKTTNKCRGYGFV 105
           G+    E      +  +GL    T +D++N  S          I  L     K RG   +
Sbjct: 1   GSKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALI 60

Query: 106 DFESGGYALAAVK 118
           + ES      A++
Sbjct: 61  EMESEQDVQKALE 73

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 38.9 bits (90), Expect = 3e-04
 Identities = 19/95 (20%), Positives = 33/95 (34%), Gaps = 7/95 (7%)

Query: 32  GTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI 91
           G+   +   +   G+   P+G  ++    L I+      T   L  +C+  G +      
Sbjct: 1   GSSGSSGKRITRPGNTDDPSGGNKV--LLLSIQNPLYPITVDVLYTVCNPVGKVQRIV-- 56

Query: 92  LDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH 126
                 +      V+FES   A  A  AL    I+
Sbjct: 57  ---IFKRNGIQAMVEFESVLCAQKAKAALNGADIY 88

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 39.3 bits (91), Expect = 4e-04
 Identities = 17/124 (13%), Positives = 36/124 (29%), Gaps = 14/124 (11%)

Query: 3   MQLYHRVSNATSPANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLY 62
           M  +H   +A +     +S  S   +       +         SP             + 
Sbjct: 1   MHHHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSP----------VLRII 50

Query: 63  IRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQD 122
           +  L    T   L  + S++G ++         T   +    + +     A  A  +L  
Sbjct: 51  VENLFYPVTLDVLHQIFSKFGTVLKII----TFTKNNQFQALLQYADPVSAQHAKLSLDG 106

Query: 123 KGIH 126
           + I+
Sbjct: 107 QNIY 110

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 40.2 bits (93), Expect = 4e-04
 Identities = 16/91 (17%), Positives = 31/91 (34%), Gaps = 15/91 (16%)

Query: 50  PTGPEQLSKTNLYIRGLTQDTTDK---------DLINMCSQYGPIISTKAILDKTTNKCR 100
             G  +     LY+ G+      K          +  + S+ G I   + +  K      
Sbjct: 126 GIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK------ 179

Query: 101 GYGFVDFESGGYALAAVKALQDKGIHAQMAR 131
             GFV F+    A  A +A+ ++ +     +
Sbjct: 180 NCGFVKFKYQANAEFAKEAMSNQTLLLPSDK 210

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 21/105 (20%), Positives = 37/105 (35%), Gaps = 2/105 (1%)

Query: 16  ANTHSSSSSNTGSQNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDL 75
            ++H     ++G    G+H  +    Q  G      GPE      + +RGL    + +D+
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDV 61

Query: 76  INMCSQYGPIISTKAI--LDKTTNKCRGYGFVDFESGGYALAAVK 118
            N  S          +  +     +  G  FV+  S      A+K
Sbjct: 62  QNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK 106

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	305
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	100.0
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	100.0
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	100.0
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.98
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.98
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.98
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.98
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.93
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.88
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.87
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.86
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.85
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.85
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.84
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.84
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.83
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.83
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.83
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.82
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.82
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.82
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.82
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.82
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.82
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.82
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.82
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.82
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.82
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.81
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.81
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.81
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.81
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.81
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.81
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.81
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.81
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.81
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.81
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.81
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.81
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.81
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.8
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.8
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.8
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.8
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.8
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.8
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.8
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.8
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.8
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.8
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.8
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.8
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.8
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.79
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.79
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.79
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.79
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.79
2div_A	99	TRNA selenocysteine associated protein; structural	99.79
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.79
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.79
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.79
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.79
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.78
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.78
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.78
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.78
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.78
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.78
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.78
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.78
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.78
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.78
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.78
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.78
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.78
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.78
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.78
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.78
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.78
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.78
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.78
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.78
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.78
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.78
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.77
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.77
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.77
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.77
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.77
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.77
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.77
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.77
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.77
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.77
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.77
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.77
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.77
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.77
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.77
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.77
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.77
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.77
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.77
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.77
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.77
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.77
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.77
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.77
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.77
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.77
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.77
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.77
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.77
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.77
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.77
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.77
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.76
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.76
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.76
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.76
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.76
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.76
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.76
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.76
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.76
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.76
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.76
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.76
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.76
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.76
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.76
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.76
2div_A	99	TRNA selenocysteine associated protein; structural	99.76
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.76
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.76
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.76
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.76
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.76
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.76
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.76
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.76
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.75
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.75
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.75
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.75
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.75
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.75
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.75
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.75
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.75
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.75
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.75
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.61
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.75
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.75
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.75
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.75
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.75
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.75
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.75
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.75
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.75
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.75
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.75
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.75
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.75
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.75
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.75
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.75
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.75
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.74
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.74
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.74
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.74
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.74
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.74
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.74
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.74
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.74
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.74
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.74
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.74
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.74
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.74
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.74
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.74
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.74
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.74
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.74
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.74
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.74
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.74
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.73
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.73
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.73
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.73
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.73
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.73
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.73
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.73
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.73
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.73
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.73
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.73
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.73
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.73
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.73
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.72
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.72
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.72
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.72
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.72
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.72
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.72
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.72
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.72
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.72
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.72
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.72
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.72
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.72
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.72
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.72
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.71
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.71
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.71
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.71
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.71
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.71
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.71
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.71
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.71
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.71
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.7
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.7
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.7
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.7
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.7
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.7
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.7
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.7
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.7
1x5p_A	97	Negative elongation factor E; structure genomics,	99.7
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.7
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.7
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.7
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.7
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.69
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.69
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.69
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.69
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.69
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.69
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.69
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.69
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.69
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.69
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.69
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.69
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.68
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.68
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.68
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.68
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.68
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.68
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.68
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.68
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.68
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.68
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.67
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.67
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.67
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.67
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.67
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.67
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.67
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.67
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.67
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.67
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.67
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.67
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.67
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.67
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.67
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.67
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.66
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.66
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.66
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.66
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.47
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.65
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.65
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.65
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.65
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.64
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.64
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.64
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.64
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.64
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.64
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.63
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.63
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.63
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.63
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.63
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.63
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.63
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.62
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.62
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.62
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.62
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.62
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.62
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.62
1x5p_A	97	Negative elongation factor E; structure genomics,	99.62
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.61
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.61
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.61
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.61
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.61
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.61
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.6
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.6
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.6
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.6
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.6
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.59
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.59
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.59
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.59
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.58
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.56
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.55
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.55
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.54
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.54
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.53
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.53
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.53
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.52
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.51
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.51
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.48
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.48
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.47
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.46
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.45
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.45
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.43
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.41
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.41
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.37
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.37
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.32
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.28
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.16
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.11
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.1
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.08
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.96
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.93
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.79
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.77
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.69
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.49
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.24
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.12
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.83
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.82
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.8
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.69
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.53
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.25
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.24
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.2
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.1
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.1
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.9
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.89
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.88
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.59
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	94.92
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.86
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	94.54
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	91.75
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	86.88

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=7.4e-38  Score=264.44  Aligned_cols=161  Identities=25%  Similarity=0.396  Sum_probs=147.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccccc---
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQE---  134 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~---  134 (305)
                      .++|||+|||+++||++|+++|++||+|++|+|++|+.+++++|||||+|.+.++|++|++.+|+..+.++.++...   
T Consensus        15 ~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~   94 (213)
T 4f02_A           15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   94 (213)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccccc
Confidence            47899999999999999999999999999999999999999999999999999999999999999988887766322   


Q ss_pred             ------CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCc
Q psy4086         135 ------QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKE  208 (305)
Q Consensus       135 ------~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~  208 (305)
                            ....+|||+|||+++++++|+++|++||.|++|+|++++. .++|||||+|.+.++|++||+.|||..|.|  +
T Consensus        95 ~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~-~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g--~  171 (213)
T 4f02_A           95 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLND--R  171 (213)
T ss_dssp             CTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESSHHHHHHHHHHHTTCEETT--E
T ss_pred             cccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCC-CCceEEEEEeCCHHHHHHHHHHhCCCEECC--E
Confidence                  2346899999999999999999999999999999999864 479999999999999999999999999999  7


Q ss_pred             cEEEEeccCCCcC
Q psy4086         209 PLLVKFADSGLKK  221 (305)
Q Consensus       209 ~l~v~~a~~~~~~  221 (305)
                      +|+|+++.++..+
T Consensus       172 ~i~V~~a~~~~~~  184 (213)
T 4f02_A          172 KVFVGRFKSRKER  184 (213)
T ss_dssp             ECEEEECCCHHHH
T ss_pred             EEEEEEcCCCccc
Confidence            8999999876543

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=100.00  E-value=3.5e-36  Score=243.58  Aligned_cols=158  Identities=32%  Similarity=0.559  Sum_probs=146.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc-----
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ-----  132 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~-----  132 (305)
                      +++|||+|||+++++++|+++|+.||+|.++++++++.+|+++|||||+|.+.++|++|++.|||..+.++.++.     
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            578999999999999999999999999999999999989999999999999999999999999998887776652     


Q ss_pred             --ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCcc
Q psy4086         133 --QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEP  209 (305)
Q Consensus       133 --~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~  209 (305)
                        .....++|||+|||..+++++|+++|++||.|.++++..++ +|.++|||||+|.+.++|.+|++.|||..+.|+..+
T Consensus        82 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~  161 (167)
T 1fxl_A           82 SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEP  161 (167)
T ss_dssp             CCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSC
T ss_pred             CcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccc
Confidence              22345789999999999999999999999999999999998 889999999999999999999999999999997677


Q ss_pred             EEEEec
Q psy4086         210 LLVKFA  215 (305)
Q Consensus       210 l~v~~a  215 (305)
                      |+|+||
T Consensus       162 i~v~~A  167 (167)
T 1fxl_A          162 ITVKFA  167 (167)
T ss_dssp             CEEEEC
T ss_pred             eEEEeC
Confidence            999986

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=100.00  E-value=4.9e-36  Score=243.23  Aligned_cols=159  Identities=32%  Similarity=0.543  Sum_probs=147.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc----
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ----  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~----  132 (305)
                      ..++|||+|||+++++++|+++|+.||+|.++++++++.+|+++|||||+|.+.++|++|++.|||..+.++.++.    
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            3578999999999999999999999999999999999989999999999999999999999999988887766552    


Q ss_pred             ---ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCc
Q psy4086         133 ---QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKE  208 (305)
Q Consensus       133 ---~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~  208 (305)
                         .....++|||+|||..+++++|+++|++||.|..+++..++ ++.++|||||+|.+.++|.+|++.|||..+.|+.+
T Consensus        82 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~  161 (168)
T 1b7f_A           82 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQ  161 (168)
T ss_dssp             CCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSS
T ss_pred             CCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCe
Confidence               22345789999999999999999999999999999999998 88999999999999999999999999999988778


Q ss_pred             cEEEEec
Q psy4086         209 PLLVKFA  215 (305)
Q Consensus       209 ~l~v~~a  215 (305)
                      +|+|+||
T Consensus       162 ~l~V~~A  168 (168)
T 1b7f_A          162 PLSVRLA  168 (168)
T ss_dssp             CCEEEEC
T ss_pred             EEEEEeC
Confidence            8999986

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=100.00  E-value=4e-36  Score=249.91  Aligned_cols=165  Identities=21%  Similarity=0.377  Sum_probs=141.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc---
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR---  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~---  131 (305)
                      ....++|||+|||+++|+++|+++|+.||.|.+|+|++++.+|+++|||||+|.+.++|++|++. ++..+.++.+.   
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            34568899999999999999999999999999999999999999999999999999999999986 55555544433   


Q ss_pred             --ccc--------CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCC
Q psy4086         132 --QQE--------QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNG  200 (305)
Q Consensus       132 --~~~--------~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g  200 (305)
                        ...        ...++|||+|||.++++++|+++|+.||.|..|+|+.++ ++.++|||||+|.+.++|.+|++. ++
T Consensus        89 ~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~  167 (196)
T 1l3k_A           89 AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KY  167 (196)
T ss_dssp             CCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SC
T ss_pred             ccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CC
Confidence              211        234789999999999999999999999999999999998 889999999999999999999986 79


Q ss_pred             CCCCCCCccEEEEeccCCCcCCC
Q psy4086         201 STLPGSKEPLLVKFADSGLKKRG  223 (305)
Q Consensus       201 ~~~~g~~~~l~v~~a~~~~~~~~  223 (305)
                      ..|+|  +.|.|+++.++.....
T Consensus       168 ~~~~G--~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          168 HTVNG--HNCEVRKALSKQEMAS  188 (196)
T ss_dssp             CEETT--EECEEEECC-------
T ss_pred             cEECC--EEEEEEecCChhHhcc
Confidence            99999  7799999998766553

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=100.00  E-value=9.2e-36  Score=243.09  Aligned_cols=160  Identities=23%  Similarity=0.429  Sum_probs=142.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCC--CccceEEEEecchhhHHHHHHHhccCcccce---e--
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTN--KCRGYGFVDFESGGYALAAVKALQDKGIHAQ---M--  129 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g--~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~---~--  129 (305)
                      +.++|||+|||+++|+++|+++|++||+|.+|+|++++.++  +++|||||+|.+.++|++|++.|||..+...   .  
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            35789999999999999999999999999999999999876  8999999999999999999999998766422   1  


Q ss_pred             ---ccc---ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCC
Q psy4086         130 ---ARQ---QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTL  203 (305)
Q Consensus       130 ---~~~---~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~  203 (305)
                         ...   .....++|||+|||.++++++|+++|++||.|.+++++.+++|.++|||||+|.+.++|.+|++.|||..+
T Consensus        82 ~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~  161 (175)
T 3nmr_A           82 MKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQT  161 (175)
T ss_dssp             EEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCC
T ss_pred             EccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcc
Confidence               111   12245789999999999999999999999999999999999899999999999999999999999999877


Q ss_pred             CC-CCccEEEEecc
Q psy4086         204 PG-SKEPLLVKFAD  216 (305)
Q Consensus       204 ~g-~~~~l~v~~a~  216 (305)
                      .+ ..++|+|+||+
T Consensus       162 ~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          162 MEGCSSPMVVKFAD  175 (175)
T ss_dssp             CTTCSSCCEEEECC
T ss_pred             cCCCCCCeEEEecC
Confidence            53 34789999985

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=100.00  E-value=1.8e-35  Score=249.69  Aligned_cols=163  Identities=20%  Similarity=0.326  Sum_probs=146.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc----
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ----  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~----  132 (305)
                      ..++|||+|||+++|+++|+++|+.||+|.+|+|++++.+++++|||||+|.+.++|++|++.||+..|.++.++.    
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            4578999999999999999999999999999999999989999999999999999999999999988887776552    


Q ss_pred             --------------ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHH
Q psy4086         133 --------------QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQL  197 (305)
Q Consensus       133 --------------~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~  197 (305)
                                    .....++|||+|||.++++++|+++|++||.|+.|+|+.++ +|.++|||||+|.+.++|.+|++.
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~  186 (216)
T 2qfj_A          107 NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS  186 (216)
T ss_dssp             CCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHH
Confidence                          12345789999999999999999999999999999999997 889999999999999999999999


Q ss_pred             hCCCCCCCCCccEEEEeccCCCcC
Q psy4086         198 FNGSTLPGSKEPLLVKFADSGLKK  221 (305)
Q Consensus       198 l~g~~~~g~~~~l~v~~a~~~~~~  221 (305)
                      |||..|.|  +.|+|.|+..+...
T Consensus       187 l~g~~~~g--~~i~V~~a~~~~~~  208 (216)
T 2qfj_A          187 MNLFDLGG--QYLRVGKAVTPPMP  208 (216)
T ss_dssp             HTTCBCSS--SBCEEEECSSCSST
T ss_pred             ccCCEeCC--cEEEEEEecCCCCC
Confidence            99999999  77999999886443

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=100.00  E-value=2.4e-36  Score=244.99  Aligned_cols=159  Identities=23%  Similarity=0.456  Sum_probs=145.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHH---hccCcccceecccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA---LQDKGIHAQMARQQ  133 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~---l~g~~i~~~~~~~~  133 (305)
                      +.++|||+|||+++|+++|+++|+.||.|.+|+|++++.+|+++|||||+|.+.++|++|++.   |+|+.|.+.+....
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~~   81 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPR   81 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCCH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccccch
Confidence            457899999999999999999999999999999999999999999999999999999999997   67777776665432


Q ss_pred             --cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         134 --EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       134 --~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                        ....++|||+|||.++++++|+++|+.||.|.+++++.++ +|.++|||||+|.+.++|.+|++ +++..+.|  +.|
T Consensus        82 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g--~~i  158 (167)
T 2cjk_A           82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKD--RKI  158 (167)
T ss_dssp             HHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSS--SCE
T ss_pred             hhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCC--eEE
Confidence              2345789999999999999999999999999999999997 89999999999999999999998 89999999  779


Q ss_pred             EEEeccCC
Q psy4086         211 LVKFADSG  218 (305)
Q Consensus       211 ~v~~a~~~  218 (305)
                      +|+|+.++
T Consensus       159 ~V~~a~pk  166 (167)
T 2cjk_A          159 EIKRAEPR  166 (167)
T ss_dssp             EEEECCCC
T ss_pred             EEeecCCC
Confidence            99999874

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.6e-35  Score=239.47  Aligned_cols=156  Identities=26%  Similarity=0.483  Sum_probs=142.9

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc------
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ------  132 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~------  132 (305)
                      ++|||+|||+++|+++|+++|++||+|.++++++++ +++++|||||+|.+.++|++|++.|||..+.++.++.      
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            579999999999999999999999999999999998 4789999999999999999999999999887776652      


Q ss_pred             ---ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCc
Q psy4086         133 ---QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKE  208 (305)
Q Consensus       133 ---~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~  208 (305)
                         .....++|||+|||.++++++|+++|++||.|.++.++.++ ++.++|||||+|.+.++|.+|++.|||..+.|  +
T Consensus        80 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~  157 (166)
T 3md3_A           80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG--R  157 (166)
T ss_dssp             CCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETT--E
T ss_pred             CCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC--c
Confidence               22345789999999999999999999999999999999996 88999999999999999999999999999999  7


Q ss_pred             cEEEEeccC
Q psy4086         209 PLLVKFADS  217 (305)
Q Consensus       209 ~l~v~~a~~  217 (305)
                      .|+|.||+.
T Consensus       158 ~i~v~~a~~  166 (166)
T 3md3_A          158 PLRINWAAK  166 (166)
T ss_dssp             ECEEEESCC
T ss_pred             EEEEEecCC
Confidence            899999863

>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=100.00  E-value=6.6e-33  Score=232.37  Aligned_cols=153  Identities=16%  Similarity=0.227  Sum_probs=132.7

Q ss_pred             CCCeEEEcCCC-CCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccccc-
Q psy4086          57 SKTNLYIRGLT-QDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQE-  134 (305)
Q Consensus        57 ~~~~l~V~~Lp-~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~-  134 (305)
                      ..++|||+||| +++|+++|+++|++||.|.+|+|+++     .+|||||+|.+.++|++|++.|||..+.++.++... 
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 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            35789999999 89999999999999999999999875     378999999999999999999998877665543110 


Q ss_pred             -------------------------------------------CCCCceEEecCCCCCCHHHHHHHHhhCCCe--EEEEE
Q psy4086         135 -------------------------------------------QDPTNLYIANLPLNFKECDLESLLAKYVTV--VSTRI  169 (305)
Q Consensus       135 -------------------------------------------~~~~~l~V~nlp~~~te~~l~~~F~~~g~v--~~v~i  169 (305)
                                                                 ...++|||+|||+++|+++|+++|++||.|  .++++
T Consensus        78 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~  157 (205)
T 3tyt_A           78 KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKV  157 (205)
T ss_dssp             SCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEE
T ss_pred             cCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE
Confidence                                                       112469999999999999999999999999  89999


Q ss_pred             eeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCC--CccEEEEec
Q psy4086         170 LRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGS--KEPLLVKFA  215 (305)
Q Consensus       170 ~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~--~~~l~v~~a  215 (305)
                      +.++ +.++|||||+|.+.++|.+||..|||..|.+.  +.++.|+|+
T Consensus       158 ~~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          158 FSGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CSCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             EcCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            8876 45679999999999999999999999999774  368888886

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=100.00  E-value=1e-32  Score=242.80  Aligned_cols=162  Identities=19%  Similarity=0.270  Sum_probs=149.0

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc-----
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ-----  132 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~-----  132 (305)
                      .++|||+|||+++|+++|+++|+.||.|..++++.++.+|+++|||||+|.+.++|.+|++.|||..+.++.+..     
T Consensus        95 ~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~  174 (284)
T 3smz_A           95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDA  174 (284)
T ss_dssp             SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCG
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCC
Confidence            467999999999999999999999999999999999999999999999999999999999999988887766551     


Q ss_pred             -----ccCCCCceEEecCCCCC-CHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCC
Q psy4086         133 -----QEQDPTNLYIANLPLNF-KECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGS  206 (305)
Q Consensus       133 -----~~~~~~~l~V~nlp~~~-te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  206 (305)
                           .....++|||+|||.++ ++++|+++|+.||.|.+++|+.+.+|.++|||||+|.+.++|.+|++.|||..|.| 
T Consensus       175 ~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g-  253 (284)
T 3smz_A          175 GQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGG-  253 (284)
T ss_dssp             GGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEETT-
T ss_pred             CCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCccCC-
Confidence                 22345789999999995 99999999999999999999999999999999999999999999999999999999 


Q ss_pred             CccEEEEeccCCCcC
Q psy4086         207 KEPLLVKFADSGLKK  221 (305)
Q Consensus       207 ~~~l~v~~a~~~~~~  221 (305)
                       ++|+|.|+.++..+
T Consensus       254 -~~l~v~~a~~~~~~  267 (284)
T 3smz_A          254 -SHLRVSFCAPGPPG  267 (284)
T ss_dssp             -EECEEEECCSSSCH
T ss_pred             -eEEEEEEecCCCcc
Confidence             78999999886654

>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=100.00  E-value=1.6e-32  Score=223.49  Aligned_cols=151  Identities=22%  Similarity=0.393  Sum_probs=135.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcc----C-------CeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQY----G-------PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGI  125 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~----G-------~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i  125 (305)
                      ..++|||+|||+++|+++|+++|++|    |       .|.++.+.      +++|||||+|.+.++|++|+ .|||..+
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            45789999999999999999999999    6       67777664      45789999999999999999 7999888


Q ss_pred             cceeccccc-------CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHH
Q psy4086         126 HAQMARQQE-------QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQL  197 (305)
Q Consensus       126 ~~~~~~~~~-------~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~  197 (305)
                      .++.++...       ...++|||+|||.++++++|+++|++||.|..+++..++ +|.++|||||+|.+.++|.+|++.
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~  155 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG  155 (172)
T ss_dssp             TTEECEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHH
T ss_pred             cCceeeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHH
Confidence            877765322       235789999999999999999999999999999999997 899999999999999999999999


Q ss_pred             hCCCCCCCCCccEEEEecc
Q psy4086         198 FNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       198 l~g~~~~g~~~~l~v~~a~  216 (305)
                      |||..+.|  +.|.|+||.
T Consensus       156 l~g~~~~g--~~l~V~~As  172 (172)
T 2g4b_A          156 LNGMQLGD--KKLLVQRAS  172 (172)
T ss_dssp             HTTCEETT--EECEEEECC
T ss_pred             cCCCEECC--eEEEEEeCC
Confidence            99999999  779999973

>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=100.00  E-value=1.5e-33  Score=230.39  Aligned_cols=156  Identities=19%  Similarity=0.330  Sum_probs=135.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccccc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQE  134 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~  134 (305)
                      ....++|||+|||+++|+++|+++|+.||.+.. .++.+..+++++|||||+|.+.++|++|++ |||..|.++.++...
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~   87 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEec
Confidence            445688999999999999999999999998766 445555678999999999999999999995 998888777665322


Q ss_pred             ---------CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCC
Q psy4086         135 ---------QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPG  205 (305)
Q Consensus       135 ---------~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  205 (305)
                               ...++|||+|||.++++++|+++|+.||.|..+    ..++.++|||||+|.+.++|.+|++.|||..|.|
T Consensus        88 ~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  163 (175)
T 1fje_B           88 PKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG  163 (175)
T ss_dssp             CCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETT
T ss_pred             CCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence                     234789999999999999999999999987765    4577899999999999999999999999999999


Q ss_pred             CCccEEEEeccCC
Q psy4086         206 SKEPLLVKFADSG  218 (305)
Q Consensus       206 ~~~~l~v~~a~~~  218 (305)
                        +.|+|+|+.++
T Consensus       164 --~~i~v~~a~~k  174 (175)
T 1fje_B          164 --RSVSLYYTGEK  174 (175)
T ss_dssp             --EEEEEEECSSC
T ss_pred             --eEEEEEecCCC
Confidence              77999999864

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=100.00  E-value=3.7e-32  Score=226.27  Aligned_cols=154  Identities=23%  Similarity=0.414  Sum_probs=135.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcc----C-------CeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQY----G-------PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH  126 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~----G-------~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~  126 (305)
                      .++|||+|||+++|+++|+++|++|    |       .|.++.+      ++++|||||+|.+.++|++|+ .|||..|.
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            5789999999999999999999999    4       5555554      456899999999999999999 79888777


Q ss_pred             ceeccccc---------------------------CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcc
Q psy4086         127 AQMARQQE---------------------------QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSK  178 (305)
Q Consensus       127 ~~~~~~~~---------------------------~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~  178 (305)
                      ++.++...                           ...++|||+|||.++++++|+++|++||.|.++++..++ ++.++
T Consensus        77 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~  156 (198)
T 2yh0_A           77 GQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK  156 (198)
T ss_dssp             TEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEE
T ss_pred             CceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcc
Confidence            76554111                           345789999999999999999999999999999999997 88999


Q ss_pred             cEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCCCc
Q psy4086         179 GVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLK  220 (305)
Q Consensus       179 g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~~~  220 (305)
                      |||||+|.+.++|.+|++.|||..|.|  +.|+|.++.++.+
T Consensus       157 g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a~~~~~  196 (198)
T 2yh0_A          157 GYAFCEYVDINVTDQAIAGLNGMQLGD--KKLLVQRASVGAK  196 (198)
T ss_dssp             EEEEEEESSSSHHHHHHHHHTTCEETT--EECEEEESCCCCC
T ss_pred             eEEEEEECCHHHHHHHHHHcCCCEECC--EEEEEEECCCCCC
Confidence            999999999999999999999999999  7799999987543

>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=99.98  E-value=1.7e-31  Score=232.34  Aligned_cols=162  Identities=19%  Similarity=0.279  Sum_probs=142.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccccc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQE  134 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~  134 (305)
                      ....++|||+|||+++|+++|+++|+.||.|.+|.|.+      ++|||||+|.+.++|.+|++.|||..|.++.++...
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            34567899999999999999999999999999999864      468999999999999999999999999888777443


Q ss_pred             -CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCC-CCCC-CCCccEE
Q psy4086         135 -QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNG-STLP-GSKEPLL  211 (305)
Q Consensus       135 -~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g-~~~~-g~~~~l~  211 (305)
                       ...++|||+|||..+|+++|+++|+.||.|.+|.|+.+.+|.++|||||+|.+.++|.+|++.||+ ..+. +..++|.
T Consensus        93 a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~  172 (261)
T 3sde_A           93 ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVI  172 (261)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCE
T ss_pred             cccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEE
Confidence             346789999999999999999999999999999999999999999999999999999999999954 4433 2228899


Q ss_pred             EEeccCCCcCC
Q psy4086         212 VKFADSGLKKR  222 (305)
Q Consensus       212 v~~a~~~~~~~  222 (305)
                      |.++.......
T Consensus       173 v~~~~~~~~~~  183 (261)
T 3sde_A          173 VEPMEQFDDED  183 (261)
T ss_dssp             EEECCCEESSS
T ss_pred             EeeccccCccC
Confidence            99998765443

>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=99.98  E-value=2.4e-31  Score=226.95  Aligned_cols=152  Identities=20%  Similarity=0.320  Sum_probs=133.8

Q ss_pred             CCCCeEEEcCCCC-CCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc--
Q psy4086          56 LSKTNLYIRGLTQ-DTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ--  132 (305)
Q Consensus        56 ~~~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~--  132 (305)
                      ...++|||+|||+ ++++++|+++|++||.|.+|+|++++     +|||||+|.+.++|++|++.|||..|.++.++.  
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            3457899999999 99999999999999999999999875     789999999999999999999887776554441  


Q ss_pred             ---c-------------------------------------cCCCCceEEecCCCCCCHHHHHHHHhhCC-CeEEEEEee
Q psy4086         133 ---Q-------------------------------------EQDPTNLYIANLPLNFKECDLESLLAKYV-TVVSTRILR  171 (305)
Q Consensus       133 ---~-------------------------------------~~~~~~l~V~nlp~~~te~~l~~~F~~~g-~v~~v~i~~  171 (305)
                         .                                     ....++|||+|||..+++++|+++|++|| .|.+|+++.
T Consensus       107 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~  186 (229)
T 2adc_A          107 SKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ  186 (229)
T ss_dssp             CSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS
T ss_pred             ecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEE
Confidence               1                                     01247799999999999999999999999 999999975


Q ss_pred             CCCCCcccEEEEEecCHHHHHHHHHHhCCCCCC-CCCccEEEEeccCC
Q psy4086         172 DNNNTSKGVGFARLESKDKCDQMIQLFNGSTLP-GSKEPLLVKFADSG  218 (305)
Q Consensus       172 ~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~~~l~v~~a~~~  218 (305)
                      +    .+|||||+|.+.++|.+|++.|||..+. |  +.|+|.|++++
T Consensus       187 ~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g--~~l~v~~a~~~  228 (229)
T 2adc_A          187 K----DRKMALIQMGSVEEAVQALIDLHNHDLGEN--HHLRVSFSKST  228 (229)
T ss_dssp             S----STTCEEEEESSHHHHHHHHHHHTTCBSSSS--CBCEEEECSSC
T ss_pred             C----CCcEEEEEECCHHHHHHHHHHHCCCccCCC--CeEEEEEecCC
Confidence            3    4789999999999999999999999998 7  77999998763

>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=99.98  E-value=1.8e-31  Score=234.56  Aligned_cols=153  Identities=20%  Similarity=0.340  Sum_probs=134.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHH----HHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLI----NMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~----~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      ....++|||+|||+++|+++|+    ++|++||.|.+|+|++   +++++|||||+|.+.++|++|++.|||..|.++.+
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            3456789999999999999976    8999999999999886   67899999999999999999999999877766544


Q ss_pred             c-----ccc-----------------------------------------------------------------------
Q psy4086         131 R-----QQE-----------------------------------------------------------------------  134 (305)
Q Consensus       131 ~-----~~~-----------------------------------------------------------------------  134 (305)
                      +     ...                                                                       
T Consensus        83 ~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~  162 (282)
T 3pgw_A           83 RIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPP  162 (282)
T ss_pred             EEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCC
Confidence            3     111                                                                       


Q ss_pred             ------------------------------------------CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeC
Q psy4086         135 ------------------------------------------QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD  172 (305)
Q Consensus       135 ------------------------------------------~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~  172 (305)
                                                                ...++|||+|||.++++++|+++|++||.|++|+|+.+
T Consensus       163 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~  242 (282)
T 3pgw_A          163 YMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG  242 (282)
T ss_pred             CCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecC
Confidence                                                      12366999999999999999999999999999999976


Q ss_pred             CCCCcccEEEEEecCHHHHHHHHHHhCCCCCC-CCCccEEEEecc
Q psy4086         173 NNNTSKGVGFARLESKDKCDQMIQLFNGSTLP-GSKEPLLVKFAD  216 (305)
Q Consensus       173 ~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~~~l~v~~a~  216 (305)
                      +    +|||||+|.+.++|.+|++.|||..|. |  +.|+|.|++
T Consensus       243 ~----~g~afV~f~~~~~A~~A~~~l~g~~~~~g--~~l~v~~ak  281 (282)
T 3pgw_A          243 R----HDIAFVEFDNEVQAGAARDALQGFKITQN--NAMKISFAK  281 (282)
T ss_pred             C----CcEEEEEeCCHHHHHHHHHHcCCcEeCCC--CEEEEEEec
Confidence            3    589999999999999999999999999 8  779999986

>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=99.98  E-value=8.7e-32  Score=237.71  Aligned_cols=163  Identities=18%  Similarity=0.273  Sum_probs=141.2

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ  133 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~  133 (305)
                      .+...++|||+|||+++|+++|+++|+.||+|.+|+|++++.+  ++|||||+|.+.++|++|++ +||..+.++.+...
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~  113 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVS  113 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEE
Confidence            4456788999999999999999999999999999999998743  58999999999999999995 99999999999888


Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCC-CeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYV-TVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g-~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....++|||+|||.++++++|+++|+.|| .|..|+++.++.+.++|||||+|.+.++|.+|++.|||..|.|  +.|.|
T Consensus       114 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v  191 (292)
T 2ghp_A          114 HLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG--YTLVT  191 (292)
T ss_dssp             ECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETT--EECEE
T ss_pred             ECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCC--cEEEE
Confidence            88899999999999999999999999999 9999999998888899999999999999999999999999999  78999


Q ss_pred             EeccCCCcC
Q psy4086         213 KFADSGLKK  221 (305)
Q Consensus       213 ~~a~~~~~~  221 (305)
                      .++.+....
T Consensus       192 ~~a~~~~~~  200 (292)
T 2ghp_A          192 KVSNPLEKS  200 (292)
T ss_dssp             EECCCC---
T ss_pred             EECCCCccc
Confidence            999875443

>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=99.97  E-value=5.6e-31  Score=231.61  Aligned_cols=155  Identities=25%  Similarity=0.392  Sum_probs=142.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccccc-C
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQE-Q  135 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~-~  135 (305)
                      .+++|||+|||+++|+++|+++|+.|| |.+|.+      ++++|||||+|.+.++|++|++.|||..+.++.+.... .
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~   93 (284)
T 3smz_A           21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP   93 (284)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC
Confidence            457899999999999999999999999 999987      45788999999999999999999999999888877443 3


Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ..++|||+|||.++++++|+++|+.||.|..++++.++ +|.++|||||+|.+.++|.+|++.|+|..+.|  +.|.|.+
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g--~~i~v~~  171 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP--RTLYVHW  171 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT--EECEEEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCC--cEEEEEE
Confidence            45789999999999999999999999999999999987 89999999999999999999999999999999  7899999


Q ss_pred             ccCCCc
Q psy4086         215 ADSGLK  220 (305)
Q Consensus       215 a~~~~~  220 (305)
                      +.....
T Consensus       172 a~~~~~  177 (284)
T 3smz_A          172 TDAGQL  177 (284)
T ss_dssp             CCGGGC
T ss_pred             CCCCCC
Confidence            987543

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.97  E-value=2.6e-31  Score=221.46  Aligned_cols=151  Identities=20%  Similarity=0.318  Sum_probs=133.1

Q ss_pred             CCCeEEEcCCCC-CCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc--
Q psy4086          57 SKTNLYIRGLTQ-DTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ--  133 (305)
Q Consensus        57 ~~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~--  133 (305)
                      ++++|||+|||+ ++++++|+++|++||.|.+|++++++     +|||||+|.+.++|++|++.|||..+.++.++..  
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            357899999999 99999999999999999999998875     7899999999999999999998877665544411  


Q ss_pred             ----------------------------------------cCCCCceEEecCCCCCCHHHHHHHHhhCC-CeEEEEEeeC
Q psy4086         134 ----------------------------------------EQDPTNLYIANLPLNFKECDLESLLAKYV-TVVSTRILRD  172 (305)
Q Consensus       134 ----------------------------------------~~~~~~l~V~nlp~~~te~~l~~~F~~~g-~v~~v~i~~~  172 (305)
                                                              ....++|||+|||..+++++|+++|++|| .|.+++++.+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~  156 (198)
T 1qm9_A           77 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK  156 (198)
T ss_dssp             CCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST
T ss_pred             cCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC
Confidence                                                    01256799999999999999999999999 9999999764


Q ss_pred             CCCCcccEEEEEecCHHHHHHHHHHhCCCCCC-CCCccEEEEeccCC
Q psy4086         173 NNNTSKGVGFARLESKDKCDQMIQLFNGSTLP-GSKEPLLVKFADSG  218 (305)
Q Consensus       173 ~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~~~l~v~~a~~~  218 (305)
                          .+|||||+|.+.++|.+|++.|||..+. |  ++|+|.|++++
T Consensus       157 ----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g--~~l~v~~a~~~  197 (198)
T 1qm9_A          157 ----DRKMALIQMGSVEEAVQALIDLHNHDLGEN--HHLRVSFSKST  197 (198)
T ss_dssp             ----TSSCEEEECSSHHHHHHHHHHHTSSCCSSC--CSCCEEEECCC
T ss_pred             ----CCcEEEEEeCCHHHHHHHHHHhcCCccCCC--CeEEEEeeccc
Confidence                3789999999999999999999999998 7  77999998763

>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=99.97  E-value=3.6e-31  Score=233.79  Aligned_cols=158  Identities=17%  Similarity=0.252  Sum_probs=137.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccC-CeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc--
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYG-PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ--  133 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G-~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~--  133 (305)
                      ..++|||+|||+++++++|+++|+.|| .|..|.++.++. +.++|||||+|.+.++|.+|++.|||..|.++.+...  
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 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            467899999999999999999999999 999999999885 8899999999999999999999999888877665521  


Q ss_pred             ------------cCCCCceEEecCCCC-CCHHHHHHHHhhCCCeEEEEEeeCCC--CCcccEEEEEecCHHHHHHHHHHh
Q psy4086         134 ------------EQDPTNLYIANLPLN-FKECDLESLLAKYVTVVSTRILRDNN--NTSKGVGFARLESKDKCDQMIQLF  198 (305)
Q Consensus       134 ------------~~~~~~l~V~nlp~~-~te~~l~~~F~~~g~v~~v~i~~~~~--g~~~g~afV~f~~~~~A~~Ai~~l  198 (305)
                                  ....++|||+|||.. +++++|+++|+.||.|..|+|+.+..  |.++|||||+|.+.++|.+|+ .|
T Consensus       195 ~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l  273 (292)
T 2ghp_A          195 NPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QM  273 (292)
T ss_dssp             CCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GG
T ss_pred             CCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-Hh
Confidence                        123478999999999 99999999999999999999999886  899999999999999999999 99


Q ss_pred             CCCCCCCCCccEEEEeccCC
Q psy4086         199 NGSTLPGSKEPLLVKFADSG  218 (305)
Q Consensus       199 ~g~~~~g~~~~l~v~~a~~~  218 (305)
                      ||..|.|  +.|.|.|+.++
T Consensus       274 ~g~~~~g--~~i~V~~a~~k  291 (292)
T 2ghp_A          274 NRSLLGN--REISVSLADKK  291 (292)
T ss_dssp             TTEEETT--EEEEEEECCCC
T ss_pred             cCCEECC--cEEEEEEecCC
Confidence            9999999  78999999875

>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=99.93  E-value=5.4e-25  Score=176.77  Aligned_cols=132  Identities=22%  Similarity=0.295  Sum_probs=110.4

Q ss_pred             EEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcc-cceec-------------------ccccCCCCceEEecCC
Q psy4086          87 STKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGI-HAQMA-------------------RQQEQDPTNLYIANLP  146 (305)
Q Consensus        87 ~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i-~~~~~-------------------~~~~~~~~~l~V~nlp  146 (305)
                      .++|+.+..  +++|||||+|.+.++|++|++.+++... ...+.                   .......++|||+|||
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~   79 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT   79 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCC
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCC
Confidence            467777764  6899999999999999999998774321 11110                   0122335789999999


Q ss_pred             CCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCCCcCC
Q psy4086         147 LNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKR  222 (305)
Q Consensus       147 ~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~~~~~  222 (305)
                      +++++++|+++|+.||.|.+|+|+.++ +|.++|||||+|.+.++|++||+.|||..|.|  ++|+|.+++....+.
T Consensus        80 ~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a~~~~~~~  154 (158)
T 2kn4_A           80 YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG--RELRVQMARYGRPPD  154 (158)
T ss_dssp             TTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSS--SEEEEEEECCSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC--eEEEEEECCCCCCCC
Confidence            999999999999999999999999997 89999999999999999999999999999999  779999998765443

>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=99.88  E-value=9.4e-23  Score=154.88  Aligned_cols=94  Identities=28%  Similarity=0.467  Sum_probs=66.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc----
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ----  133 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~----  133 (305)
                      .++|||+|||+++|+++|+++|++||.|.+|+|++++  +.++|||||+|.+.++|++|++.|||..|.++.++..    
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            4679999999999999999999999999999999986  4589999999999999999999999988877765521    


Q ss_pred             -----------cCCCCceEEecCCCCCCHHH
Q psy4086         134 -----------EQDPTNLYIANLPLNFKECD  153 (305)
Q Consensus       134 -----------~~~~~~l~V~nlp~~~te~~  153 (305)
                                 .....+|||+|||+++|++.
T Consensus        83 ~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           83 RKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CCC----------------------------
T ss_pred             ccccccccccccCCCCceEeCCCCCCccccc
Confidence                       11235799999999999864

>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=99.87  E-value=4.3e-22  Score=158.42  Aligned_cols=116  Identities=19%  Similarity=0.270  Sum_probs=101.7

Q ss_pred             CCccceEEEEecchhhHHHHHHHh-ccCcccceecc-----------------------cccCCCCceEEecCCCCCCHH
Q psy4086          97 NKCRGYGFVDFESGGYALAAVKAL-QDKGIHAQMAR-----------------------QQEQDPTNLYIANLPLNFKEC  152 (305)
Q Consensus        97 g~~~G~afV~f~~~~~A~~a~~~l-~g~~i~~~~~~-----------------------~~~~~~~~l~V~nlp~~~te~  152 (305)
                      ...+|+++|+|.+.++|++|++.+ ||..+.+ .+.                       ......++|||+|||++++++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~   88 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKT   88 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCH
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHH
Confidence            467899999999999999999999 8877766 332                       111234789999999999999


Q ss_pred             HHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCCC
Q psy4086         153 DLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGL  219 (305)
Q Consensus       153 ~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~~  219 (305)
                      +|+++|++||.|.+|+|+.+    ++|||||+|.+.++|.+|++.|||..|.|  ++|+|+|+.++.
T Consensus        89 ~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~a~~~~  149 (150)
T 2i2y_A           89 ELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCG--CRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSS--SCCEEEECCCCC
T ss_pred             HHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECC--eEEEEEEcCCCC
Confidence            99999999999999999876    58999999999999999999999999999  779999998753

>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=99.86  E-value=1.8e-21  Score=143.67  Aligned_cols=80  Identities=29%  Similarity=0.476  Sum_probs=76.1

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ..++|||+|||.++|+++|+++|++||.|.+|+|++++ +|.++|||||+|.+.++|++|++.|||..|.|  ++|+|+|
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g--r~l~V~~   95 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQS--KTIKVSY   95 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETT--EECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECC--EEEEEEE
Confidence            45789999999999999999999999999999999998 79999999999999999999999999999999  7899999


Q ss_pred             ccC
Q psy4086         215 ADS  217 (305)
Q Consensus       215 a~~  217 (305)
                      |++
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            864

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.85  E-value=1.3e-21  Score=152.70  Aligned_cols=119  Identities=19%  Similarity=0.223  Sum_probs=80.5

Q ss_pred             eEEEEecchhhHHHHHHHhccCcccceecc------cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-C
Q psy4086         102 YGFVDFESGGYALAAVKALQDKGIHAQMAR------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-N  174 (305)
Q Consensus       102 ~afV~f~~~~~A~~a~~~l~g~~i~~~~~~------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~  174 (305)
                      ++|++|.+...+..|++.++|....++...      ......++|||+|||+++++++|+++|++||.|..|+|+.++ +
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~   85 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYT   85 (135)
T ss_dssp             -----------------------------CCSCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSS
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCCCCcCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCC
Confidence            688999999999999999887654443222      333446789999999999999999999999999999999987 8


Q ss_pred             CCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCCCcCC
Q psy4086         175 NTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKR  222 (305)
Q Consensus       175 g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~~~~~  222 (305)
                      +.++|||||+|.+.++|++||+.|||..|.|  +.|+|++++......
T Consensus        86 g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g--~~l~V~~a~~~~~~~  131 (135)
T 2lea_A           86 KESRGFAFVRFHDKRDAEDAMDAMDGAVLDG--RELRVQMARYGRPPD  131 (135)
T ss_dssp             SSCCSCCEEECSCHHHHHHHHTTTTTCCSSS--SCCEEEECCCCCCCT
T ss_pred             CccceEEEEEECCHHHHHHHHHHcCCCEECC--EEEEEEECCCCCCCc
Confidence            8999999999999999999999999999999  779999998765443

>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=99.85  E-value=2.1e-21  Score=179.78  Aligned_cols=145  Identities=17%  Similarity=0.253  Sum_probs=106.5

Q ss_pred             HHHHHhccCCeeEEEEee----CC-CCCCccceE--EEEecchhhHHHHHHHhccCccc------------------cee
Q psy4086          75 LINMCSQYGPIISTKAIL----DK-TTNKCRGYG--FVDFESGGYALAAVKALQDKGIH------------------AQM  129 (305)
Q Consensus        75 L~~~f~~~G~i~~~~i~~----~~-~~g~~~G~a--fV~f~~~~~A~~a~~~l~g~~i~------------------~~~  129 (305)
                      |.+||..+++|..|..+.    ++ .+....|++  |++|.+..++..++..++.....                  ...
T Consensus         9 L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~~~~~~   88 (437)
T 3pgw_S            9 LLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKM   88 (437)
T ss_pred             HHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            788999999998874332    22 112222333  78887765554433222111100                  000


Q ss_pred             ------cccccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCC
Q psy4086         130 ------ARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGST  202 (305)
Q Consensus       130 ------~~~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~  202 (305)
                            ........++|||+|||+.+|+++|+++|++||.|+.|.|+.++ ++.++|||||+|.+.++|++||+.|||..
T Consensus        89 ~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~  168 (437)
T 3pgw_S           89 WDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKK  168 (437)
T ss_pred             cCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCE
Confidence                  00122334789999999999999999999999999999999997 88999999999999999999999999999


Q ss_pred             CCCCCccEEEEeccCCCcC
Q psy4086         203 LPGSKEPLLVKFADSGLKK  221 (305)
Q Consensus       203 ~~g~~~~l~v~~a~~~~~~  221 (305)
                      |.|  +.|.|.|+.....+
T Consensus       169 i~g--r~i~V~~a~~~~~~  185 (437)
T 3pgw_S          169 IDG--RRVLVDVERGRTVK  185 (437)
T ss_pred             ECC--EEEEEEEeCCCCCC
Confidence            999  77999999875543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=4.5e-20  Score=134.99  Aligned_cols=86  Identities=22%  Similarity=0.439  Sum_probs=79.6

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||.++++++|+++|++||.|.+|+|+.++ ++.++|||||+|.+.++|++|++.|||..|.|  +.|+|+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~V~   80 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAG--RPMRVG   80 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSS--SCCEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCC--cEEEEE
Confidence            356899999999999999999999999999999999998 78999999999999999999999999999999  779999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      ++..+....
T Consensus        81 ~a~~~~~~~   89 (95)
T 2dnz_A           81 HVTERLDGG   89 (95)
T ss_dssp             ESSCCCCCC
T ss_pred             EcccccCCC
Confidence            998865543

>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=99.84  E-value=4.6e-20  Score=140.15  Aligned_cols=87  Identities=21%  Similarity=0.348  Sum_probs=80.7

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||.++++++|+++|++||.|++|.|+.++++.++|||||+|.+.++|++|++.|||..|.|  +.|+|+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g--~~l~V~   81 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHG--KAIKVE   81 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSS--SBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECC--EEEEEE
Confidence            345689999999999999999999999999999999999888999999999999999999999999999999  779999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      +++......
T Consensus        82 ~a~~~~~~~   90 (116)
T 2fy1_A           82 QAKKPSFQS   90 (116)
T ss_dssp             ECCCSSCSS
T ss_pred             ECCCCCCCC
Confidence            999866554

>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=99.83  E-value=1.4e-20  Score=138.79  Aligned_cols=76  Identities=29%  Similarity=0.434  Sum_probs=71.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      +.++|||+|||+++|+++|+++|++||+|.+|+|++|+.+|+++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V   93 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKV   93 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            4578999999999999999999999999999999999999999999999999999999999999999988876653

>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=1.2e-20  Score=141.83  Aligned_cols=85  Identities=16%  Similarity=0.198  Sum_probs=79.2

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+||++++++++|+++|++||.|++|+|+.|+ +++++|||||+|.+.++|++||+.|||..|.|  +.|+|.
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~g--r~i~V~   81 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMG--NIIHAQ   81 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECC--eEEEEE
Confidence            456899999999999999999999999999999999998 79999999999999999999999999999999  779999


Q ss_pred             eccCCCcC
Q psy4086         214 FADSGLKK  221 (305)
Q Consensus       214 ~a~~~~~~  221 (305)
                      ++.....+
T Consensus        82 ~a~~~~~~   89 (110)
T 3s8s_A           82 LDIKGQQR   89 (110)
T ss_dssp             ECSTTHHH
T ss_pred             ECCCCcHH
Confidence            99765443

>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=99.83  E-value=6e-20  Score=136.93  Aligned_cols=88  Identities=24%  Similarity=0.344  Sum_probs=81.4

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....++|||+|||+++++++|+++|++||.|..|+|+.++ ++.++|||||+|.+.++|++|++.||+..|.|  +.|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v   89 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYG--KPIRV   89 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSS--CBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECC--eEEEE
Confidence            3456899999999999999999999999999999999998 88999999999999999999999999999999  77999


Q ss_pred             EeccCCCcCCC
Q psy4086         213 KFADSGLKKRG  223 (305)
Q Consensus       213 ~~a~~~~~~~~  223 (305)
                      .++..+..+..
T Consensus        90 ~~a~~~~~~~~  100 (105)
T 1x5u_A           90 NKASAHNKNLS  100 (105)
T ss_dssp             EETTTTSCCCC
T ss_pred             EECCCCCcCCC
Confidence            99998766553

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=5.9e-20  Score=136.23  Aligned_cols=87  Identities=24%  Similarity=0.487  Sum_probs=80.4

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ..+.++|||+|||.++++++|+++|++||.|..|+|+.++ ++.+++||||+|.+.++|++|++.||+..|.+  +.|+|
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v   86 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDG--RQIRV   86 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTS--CCCEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECC--eEEEE
Confidence            3456899999999999999999999999999999999987 78899999999999999999999999999999  77999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      .++..+...+
T Consensus        87 ~~a~~~~~~~   96 (102)
T 1x5s_A           87 DQAGKSSDNR   96 (102)
T ss_dssp             EEEECCCCCC
T ss_pred             EECCCCCCCC
Confidence            9999876655

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=9.8e-20  Score=134.30  Aligned_cols=86  Identities=21%  Similarity=0.404  Sum_probs=79.4

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....++|||+|||.++++++|+++|++||.|.+|+|+.++ ++.++|||||+|.+.++|++|++ ||+..|.|  +.|+|
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g--~~l~V   83 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMG--KKVEV   83 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSS--CBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECC--eEEEE
Confidence            3456899999999999999999999999999999999997 78999999999999999999998 99999999  77999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      +++..+..+.
T Consensus        84 ~~a~~~~~~~   93 (99)
T 2dgs_A           84 KRAEPRDSKS   93 (99)
T ss_dssp             EECCCCCCCC
T ss_pred             EECCCCcccC
Confidence            9999866654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.82  E-value=6.7e-20  Score=143.74  Aligned_cols=88  Identities=27%  Similarity=0.453  Sum_probs=81.1

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      .....++|||+|||.++++++|+++|+.||.|++|+|+.++ ++.++|||||+|.+.++|++||+.|||..|.|  +.|+
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~  115 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN--KRLK  115 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSS--CEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC--eEEE
Confidence            34456899999999999999999999999999999999998 78899999999999999999999999999999  7799


Q ss_pred             EEeccCCCcCC
Q psy4086         212 VKFADSGLKKR  222 (305)
Q Consensus       212 v~~a~~~~~~~  222 (305)
                      |++++.+..+.
T Consensus       116 v~~a~~~~~~~  126 (139)
T 1u6f_A          116 VALAASGHQRP  126 (139)
T ss_dssp             EEESSCCCCCC
T ss_pred             EEECCCCCCCC
Confidence            99999876654

>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=9.9e-20  Score=134.24  Aligned_cols=86  Identities=20%  Similarity=0.264  Sum_probs=80.4

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      .+.++|||+|||+++++++|+++|++||.|.+|+|+.++ ++.++|||||+|.+.++|++|++.|||..|.+  +.|+|.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~V~   83 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG--RMLHVL   83 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSS--CEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECC--cEEEEE
Confidence            456889999999999999999999999999999999998 88999999999999999999999999999999  779999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      ++..+..+.
T Consensus        84 ~a~~~~~~~   92 (99)
T 1whw_A           84 PSTIKKEAS   92 (99)
T ss_dssp             ECCCCSTTC
T ss_pred             EcCCCcccc
Confidence            999876654

>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=99.82  E-value=6.3e-20  Score=146.83  Aligned_cols=87  Identities=18%  Similarity=0.271  Sum_probs=80.6

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||.++++++|+++|++||.|+.|+|+.++ ++.+++||||+|.+.++|++||+.||+..|.+  +.|+|+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~l~V~  114 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD--RIIRTD  114 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETT--EECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC--eEEEEE
Confidence            456899999999999999999999999999999999998 78899999999999999999999999999999  779999


Q ss_pred             eccCCCcCCC
Q psy4086         214 FADSGLKKRG  223 (305)
Q Consensus       214 ~a~~~~~~~~  223 (305)
                      |+......+.
T Consensus       115 ~a~~~~~~~~  124 (156)
T 1h2v_Z          115 WDAGFKEGRQ  124 (156)
T ss_dssp             EESCCCTTCC
T ss_pred             ECCCCCCcCC
Confidence            9998666554

>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=99.82  E-value=4.6e-21  Score=162.83  Aligned_cols=81  Identities=20%  Similarity=0.329  Sum_probs=75.7

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCC--CeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYV--TVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g--~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ..++|||+||++++|+++|+++|++||  .|++|+|++++ +++++|||||+|.+.++|++||+.||+..|.+  +.|+|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~G--r~l~V  144 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHG--QNPVV  144 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTT--BCCEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECC--EEeEE
Confidence            567899999999999999999999999  99999999998 89999999999999999999999999999999  77999


Q ss_pred             EeccCC
Q psy4086         213 KFADSG  218 (305)
Q Consensus       213 ~~a~~~  218 (305)
                      +++...
T Consensus       145 ~~a~~~  150 (229)
T 3q2s_C          145 TPVNKQ  150 (229)
T ss_dssp             EECCHH
T ss_pred             EECCCC
Confidence            998754

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.82  E-value=1.1e-20  Score=137.22  Aligned_cols=83  Identities=16%  Similarity=0.286  Sum_probs=75.3

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCC-CeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhC-CCCCCCCCccEEEE
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYV-TVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFN-GSTLPGSKEPLLVK  213 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g-~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~-g~~~~g~~~~l~v~  213 (305)
                      +++|||+|||.++||++|+++|++|| .|.+|+|++++ ++.++|||||+|.+.++|++|++.++ +..+.|  ++|+|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~g--r~i~V~   78 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILG--QKVSMH   78 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETT--EEEEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECC--EEEEEE
Confidence            36899999999999999999999999 79999999998 79999999999999999999999874 567999  789999


Q ss_pred             eccCCCcC
Q psy4086         214 FADSGLKK  221 (305)
Q Consensus       214 ~a~~~~~~  221 (305)
                      |+.++...
T Consensus        79 ~a~~~~~~   86 (91)
T 2lxi_A           79 YSDPKPKI   86 (91)
T ss_dssp             CCCSCCCC
T ss_pred             EcCCCCCC
Confidence            99875443

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.2e-19  Score=134.73  Aligned_cols=87  Identities=23%  Similarity=0.440  Sum_probs=80.5

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||+++++++|+++|++||.|..|+|+.+ ++.+++||||+|.+.++|++|++.||+..|.+  +.|+|.
T Consensus        12 ~~~~~~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           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVAT--KPLYVA   88 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSS--SBCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCC--cEEEEE
Confidence            446789999999999999999999999999999999999 88999999999999999999999999999999  779999


Q ss_pred             eccCCCcCCC
Q psy4086         214 FADSGLKKRG  223 (305)
Q Consensus       214 ~a~~~~~~~~  223 (305)
                      ++..+..+..
T Consensus        89 ~a~~~~~~~~   98 (103)
T 2d9p_A           89 LAQRKEERQS   98 (103)
T ss_dssp             ECSSCCCCCC
T ss_pred             EecccccCCC
Confidence            9998766553

>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=99.82  E-value=1.1e-19  Score=135.81  Aligned_cols=87  Identities=23%  Similarity=0.404  Sum_probs=79.4

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCC---CCCCcc
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTL---PGSKEP  209 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~---~g~~~~  209 (305)
                      ....++|||+|||.++++++|+++|++||.|.+|+|+.++ ++.++|||||+|.+.++|++|++.||+..+   .+  ++
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g--~~   87 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMN--RP   87 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCS--SC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCC--ce
Confidence            4456889999999999999999999999999999999998 789999999999999999999999999886   66  77


Q ss_pred             EEEEeccCCCcCC
Q psy4086         210 LLVKFADSGLKKR  222 (305)
Q Consensus       210 l~v~~a~~~~~~~  222 (305)
                      |+|++++.+..+.
T Consensus        88 l~v~~a~~~~~~~  100 (106)
T 2dgp_A           88 IQVKPADSESRGG  100 (106)
T ss_dssp             CEEEECCCCSCCC
T ss_pred             EEEEECCcccccC
Confidence            9999999866554

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=6.2e-20  Score=134.54  Aligned_cols=86  Identities=28%  Similarity=0.417  Sum_probs=79.7

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEE-EEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVST-RILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v-~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ...++|||+|||.++++++|+++|++||.|.++ +|+.++ ++.++|||||+|.+.++|++|++.||+..|.|  ++|+|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v   80 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCN--RPITV   80 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETT--EECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECC--EEEEE
Confidence            356899999999999999999999999999999 999996 88999999999999999999999999999999  77999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      +++..+..+.
T Consensus        81 ~~a~~~~~~~   90 (96)
T 1x5t_A           81 SYAFKKDSKG   90 (96)
T ss_dssp             EESCCCCCCC
T ss_pred             EEecccCCCC
Confidence            9998866554

>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=99.81  E-value=1.1e-19  Score=137.77  Aligned_cols=86  Identities=28%  Similarity=0.423  Sum_probs=80.2

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++++++|+++|++||.|++|+|+.++ ++.+++||||+|.+.++|++||+.||+..|.+  +.|+|+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~V~  100 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM--KRLKVQ  100 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECC--EEEEEE
Confidence            456899999999999999999999999999999999998 89999999999999999999999999999999  779999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      |++.+..+.
T Consensus       101 ~a~~~~~~~  109 (115)
T 2cpz_A          101 LKRSKNDSK  109 (115)
T ss_dssp             CCCCSCCCC
T ss_pred             EcCCCCcCC
Confidence            999876554

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.81  E-value=8.1e-20  Score=137.32  Aligned_cols=75  Identities=23%  Similarity=0.312  Sum_probs=71.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||+|.+|+|++|+.|++++|||||+|.+.++|++|++.|||+.|.++.++
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~   79 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIH   79 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            357799999999999999999999999999999999999999999999999999999999999999999888765

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.81  E-value=2.4e-20  Score=136.29  Aligned_cols=81  Identities=21%  Similarity=0.414  Sum_probs=74.5

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCC--eEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCC----CCCCC
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVT--VVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGST----LPGSK  207 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~--v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~----~~g~~  207 (305)
                      ..-.+|||+|||+++|+++|+++|++||.  |.+|++++|+ +|++||||||+|.+.++|++|++.|||..    |+|  
T Consensus         7 ~~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            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG--   84 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT--
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC--
Confidence            44578999999999999999999999995  6799999998 89999999999999999999999999974    788  


Q ss_pred             ccEEEEeccC
Q psy4086         208 EPLLVKFADS  217 (305)
Q Consensus       208 ~~l~v~~a~~  217 (305)
                      ++|.|+||++
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            8899999875

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=1.7e-19  Score=134.16  Aligned_cols=87  Identities=17%  Similarity=0.326  Sum_probs=80.1

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhh-CCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCC-CCCCCccEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAK-YVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGST-LPGSKEPLL  211 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~-~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~-~~g~~~~l~  211 (305)
                      ....++|||+|||+++++++|+++|++ ||.|.+|+|+.++++.++|||||+|.+.++|++|++.||+.. |.|  +.|+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g--~~l~   83 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGS--KPVR   83 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSS--SCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCC--EeEE
Confidence            345689999999999999999999999 999999999999988999999999999999999999999999 999  7799


Q ss_pred             EEeccCCCcCC
Q psy4086         212 VKFADSGLKKR  222 (305)
Q Consensus       212 v~~a~~~~~~~  222 (305)
                      |.++..+..+.
T Consensus        84 v~~a~~~~~~~   94 (104)
T 2dhg_A           84 LSVAIPKASRV   94 (104)
T ss_dssp             CCBCCCCCSCC
T ss_pred             EEEccCCCcCC
Confidence            99998765554

>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=6.7e-20  Score=135.92  Aligned_cols=87  Identities=20%  Similarity=0.282  Sum_probs=80.7

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++++++|+++|++||.|++|+|+.++ ++.++|||||+|.+.++|++|++.||+..|.+  +.|+|.
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~V~   87 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG--RTIRVN   87 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETT--EEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC--cEEEEE
Confidence            456899999999999999999999999999999999997 78999999999999999999999999999999  779999


Q ss_pred             eccCCCcCCC
Q psy4086         214 FADSGLKKRG  223 (305)
Q Consensus       214 ~a~~~~~~~~  223 (305)
                      ++..+..+..
T Consensus        88 ~a~~~~~~~~   97 (102)
T 2cqb_A           88 LAKPMRIKES   97 (102)
T ss_dssp             ECCCCCCCCC
T ss_pred             eCCCCCCCCC
Confidence            9998766653

>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=99.81  E-value=8.8e-20  Score=140.63  Aligned_cols=88  Identities=18%  Similarity=0.278  Sum_probs=80.7

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....++|||+|||+++++++|+++|++||.|.+|.|+.++ ++.++|||||+|.+.++|++||+.|||..|.|  +.|.|
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v   96 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG--QPISV   96 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSS--SBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCC--eEEEE
Confidence            3446789999999999999999999999999999999998 88999999999999999999999999999999  77999


Q ss_pred             EeccCCCcCCC
Q psy4086         213 KFADSGLKKRG  223 (305)
Q Consensus       213 ~~a~~~~~~~~  223 (305)
                      +|+..+..++.
T Consensus        97 ~~a~~~~~~~~  107 (126)
T 3ex7_B           97 DWCFVRGPPKG  107 (126)
T ss_dssp             EESEESSSCCC
T ss_pred             EEecCCCCCCC
Confidence            99987666553

>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=1.1e-19  Score=135.02  Aligned_cols=87  Identities=22%  Similarity=0.337  Sum_probs=80.0

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....++|||+|||.++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|++.|||..|.|  +.|+|
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~V   87 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDG--RELRV   87 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTT--BCCEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECC--cEEEE
Confidence            3456899999999999999999999999999999999998 68999999999999999999999999999999  77999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      .+++......
T Consensus        88 ~~a~~~~~~~   97 (103)
T 2dnm_A           88 QVARYGRRDL   97 (103)
T ss_dssp             EECSSCCSCC
T ss_pred             EECCcCCCCC
Confidence            9998765443

>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=2.6e-19  Score=133.86  Aligned_cols=88  Identities=17%  Similarity=0.454  Sum_probs=80.6

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeC-C-CCCcccEEEEEecCHHHHHHHHHHh-CCCCCCCCCcc
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-N-NNTSKGVGFARLESKDKCDQMIQLF-NGSTLPGSKEP  209 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~-~-~g~~~g~afV~f~~~~~A~~Ai~~l-~g~~~~g~~~~  209 (305)
                      .....++|||+|||.++++++|+++|++||.|..|+|+.+ + ++.++|||||+|.+.++|++||+.| |+..|.|  +.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g--~~   88 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG--RR   88 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSS--CB
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECC--CE
Confidence            3456689999999999999999999999999999999998 4 8899999999999999999999999 9999999  77


Q ss_pred             EEEEeccCCCcCC
Q psy4086         210 LLVKFADSGLKKR  222 (305)
Q Consensus       210 l~v~~a~~~~~~~  222 (305)
                      |+|+|+..+....
T Consensus        89 l~v~~a~~~~~~~  101 (107)
T 2cph_A           89 LVLEWADSEVTVQ  101 (107)
T ss_dssp             CEEEECCCCCCCC
T ss_pred             EEEEeCCCCCCCC
Confidence            9999999866554

>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=99.81  E-value=3.3e-19  Score=132.89  Aligned_cols=88  Identities=24%  Similarity=0.388  Sum_probs=80.1

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCC-CCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPG-SKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-~~~~l~v~  213 (305)
                      ...++|||+|||.++++++|+++|++||.|.+|+|+.++++.++|||||+|.+.++|++||+.|||..+.+ ..++|+|+
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~   92 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVK   92 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEE
Confidence            45689999999999999999999999999999999999988999999999999999999999999999876 22459999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      +++.+..++
T Consensus        93 ~a~~~~~~~  101 (105)
T 2dnh_A           93 FADTDKESG  101 (105)
T ss_dssp             ESCSSCCCS
T ss_pred             ECccCcccC
Confidence            999876654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.81  E-value=3.7e-19  Score=135.50  Aligned_cols=78  Identities=32%  Similarity=0.491  Sum_probs=72.3

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +....++|||+|||+++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  113 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLK  113 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            344568899999999999999999999999999999999998999999999999999999999999999988887664

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=2.3e-19  Score=132.59  Aligned_cols=85  Identities=21%  Similarity=0.405  Sum_probs=79.2

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||.++++++|+++|++||.|.+|+|+.++++.++|||||+|.+.++|++|++.||+..|.|  +.|+|.
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~   91 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKE--NIIKVA   91 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSS--CEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECC--EEEEEE
Confidence            345689999999999999999999999999999999999988999999999999999999999999999999  779999


Q ss_pred             eccCCCc
Q psy4086         214 FADSGLK  220 (305)
Q Consensus       214 ~a~~~~~  220 (305)
                      +++++..
T Consensus        92 ~a~~~~~   98 (100)
T 2do4_A           92 ISNSGPS   98 (100)
T ss_dssp             ECCCCSC
T ss_pred             ECCCCCC
Confidence            9987543

>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=99.81  E-value=8.9e-20  Score=147.32  Aligned_cols=116  Identities=17%  Similarity=0.260  Sum_probs=77.9

Q ss_pred             EEecchhhHHHHHHHhccCcccce-------e----------------------cccccCCCCceEEecCCCCCCHHHHH
Q psy4086         105 VDFESGGYALAAVKALQDKGIHAQ-------M----------------------ARQQEQDPTNLYIANLPLNFKECDLE  155 (305)
Q Consensus       105 V~f~~~~~A~~a~~~l~g~~i~~~-------~----------------------~~~~~~~~~~l~V~nlp~~~te~~l~  155 (305)
                      .+|.+.++|+.|+..|+++....+       .                      ........++|||+|||+.+++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            667777777777777765433210       0                      00122234679999999999999999


Q ss_pred             HHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCCCcCC
Q psy4086         156 SLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKR  222 (305)
Q Consensus       156 ~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~~~~~  222 (305)
                      ++|++||.|..|.|+.++ +|.++|||||+|.+.++|++||+.|||..|.|  +.|.|.|+..+..++
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~l~V~~a~~~~~~~  156 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG--QTIQVDWCFVKGPKR  156 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETT--EECEEEESEECC---
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECC--EEEEEEEecCCCCCC
Confidence            999999999999999997 88999999999999999999999999999999  789999998765544

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=3e-19  Score=135.58  Aligned_cols=87  Identities=18%  Similarity=0.373  Sum_probs=78.8

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      .....++|||+|||+++++++|+++|++||.|.+|+|+.++ ++.+++||||+|.+.++|++||+.|++ .|.+  +.|+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g--~~l~   89 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDG--RKAN   89 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETT--EECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCC--EEEE
Confidence            34556899999999999999999999999999999999997 789999999999999999999999998 8999  7799


Q ss_pred             EEeccCCCcCC
Q psy4086         212 VKFADSGLKKR  222 (305)
Q Consensus       212 v~~a~~~~~~~  222 (305)
                      |+++......+
T Consensus        90 V~~a~~~~~~~  100 (116)
T 2cqd_A           90 VNLAYLGAKPR  100 (116)
T ss_dssp             EEESTTTCCCC
T ss_pred             EEEcccCCCcc
Confidence            99998754443

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.80  E-value=5.4e-19  Score=133.95  Aligned_cols=87  Identities=20%  Similarity=0.360  Sum_probs=80.5

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....++|||+|||+++++++|+++|+.||.|..|+|+.++ ++.++|||||+|.+.++|++||+.|||..|.|  +.|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~V   89 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG--RQIRT   89 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETT--EECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC--EEEEE
Confidence            3456889999999999999999999999999999999997 88999999999999999999999999999999  77999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      .|+..+....
T Consensus        90 ~~a~~~~~~~   99 (115)
T 2dgo_A           90 NWATRKPPAP   99 (115)
T ss_dssp             EESSCCCCCS
T ss_pred             EEccCCCCCC
Confidence            9999866554

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.4e-19  Score=134.52  Aligned_cols=87  Identities=20%  Similarity=0.329  Sum_probs=80.4

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....++|||+|||.++++++|+++|++||.|..|+|+.++ ++.++|||||+|.+.++|++||+.||+..|.+  +.|+|
T Consensus        12 ~~~~~~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           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDH--LILNV   89 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETT--EECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCC--cEEEE
Confidence            4456889999999999999999999999999999999997 88999999999999999999999999999999  77999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      .++..+..+.
T Consensus        90 ~~a~~~~~~~   99 (103)
T 2cq0_A           90 EWAKPSTNSG   99 (103)
T ss_dssp             EESSCCCCSC
T ss_pred             EECCCCCCCC
Confidence            9998865543

>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=99.80  E-value=2.1e-19  Score=127.96  Aligned_cols=80  Identities=24%  Similarity=0.487  Sum_probs=75.9

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      .+|||+|||.++++++|+++|++||.|.++.++.++ ++.++|||||+|.+.++|++|++.|||..+.|  +.|+|+++.
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g--~~l~v~~a~   79 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG--RPLRINWAA   79 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETT--EECEEEECC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCC--cEEEEEecC
Confidence            589999999999999999999999999999999996 88999999999999999999999999999999  779999998


Q ss_pred             CCC
Q psy4086         217 SGL  219 (305)
Q Consensus       217 ~~~  219 (305)
                      ++.
T Consensus        80 ~~~   82 (83)
T 3md1_A           80 KLE   82 (83)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            753

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=7.1e-19  Score=133.06  Aligned_cols=86  Identities=28%  Similarity=0.422  Sum_probs=79.4

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||+++++++|+++|++||.|++|+|+.++++.+++||||+|.+.++|++|++.||+..|.+  +.|+|+
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~   89 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFD--RPMHVK   89 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC--CEEEEE
Confidence            345689999999999999999999999999999999999988999999999999999999999999999999  779999


Q ss_pred             eccCCCcC
Q psy4086         214 FADSGLKK  221 (305)
Q Consensus       214 ~a~~~~~~  221 (305)
                      +++....+
T Consensus        90 ~a~~~~~~   97 (114)
T 2do0_A           90 MDERALPK   97 (114)
T ss_dssp             ECSCCCCC
T ss_pred             EcccCCCC
Confidence            99865444

>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=99.80  E-value=6.7e-20  Score=132.80  Aligned_cols=82  Identities=20%  Similarity=0.311  Sum_probs=71.1

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCC--CeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYV--TVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g--~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      .+|||+|||+++++++|+++|++||  .|.+++|+.++ +|+++|||||+|.+.++|++|++.|||..|.|  +.|+|++
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~g--r~i~V~~   79 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHG--QNPVVTP   79 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSS--CCCEECC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCC--EEEEEEE
Confidence            4799999999999999999999999  99999999998 89999999999999999999999999999999  6799999


Q ss_pred             ccCCCcC
Q psy4086         215 ADSGLKK  221 (305)
Q Consensus       215 a~~~~~~  221 (305)
                      +.+....
T Consensus        80 ~~~~~~~   86 (90)
T 3p5t_L           80 SNKLEHH   86 (90)
T ss_dssp             C------
T ss_pred             CCCCccc
Confidence            9875443

>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=1.5e-19  Score=137.15  Aligned_cols=82  Identities=24%  Similarity=0.431  Sum_probs=75.0

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      ..+|||+|||+++++++|+++|++||.|.+|+|+.++. .++|||||+|.+.++|++||+.|||..|.|  +.|+|.++.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~-~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g--~~i~V~~a~   81 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLND--RKVFVGRFK   81 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-EEEEEEEEEESCHHHHHHHHHHHTTCEETT--EECEEEESS
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC-CCCceEEEEECCHHHHHHHHHHcCCCEECC--EEEEEEECC
Confidence            46899999999999999999999999999999999864 479999999999999999999999999999  779999998


Q ss_pred             CCCcC
Q psy4086         217 SGLKK  221 (305)
Q Consensus       217 ~~~~~  221 (305)
                      .+..+
T Consensus        82 ~~~~~   86 (115)
T 4f25_A           82 SRKER   86 (115)
T ss_dssp             CCCC-
T ss_pred             Ccccc
Confidence            75443

>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=99.80  E-value=4.5e-19  Score=131.72  Aligned_cols=86  Identities=16%  Similarity=0.346  Sum_probs=78.3

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||+++++++|+++|++||.|.+|+|+.++.+ +++||||+|.+.++|++|++.||+..|.|  +.|+|+
T Consensus        12 ~~~~~~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           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILG--KEVKVN   88 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETT--EEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCcCC--CeEEEE
Confidence            445689999999999999999999999999999999998643 68999999999999999999999999999  789999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      |+..+..++
T Consensus        89 ~a~~~~~~~   97 (103)
T 2cqi_A           89 WATTPSSQK   97 (103)
T ss_dssp             ECCCTTCCC
T ss_pred             ECCCCcccc
Confidence            999866554

>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=99.80  E-value=2.3e-19  Score=128.93  Aligned_cols=81  Identities=20%  Similarity=0.385  Sum_probs=75.1

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ..++|||+|||.++++++|+++|++||.|.+++++.++ ++.++|||||+|.+.++|++|++.|||..+.|  +.|+|++
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v~~   82 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG--RQIRTNW   82 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT--EECEEEE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC--eEEEEEe
Confidence            46789999999999999999999999999999999997 88999999999999999999999999999999  7799999


Q ss_pred             ccCC
Q psy4086         215 ADSG  218 (305)
Q Consensus       215 a~~~  218 (305)
                      ++.+
T Consensus        83 a~~k   86 (87)
T 3bs9_A           83 ATRK   86 (87)
T ss_dssp             EC--
T ss_pred             cCCC
Confidence            8764

>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=3.1e-19  Score=131.33  Aligned_cols=86  Identities=23%  Similarity=0.423  Sum_probs=78.4

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCC--C--CcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN--N--TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~--g--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      .+.++|||+|||+++++++|+++|++||.|..|+|+.++.  |  .+++||||+|.+.++|++|++.|||..|.+  +.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l   80 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDG--HKL   80 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETT--EEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCC--eEE
Confidence            3568999999999999999999999999999999998763  3  789999999999999999999999999999  779


Q ss_pred             EEEeccCCCcCC
Q psy4086         211 LVKFADSGLKKR  222 (305)
Q Consensus       211 ~v~~a~~~~~~~  222 (305)
                      +|++++.....+
T Consensus        81 ~V~~a~~~~~~~   92 (98)
T 2cpf_A           81 EVRISERATKPA   92 (98)
T ss_dssp             EEECSSCSSCCC
T ss_pred             EEEEccCCCCCC
Confidence            999998866554

>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=2.4e-19  Score=133.42  Aligned_cols=84  Identities=24%  Similarity=0.419  Sum_probs=77.8

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-C-CCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-N-NTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~-g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ...++|||+|||+++++++|+++|+.|| |.+|+|+.++ + +.++|||||+|.+.++|++|| .||+..|.+  +.|+|
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g--~~l~V   88 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN--KRIRV   88 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETT--EECEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCC--cEEEE
Confidence            4568999999999999999999999999 9999999998 4 899999999999999999999 999999999  77999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      +++..+..+.
T Consensus        89 ~~a~~~~~~~   98 (104)
T 1wi8_A           89 DVADQAQDKD   98 (104)
T ss_dssp             EECCCCCCCC
T ss_pred             EEccCCCCCC
Confidence            9999876654

>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=99.80  E-value=5e-19  Score=133.23  Aligned_cols=88  Identities=20%  Similarity=0.342  Sum_probs=80.4

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhC------CCCCCC
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFN------GSTLPG  205 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~------g~~~~g  205 (305)
                      .....++|||+|||+++++++|+++|+.||.|.+|+|+.++ ++.++|||||+|.+.++|++|++.||      +..|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            34456899999999999999999999999999999999998 78999999999999999999999999      999999


Q ss_pred             CCccEEEEeccCCCcCC
Q psy4086         206 SKEPLLVKFADSGLKKR  222 (305)
Q Consensus       206 ~~~~l~v~~a~~~~~~~  222 (305)
                        +.|+|.++..+....
T Consensus        91 --~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           91 --RQLKVDLAVTRDEAA  105 (111)
T ss_dssp             --CEEEEECCCCCCCCC
T ss_pred             --EEEEEEECCCCccCC
Confidence              779999998865543

>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=5.6e-19  Score=131.16  Aligned_cols=87  Identities=22%  Similarity=0.505  Sum_probs=79.1

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      .....++|||+|||+++++++|+++|++||.|.+|+|+.++.+ +++||||+|.+.++|++|++.||+..|.+  +.|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v   87 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEG--RKIEV   87 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETT--EECEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECC--EEEEE
Confidence            3445689999999999999999999999999999999998754 89999999999999999999999999999  77999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      .++..+..+.
T Consensus        88 ~~a~~~~~~~   97 (103)
T 2cq3_A           88 NNATARVMTN   97 (103)
T ss_dssp             EECCSSCCCC
T ss_pred             EEcccCCCCC
Confidence            9999866554

>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=99.80  E-value=4.2e-19  Score=133.28  Aligned_cols=85  Identities=20%  Similarity=0.354  Sum_probs=76.3

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||.++++++|+++|++||.|+.|+|..+  +.+++||||+|.+.++|++||+.||+..|.+  +.|+|+
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~V~   94 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDG--YRLRVE   94 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECC--eEEEEE
Confidence            445689999999999999999999999999999999765  3579999999999999999999999999999  779999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      +++......
T Consensus        95 ~a~~~~~~~  103 (109)
T 1x4a_A           95 FPRSGRGTG  103 (109)
T ss_dssp             CCCCCCCCC
T ss_pred             EcccCCCCC
Confidence            998865443

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=2.7e-19  Score=135.22  Aligned_cols=88  Identities=19%  Similarity=0.296  Sum_probs=80.2

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeE--------EEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCC
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVV--------STRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTL  203 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~--------~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~  203 (305)
                      .....++|||+|||+++++++|+++|++||.|.        .|+|+.++ ++.++|||||+|.+.++|++||+.|||..|
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            344678999999999999999999999999999        69999996 899999999999999999999999999999


Q ss_pred             CCCCccEEEEeccCCCcCC
Q psy4086         204 PGSKEPLLVKFADSGLKKR  222 (305)
Q Consensus       204 ~g~~~~l~v~~a~~~~~~~  222 (305)
                      .|  +.|+|+++..+..+.
T Consensus        91 ~g--~~l~V~~a~~~~~~~  107 (113)
T 2cpe_A           91 QG--SKLKVSLARKKPPMN  107 (113)
T ss_dssp             TT--EECEEECSSCCCCST
T ss_pred             CC--CEEEEEECCCCCCCC
Confidence            99  779999998865543

>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=99.79  E-value=3.8e-19  Score=130.35  Aligned_cols=82  Identities=17%  Similarity=0.304  Sum_probs=77.4

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||.++++++|+++|++||.|.+|+|+.++ +|.++|||||+|.+.++|++|++.|||..|.|  +.|+|+++
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   79 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGS--RFLKCGYS   79 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETT--EECEEEEC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECC--eEEEEEEc
Confidence            5789999999999999999999999999999999997 78999999999999999999999999999999  77999999


Q ss_pred             cCCCc
Q psy4086         216 DSGLK  220 (305)
Q Consensus       216 ~~~~~  220 (305)
                      ..+..
T Consensus        80 ~~~~~   84 (96)
T 2x1f_A           80 SNSDI   84 (96)
T ss_dssp             SCSSG
T ss_pred             CCCCC
Confidence            87543

>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=99.79  E-value=9.2e-19  Score=132.69  Aligned_cols=77  Identities=30%  Similarity=0.495  Sum_probs=71.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ...++|||+|||+++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++.||+..|.++.++.
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   99 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   99 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34578999999999999999999999999999999999999999999999999999999999999999888776653

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=4.7e-19  Score=132.28  Aligned_cols=83  Identities=18%  Similarity=0.262  Sum_probs=77.5

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||.++++++|+++|+.||.|.+|.|+.++ ++.++|||||+|.+.++|++|++.|||..|.|  +.|+|+
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~V~   98 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG--QPISVD   98 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSS--SBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECC--cEEEEE
Confidence            345789999999999999999999999999999999998 78999999999999999999999999999999  779999


Q ss_pred             eccCCC
Q psy4086         214 FADSGL  219 (305)
Q Consensus       214 ~a~~~~  219 (305)
                      ++..+.
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            998754

>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=99.79  E-value=5.3e-20  Score=143.72  Aligned_cols=117  Identities=8%  Similarity=0.046  Sum_probs=75.0

Q ss_pred             ceEEEEecchhhHHHHHHHhccC----cccc----eecccccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeC
Q psy4086         101 GYGFVDFESGGYALAAVKALQDK----GIHA----QMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD  172 (305)
Q Consensus       101 G~afV~f~~~~~A~~a~~~l~g~----~i~~----~~~~~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~  172 (305)
                      |+||.+|..++.+..++..+...    ....    ..........++|||+|||+++||++|+++|++|| |++|+|+.+
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~gg~~~g~~~g~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d   80 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIG   80 (139)
T ss_dssp             -------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCS
T ss_pred             CcccccccCccccchhcccchhccCCCCCCCCCCCcccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEEC
Confidence            57888888887777776653211    1110    01112334567899999999999999999999999 779999999


Q ss_pred             CCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCCCcC
Q psy4086         173 NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKK  221 (305)
Q Consensus       173 ~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~~~~  221 (305)
                      ++++++|||||+|.+.++|++|| .+|+..|.+  +.|+|..+......
T Consensus        81 ~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~g--R~i~V~~a~~~~~~  126 (139)
T 2hgn_A           81 PDGRVTGEADVEFATHEEAVAAM-SKDRANMQH--RYIELFLNSTTGAS  126 (139)
T ss_dssp             SSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSS--CCCCCEECCCSCC-
T ss_pred             CCCCCceEEEEEeCCHHHHHHHH-hhCCCEECC--EEEEEEECCCCCCC
Confidence            98999999999999999999999 789999999  67999998875543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=3.7e-19  Score=131.14  Aligned_cols=83  Identities=19%  Similarity=0.348  Sum_probs=77.4

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeE-EEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCcc---
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVV-STRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEP---  209 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~-~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~---  209 (305)
                      ...++|||+|||+++++++|+++|++||.|. +|+|+.++ ++.++|||||+|.+.++|++|++.|||..|.+  +.   
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~~~~   84 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPG--ATPAK   84 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESS--CSSCE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCC--CCcce
Confidence            4568999999999999999999999999999 99999998 88999999999999999999999999999999  66   


Q ss_pred             -EEEEeccCCC
Q psy4086         210 -LLVKFADSGL  219 (305)
Q Consensus       210 -l~v~~a~~~~  219 (305)
                       |+|.|+....
T Consensus        85 ~l~v~~a~~~~   95 (99)
T 2div_A           85 RFKLNYATYSG   95 (99)
T ss_dssp             ECCEEETTCCS
T ss_pred             eEEEeecCCCC
Confidence             9999988753

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=3.7e-19  Score=132.02  Aligned_cols=82  Identities=20%  Similarity=0.337  Sum_probs=76.2

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      .....++|||+|||+++|+++|+++|+.||.|.+|+|+.++.+.++|||||+|.+.++|.+||. +++..|.|  +.|.|
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~g--r~l~V   83 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKE--TDLLI   83 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTT--TTCEE
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECC--EEEEE
Confidence            4455689999999999999999999999999999999999888999999999999999999998 89999999  77999


Q ss_pred             EeccC
Q psy4086         213 KFADS  217 (305)
Q Consensus       213 ~~a~~  217 (305)
                      .++..
T Consensus        84 ~~~~~   88 (103)
T 1s79_A           84 LFKDD   88 (103)
T ss_dssp             EEHHH
T ss_pred             EEchH
Confidence            99765

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.79  E-value=5e-19  Score=131.47  Aligned_cols=84  Identities=23%  Similarity=0.502  Sum_probs=77.3

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++++++|+++|++|| |.+|+|+.++ ++.++|||||+|.+.++|++|+ .||+..|.|  +.|+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g--~~l~V~   88 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGD--RSLRVD   88 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETT--EECEEE
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECC--eEEEEE
Confidence            4568899999999999999999999996 9999999998 7899999999999999999999 899999999  779999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      ++..+..++
T Consensus        89 ~a~~~~~~~   97 (103)
T 2dng_A           89 IAEGRKQDK   97 (103)
T ss_dssp             ECCCCCCCC
T ss_pred             EecCCCCCC
Confidence            998865544

>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=99.79  E-value=3.3e-19  Score=127.53  Aligned_cols=80  Identities=20%  Similarity=0.321  Sum_probs=75.5

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||.++++++|+++|++||.|.+++++.++ ++.++|||||+|.+.++|++|++.|||..+.|  +.|+|+
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~   82 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG--RTIRVN   82 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECC--cEEEEE
Confidence            456899999999999999999999999999999999986 88899999999999999999999999999999  779999


Q ss_pred             ecc
Q psy4086         214 FAD  216 (305)
Q Consensus       214 ~a~  216 (305)
                      |++
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            974

>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=5.8e-19  Score=136.53  Aligned_cols=86  Identities=24%  Similarity=0.349  Sum_probs=79.2

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      .....++|||+|||+++++++|+++|++||.|..|+|+.++ ++.++|||||+|.+.++|++||+.|||..|.|  +.|+
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g--~~l~  119 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG--RRIR  119 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSS--SCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC--EEEE
Confidence            34456899999999999999999999999999999999997 78999999999999999999999999999999  7799


Q ss_pred             EEeccCCCc
Q psy4086         212 VKFADSGLK  220 (305)
Q Consensus       212 v~~a~~~~~  220 (305)
                      |+|+..+..
T Consensus       120 V~~a~~~~p  128 (129)
T 2kxn_B          120 VDFSITKRP  128 (129)
T ss_dssp             ESCCSSSSC
T ss_pred             EEEecCCCC
Confidence            999987543

>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=99.78  E-value=4.5e-19  Score=133.32  Aligned_cols=87  Identities=15%  Similarity=0.243  Sum_probs=79.8

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      .....++|||+|||.++++++|+++|+.||.|.+|+|+.++ ++.++|||||+|.+.++|++|++.|||..|.|  +.|+
T Consensus        22 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~l~   99 (110)
T 1oo0_B           22 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG--QTIQ   99 (110)
T ss_dssp             CBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETT--EECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECC--cEEE
Confidence            34456789999999999999999999999999999999997 88999999999999999999999999999999  7799


Q ss_pred             EEeccCCCcC
Q psy4086         212 VKFADSGLKK  221 (305)
Q Consensus       212 v~~a~~~~~~  221 (305)
                      |.|+..+..+
T Consensus       100 V~~a~~~~~~  109 (110)
T 1oo0_B          100 VDWCFVKGPK  109 (110)
T ss_dssp             EEESEESSCC
T ss_pred             EEEcccCCCC
Confidence            9999876543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.78  E-value=1e-18  Score=126.93  Aligned_cols=84  Identities=23%  Similarity=0.408  Sum_probs=77.3

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...++|||+|||.++++++|+++|++||.|..++|..+ ++.+++||||+|.+.++|++|++.||+..|.|  +.|+|++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g--~~l~v~~   82 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSG--REIDVRI   82 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTT--BCCCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECC--cEEEEEE
Confidence            45689999999999999999999999999999999985 67899999999999999999999999999999  7799999


Q ss_pred             ccCCCcC
Q psy4086         215 ADSGLKK  221 (305)
Q Consensus       215 a~~~~~~  221 (305)
                      ++.....
T Consensus        83 a~~~~~~   89 (92)
T 2dgv_A           83 DRNASGP   89 (92)
T ss_dssp             CSCCSSC
T ss_pred             cCCCCCC
Confidence            9876543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.78  E-value=9.3e-19  Score=129.04  Aligned_cols=81  Identities=17%  Similarity=0.356  Sum_probs=75.8

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEE--------EEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCC
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVS--------TRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLP  204 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~--------v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~  204 (305)
                      ....++|||+|||.++++++|+++|++||.|.+        ++|+.++ ++.++|||||+|.+.++|++|++.|||..|.
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            345688999999999999999999999999999        9999997 7899999999999999999999999999999


Q ss_pred             CCCccEEEEecc
Q psy4086         205 GSKEPLLVKFAD  216 (305)
Q Consensus       205 g~~~~l~v~~a~  216 (305)
                      |  +.|+|++|+
T Consensus        90 g--~~l~V~~A~   99 (99)
T 2la6_A           90 G--NPIKVSFAT   99 (99)
T ss_dssp             S--SBCEEEECC
T ss_pred             C--cEEEEEecC
Confidence            9  779999974

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.78  E-value=3.6e-19  Score=142.14  Aligned_cols=76  Identities=18%  Similarity=0.295  Sum_probs=70.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccC--CeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYG--PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G--~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ..++|||+|||+++|+++|+++|+.||  .|.+|+|+.|+.+|+++|||||+|.+.++|++||+.|||..|.++.++.
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V  131 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDV  131 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEE
Confidence            457899999999999999999999999  9999999999999999999999999999999999999999998887653

>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=99.78  E-value=1.8e-19  Score=130.50  Aligned_cols=74  Identities=26%  Similarity=0.372  Sum_probs=67.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccC--CeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYG--PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G--~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      .+|||+|||+++|+++|+++|++||  .|.+++|+.++.+|+++|||||+|.+.++|++|++.|||..+.++.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V   77 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVV   77 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEE
Confidence            5699999999999999999999999  9999999999999999999999999999999999999999988877653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.78  E-value=9.2e-19  Score=132.68  Aligned_cols=78  Identities=22%  Similarity=0.413  Sum_probs=71.5

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +....++|||+|||+++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR   88 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            344568899999999999999999999999999999999998999999999999999999999999998887776655

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=9.1e-19  Score=127.96  Aligned_cols=76  Identities=29%  Similarity=0.439  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++++++|+++|++||.|.+|.+++++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   88 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3457799999999999999999999999999999999999999999999999999999999999999988877665

>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=99.78  E-value=4.8e-19  Score=129.49  Aligned_cols=81  Identities=23%  Similarity=0.359  Sum_probs=76.5

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...++|||+|||+++++++|+++|++||.|.+|+|+.++++.++|||||+|.+.++|++|++.||+..|.+  +.|+|++
T Consensus        14 ~~~~~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           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYG--RPINVSG   91 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETT--EECEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECC--CEEEEEE
Confidence            44578999999999999999999999999999999999888999999999999999999999999999999  7799999


Q ss_pred             ccC
Q psy4086         215 ADS  217 (305)
Q Consensus       215 a~~  217 (305)
                      ++.
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>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=99.78  E-value=8.3e-19  Score=130.68  Aligned_cols=77  Identities=27%  Similarity=0.437  Sum_probs=71.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++.||+..|.++.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIR   88 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            34557899999999999999999999999999999999998999999999999999999999999998888776665

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=6.3e-19  Score=128.60  Aligned_cols=81  Identities=28%  Similarity=0.482  Sum_probs=76.0

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....++|||+|||.++++++|+++|++||.|.+|+|+.++ ++.+++||||+|.+.++|++|++.||+..|.+  +.|+|
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v   90 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFG--RVIKA   90 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETT--EEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCC--cEEEE
Confidence            3456899999999999999999999999999999999998 68899999999999999999999999999999  77999


Q ss_pred             Eecc
Q psy4086         213 KFAD  216 (305)
Q Consensus       213 ~~a~  216 (305)
                      +||+
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9974

>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=99.78  E-value=7.6e-19  Score=128.78  Aligned_cols=83  Identities=11%  Similarity=0.174  Sum_probs=75.8

Q ss_pred             CCCCceEEecCCCCCCHHHHH----HHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         135 QDPTNLYIANLPLNFKECDLE----SLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~----~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      .+.++|||+|||+++++++|+    ++|++||.|.+|+|+.++.+  ++||||+|.+.++|++||+.|||..|.|  +.|
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~g--r~l   82 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGS--KKI   82 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETT--EEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECC--eEE
Confidence            345789999999999999999    99999999999999998854  8899999999999999999999999999  779


Q ss_pred             EEEeccCCCcC
Q psy4086         211 LVKFADSGLKK  221 (305)
Q Consensus       211 ~v~~a~~~~~~  221 (305)
                      +|++++....+
T Consensus        83 ~V~~a~~~~~~   93 (96)
T 2dgx_A           83 LVSLATGASGP   93 (96)
T ss_dssp             EEEECCCSSCC
T ss_pred             EEEEcCCCCCC
Confidence            99999875443

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=9.9e-19  Score=127.54  Aligned_cols=75  Identities=27%  Similarity=0.502  Sum_probs=70.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||+|.+|+|+.++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   89 (94)
T 2e5h_A           15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIK   89 (94)
T ss_dssp             CTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            457799999999999999999999999999999999999999999999999999999999999999888877654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=4.6e-19  Score=126.85  Aligned_cols=77  Identities=61%  Similarity=1.002  Sum_probs=72.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ  133 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~  133 (305)
                      ..++|||+|||+++++++|+++|++||+|.+++|+.++.+++++|||||+|.+.++|++|++.|||..|.++.++..
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   80 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQS   80 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeec
Confidence            34789999999999999999999999999999999999899999999999999999999999999999999887643

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=6.9e-19  Score=128.60  Aligned_cols=81  Identities=26%  Similarity=0.352  Sum_probs=76.2

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||.++++++|+++|++||.|.+|+|+.++ ++.++|||||+|.+.++|++|++.|||..|.+  +.|+|+
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v~   90 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG--RRIRVS   90 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETT--EEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECC--EEEEEE
Confidence            345789999999999999999999999999999999998 68999999999999999999999999999999  779999


Q ss_pred             eccC
Q psy4086         214 FADS  217 (305)
Q Consensus       214 ~a~~  217 (305)
                      +++.
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9875

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=1.7e-18  Score=127.89  Aligned_cols=76  Identities=24%  Similarity=0.482  Sum_probs=69.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++|+++|+++|++||.|.+|+|+.++ +++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   89 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIK   89 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3455779999999999999999999999999999999999 899999999999999999999999998888776654

>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=99.78  E-value=9.7e-19  Score=131.06  Aligned_cols=85  Identities=24%  Similarity=0.464  Sum_probs=78.6

Q ss_pred             cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       132 ~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      ......++|||+|||..+++++|+++|++||.|.+|+|+.++ ++.++|||||+|.+.++|++|++.|||..|.|  +.|
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g--~~l   98 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAG--RPM   98 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSS--SCC
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC--EEE
Confidence            344556889999999999999999999999999999999997 78999999999999999999999999999999  779


Q ss_pred             EEEeccCC
Q psy4086         211 LVKFADSG  218 (305)
Q Consensus       211 ~v~~a~~~  218 (305)
                      +|+++..+
T Consensus        99 ~V~~a~~k  106 (108)
T 2jrs_A           99 KVGHVTER  106 (108)
T ss_dssp             EEECSCSS
T ss_pred             EEEEcccC
Confidence            99999875

>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=99.78  E-value=6.1e-19  Score=130.73  Aligned_cols=83  Identities=7%  Similarity=0.092  Sum_probs=74.7

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||+++|+++|+++|+.||. ++|+|+.+++++++|||||+|.+.++|++||+ +|+..|.+  +.|+|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~g--r~i~V~   87 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQH--RYVELF   87 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSS--SCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECC--cEEEEE
Confidence            345678999999999999999999999994 59999999999999999999999999999995 79999999  679999


Q ss_pred             eccCCCc
Q psy4086         214 FADSGLK  220 (305)
Q Consensus       214 ~a~~~~~  220 (305)
                      .+.....
T Consensus        88 ~~~~~~~   94 (102)
T 1wez_A           88 LNSTAGT   94 (102)
T ss_dssp             EECCCCC
T ss_pred             ECCCCCC
Confidence            9876543

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=2.5e-18  Score=124.39  Aligned_cols=79  Identities=27%  Similarity=0.423  Sum_probs=72.8

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...++|||+|||.++++++|+++|++||.|.+|++.       ++||||+|.+.++|++|++.||+..|.+  +.|+|++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v~~   76 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHG--VNINVEA   76 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBCSS--CBCEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCccCC--cEEEEEE
Confidence            456899999999999999999999999999999987       6799999999999999999999999999  7799999


Q ss_pred             ccCCCcCC
Q psy4086         215 ADSGLKKR  222 (305)
Q Consensus       215 a~~~~~~~  222 (305)
                      +..+....
T Consensus        77 a~~~~~~~   84 (90)
T 2dnq_A           77 SKNKSKAS   84 (90)
T ss_dssp             SSCCCCCC
T ss_pred             CCCCCCCC
Confidence            99866554

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=5e-19  Score=130.76  Aligned_cols=82  Identities=20%  Similarity=0.410  Sum_probs=73.4

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCC--CCCCCCCccEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNG--STLPGSKEPLL  211 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g--~~~~g~~~~l~  211 (305)
                      ....++|||+|||++++|++|+++|++||.|++|+|+++     ||||||+|++.++|++|++.|++  ..|.|  ++|+
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~G--r~l~   85 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRG--QPIY   85 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEETT--EECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceECC--EEEE
Confidence            345689999999999999999999999999999999965     79999999999999999998864  67899  8899


Q ss_pred             EEeccCCCcCC
Q psy4086         212 VKFADSGLKKR  222 (305)
Q Consensus       212 v~~a~~~~~~~  222 (305)
                      |.|++.+..+.
T Consensus        86 V~~A~~~~~~~   96 (105)
T 1sjq_A           86 IQFSNHKELKT   96 (105)
T ss_dssp             BCCCSSSSCCC
T ss_pred             EEEcCCCCCCc
Confidence            99998765554

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=9.1e-19  Score=130.03  Aligned_cols=78  Identities=22%  Similarity=0.386  Sum_probs=72.1

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +....++|||+|||+++++++|+++|++||+|.+|.|++++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN   88 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            344568899999999999999999999999999999999998999999999999999999999999999888877665

>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=99.78  E-value=4.4e-19  Score=134.47  Aligned_cols=103  Identities=23%  Similarity=0.271  Sum_probs=86.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccccCC
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQD  136 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~~~  136 (305)
                      ..++|||+|||+++++++|+++|+.||.|.+|.|+++   +.++|||||+|.+.++|++|++.|||..+.++.++.....
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            3467999999999999999999999999999999975   4569999999999999999999999988887766643332


Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCC
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVT  163 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~  163 (305)
                      ...- ..+++...++++|+++|++||.
T Consensus        84 ~~~~-~~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           84 ANRA-FQKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             HHHH-TTTSCHHHHHHHHHHHHHHHCC
T ss_pred             CChh-hhhhhHhHhHHHHHHHHHHhCC
Confidence            2111 1577888899999999999984

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.78  E-value=2.6e-19  Score=130.75  Aligned_cols=72  Identities=24%  Similarity=0.375  Sum_probs=65.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCC--eeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCc----ccceec
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGP--IISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG----IHAQMA  130 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~--i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~----i~~~~~  130 (305)
                      .||||+|||+++|+++|+++|++||.  |.+|+|++|+.+|++||||||+|.+.++|++|++.|||..    |.++.+
T Consensus        10 ~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A           10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            46999999999999999999999995  6799999999999999999999999999999999999863    555544

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=4.9e-19  Score=131.94  Aligned_cols=86  Identities=21%  Similarity=0.342  Sum_probs=79.2

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....++|||+|||+++++++|+++|++||.|.+|+|+.++ ++.++|||||+|.+.++|++||+. ++..|.|  +.|+|
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g--~~l~V   89 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDG--RNIDP   89 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETT--EEEBC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECC--EEEEE
Confidence            4556899999999999999999999999999999999997 889999999999999999999998 9999999  77999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      +++..+....
T Consensus        90 ~~a~~~~~~~   99 (105)
T 2dh8_A           90 KPCTPRGMQP   99 (105)
T ss_dssp             CCSCCSSCCT
T ss_pred             EEccCCCCCC
Confidence            9998765544

>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=99.77  E-value=6.9e-19  Score=126.68  Aligned_cols=82  Identities=16%  Similarity=0.336  Sum_probs=75.5

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCC-cccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNT-SKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~-~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ..++|||+|||.++++++|+++|++||.|.++.|+.++ ++. ++|||||+|.+.++|++|++.|||..+.|  +.|+|+
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~   80 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDG--QEITAT   80 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECC--eEEEEE
Confidence            46899999999999999999999999999999999987 333 89999999999999999999999999999  779999


Q ss_pred             eccCCC
Q psy4086         214 FADSGL  219 (305)
Q Consensus       214 ~a~~~~  219 (305)
                      ++....
T Consensus        81 ~a~~~~   86 (88)
T 4a8x_A           81 AVLAPW   86 (88)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            997654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.77  E-value=2e-18  Score=127.25  Aligned_cols=75  Identities=21%  Similarity=0.335  Sum_probs=70.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeE--------EEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccce
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIIS--------TKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ  128 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~--------~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~  128 (305)
                      ..++|||+|||+++++++|+++|++||.|.+        ++|++++.+|+++|||||+|.+.++|++|++.|||..+.++
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~   91 (99)
T 2la6_A           12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGN   91 (99)
T ss_dssp             CCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            4578999999999999999999999999999        99999999999999999999999999999999999988876


Q ss_pred             ecc
Q psy4086         129 MAR  131 (305)
Q Consensus       129 ~~~  131 (305)
                      .++
T Consensus        92 ~l~   94 (99)
T 2la6_A           92 PIK   94 (99)
T ss_dssp             BCE
T ss_pred             EEE
Confidence            554

>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=99.77  E-value=1.1e-18  Score=124.84  Aligned_cols=76  Identities=32%  Similarity=0.509  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++++++|+++|++||.|.++.+++++.+++++|||||+|.+.++|++|++.|||..+.++.++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   80 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR   80 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            3457899999999999999999999999999999999988999999999999999999999999999988877654

>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=8.3e-19  Score=133.14  Aligned_cols=83  Identities=19%  Similarity=0.307  Sum_probs=77.2

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||+++++++|+++|+.||.|..|+|+.++ ++.++|||||+|.+.++|++||+. ++..|.|  +.|+|.++
T Consensus        27 ~~~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           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDG--RVVEPKRA  103 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETT--EEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECC--EEEEEEEC
Confidence            4789999999999999999999999999999999997 789999999999999999999997 9999999  77999999


Q ss_pred             cCCCcCC
Q psy4086         216 DSGLKKR  222 (305)
Q Consensus       216 ~~~~~~~  222 (305)
                      ..+....
T Consensus       104 ~~~~~~~  110 (116)
T 1x4b_A          104 VAREESG  110 (116)
T ss_dssp             SSCCCCC
T ss_pred             CCCccCC
Confidence            8865544

>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=99.77  E-value=1.8e-18  Score=130.79  Aligned_cols=88  Identities=56%  Similarity=0.929  Sum_probs=78.9

Q ss_pred             ccccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCC-----
Q psy4086         131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPG-----  205 (305)
Q Consensus       131 ~~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g-----  205 (305)
                      .......++|||+|||.++++++|+++|+.||.|.+|+|+.++++.++|||||+|.+.++|++|++.|||..|.+     
T Consensus        19 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~   98 (114)
T 1x5o_A           19 KQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   98 (114)
T ss_dssp             SCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCcccc
Confidence            344556789999999999999999999999999999999999988999999999999999999999999999953     


Q ss_pred             -CCccEEEEeccCC
Q psy4086         206 -SKEPLLVKFADSG  218 (305)
Q Consensus       206 -~~~~l~v~~a~~~  218 (305)
                       ..++|.|+|+++.
T Consensus        99 ~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           99 APTEPLLCKFSGPS  112 (114)
T ss_dssp             CCSSCBEEEECCCS
T ss_pred             CCCCceeEEccCCC
Confidence             1277999999853

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.3e-18  Score=129.18  Aligned_cols=77  Identities=22%  Similarity=0.264  Sum_probs=71.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++++++|+++|++||.|.+|.|+.++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELR   86 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            34557899999999999999999999999999999999999999999999999999999999999998888776654

>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=99.77  E-value=1.4e-18  Score=129.87  Aligned_cols=81  Identities=21%  Similarity=0.408  Sum_probs=76.5

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||+.+++++|+++|++||.|.+|+|+.++++.++|||||+|.+.++|++|++.|||..|.|  +.|+|+
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~V~  103 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDG--RPMNIQ  103 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCC--cEEEEE
Confidence            345688999999999999999999999999999999999989999999999999999999999999999999  779999


Q ss_pred             ecc
Q psy4086         214 FAD  216 (305)
Q Consensus       214 ~a~  216 (305)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            986

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.9e-18  Score=127.32  Aligned_cols=75  Identities=19%  Similarity=0.424  Sum_probs=69.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||.++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++ ||+..|.++.++
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~   82 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVE   82 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEE
Confidence            355789999999999999999999999999999999999999999999999999999999999 888877766554

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.77  E-value=1.7e-18  Score=129.39  Aligned_cols=77  Identities=19%  Similarity=0.376  Sum_probs=70.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeC-CCCCCccceEEEEecchhhHHHHHHHh-ccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILD-KTTNKCRGYGFVDFESGGYALAAVKAL-QDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~-~~~g~~~G~afV~f~~~~~A~~a~~~l-~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++++++|+++|++||.|..|+|+++ +.+++++|||||+|.+.++|++|++.| |+..|.++.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            345578999999999999999999999999999999999 788999999999999999999999999 88887776554

>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=1e-18  Score=132.19  Aligned_cols=77  Identities=17%  Similarity=0.278  Sum_probs=70.7

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ++...++|||+|||+++++++|+++|++||.|.+|+|+.++.+++++|||||+|.+.++|++|+ .|||..|.++.++
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   97 (114)
T 2cq4_A           21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPII   97 (114)
T ss_dssp             THHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEE
Confidence            3445688999999999999999999999999999999999999999999999999999999999 8999888776654

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.77  E-value=1.1e-18  Score=139.31  Aligned_cols=81  Identities=20%  Similarity=0.312  Sum_probs=75.9

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCC--CeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYV--TVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g--~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ..++|||+|||+++++++|+++|+.||  .|.+|+|+.|+ +|+++|||||+|.+.++|++||+.|||..|.|  +.|+|
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~G--r~l~V  131 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNG--EKVDV  131 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETT--EECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC--eEeEE
Confidence            457999999999999999999999999  99999999998 89999999999999999999999999999999  78999


Q ss_pred             EeccCC
Q psy4086         213 KFADSG  218 (305)
Q Consensus       213 ~~a~~~  218 (305)
                      +++...
T Consensus       132 ~~a~~~  137 (156)
T 3n9u_C          132 RPATRQ  137 (156)
T ss_dssp             EECCHH
T ss_pred             EEcCCC
Confidence            999764

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.77  E-value=5.2e-19  Score=137.29  Aligned_cols=84  Identities=21%  Similarity=0.415  Sum_probs=77.4

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEE--EEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCC----CCCCCC
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVS--TRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGS----TLPGSK  207 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~--v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~----~~~g~~  207 (305)
                      ...++|||+|||+++|+++|+++|++||.|..  |+|++|+ +|+++|||||+|.+. +|.+|++.|||.    .|.|  
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g--   97 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG--   97 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG--
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC--
Confidence            45678999999999999999999999999977  9999999 899999999999999 999999999999    9999  


Q ss_pred             ccEEEEeccCCCcC
Q psy4086         208 EPLLVKFADSGLKK  221 (305)
Q Consensus       208 ~~l~v~~a~~~~~~  221 (305)
                      +.|+|++++....+
T Consensus        98 r~l~V~~a~~~~~~  111 (131)
T 2m2b_A           98 KTINVEFAKGSKRD  111 (131)
T ss_dssp             CCCCCEECCCSCCC
T ss_pred             EEEEEEECCCCCCC
Confidence            77999999875443

>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=99.77  E-value=3.2e-18  Score=127.50  Aligned_cols=70  Identities=21%  Similarity=0.392  Sum_probs=66.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      ..++|||+|||+++++++|+++|++||.|.+|+|++++ +++++|||||+|.+.++|++|++.|||..+.+
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   83 (105)
T 2dnh_A           14 RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMP   83 (105)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCC
Confidence            45789999999999999999999999999999999998 79999999999999999999999999887766

>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=99.77  E-value=1.5e-18  Score=124.60  Aligned_cols=75  Identities=23%  Similarity=0.409  Sum_probs=70.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||.++++++|+++|++||.|.++++++++.+++++|||||+|.+.++|++|++.|||..+.++.++
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   79 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIR   79 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            457899999999999999999999999999999999998999999999999999999999999999888877654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.77  E-value=4.6e-19  Score=130.99  Aligned_cols=75  Identities=21%  Similarity=0.313  Sum_probs=70.1

Q ss_pred             CCCeEEEcCCCC------CCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccc-ee
Q psy4086          57 SKTNLYIRGLTQ------DTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA-QM  129 (305)
Q Consensus        57 ~~~~l~V~~Lp~------~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~-~~  129 (305)
                      ..++|||+|||+      ++++++|+++|++||.|.+|+|++++.||+++|||||+|.+.++|++|++.|||..|.+ +.
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            457899999999      99999999999999999999999999999999999999999999999999999998887 65


Q ss_pred             cc
Q psy4086         130 AR  131 (305)
Q Consensus       130 ~~  131 (305)
                      ++
T Consensus        85 l~   86 (100)
T 3ns6_A           85 LF   86 (100)
T ss_dssp             CE
T ss_pred             EE
Confidence            44

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.77  E-value=1e-18  Score=123.55  Aligned_cols=73  Identities=14%  Similarity=0.252  Sum_probs=69.1

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      ...|||+||++.+||++|+++|.+||+|.++++..     +||||||+|.+.++|++|++.||+..+.|  ++|+|++|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln~~~l~g--r~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCVLAN--TTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEEETT--EEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCEECC--cEEEEEECC
Confidence            56799999999999999999999999999999974     69999999999999999999999999999  789999985

>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=99.77  E-value=1.8e-18  Score=133.76  Aligned_cols=78  Identities=28%  Similarity=0.421  Sum_probs=71.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ....++|||+|||+++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|++.|||..|.++.++.
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  120 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            334577999999999999999999999999999999999999999999999999999999999999998888776553

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.77  E-value=2e-18  Score=126.34  Aligned_cols=78  Identities=15%  Similarity=0.207  Sum_probs=71.0

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCC--CCCCCccEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGST--LPGSKEPLLV  212 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~--~~g~~~~l~v  212 (305)
                      .+.++|||+|||+++|+++|+++|++||.|++|++++     .||||||+|++.++|.+|++.|++..  |.|  ++|+|
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~AFVef~~~~~A~~Av~~ln~~~~~i~G--r~i~V   91 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAADNQIYIAG--HPAFV   91 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHHHSCEEETT--EEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc-----CCCEEEEEECCHHHHHHHHHHhcCCCceeCC--cEEEE
Confidence            4567899999999999999999999999999999984     47899999999999999999999886  678  88999


Q ss_pred             EeccCCC
Q psy4086         213 KFADSGL  219 (305)
Q Consensus       213 ~~a~~~~  219 (305)
                      .|++.++
T Consensus        92 ~~S~~k~   98 (100)
T 3r27_A           92 NYSTSQK   98 (100)
T ss_dssp             EECSCSC
T ss_pred             Eeccccc
Confidence            9998753

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.2e-18  Score=128.96  Aligned_cols=84  Identities=17%  Similarity=0.311  Sum_probs=75.0

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||+++++++|+++|++||.|   +++.+.++.++|||||+|.+.++|++||+.||+..|.+  +.|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v~   86 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEG--RAIRLE   86 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETT--EEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCC--eEEEEE
Confidence            3456899999999999999999999999976   56777788999999999999999999999999999999  779999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      +++.+...+
T Consensus        87 ~a~~~~~~~   95 (101)
T 2fc9_A           87 LQGPRGSPN   95 (101)
T ss_dssp             ECSSCCCCC
T ss_pred             EcCCCCCCC
Confidence            998865443

>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=99.77  E-value=1.1e-18  Score=129.78  Aligned_cols=84  Identities=25%  Similarity=0.436  Sum_probs=78.5

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ..++|||+|||.++++++|+++|+.||.|..++|+.++ ++.++|||||+|.+.++|++|++.|||..|.|  +.|+|++
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~   84 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSG--RALRVDN   84 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSS--SCBEEEE
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCC--cEEEEEe
Confidence            34789999999999999999999999999999999997 88999999999999999999999999999999  7799999


Q ss_pred             ccCCCcC
Q psy4086         215 ADSGLKK  221 (305)
Q Consensus       215 a~~~~~~  221 (305)
                      +.....+
T Consensus        85 a~~~~~~   91 (104)
T 1p1t_A           85 AASEKNK   91 (104)
T ss_dssp             TTCTTHH
T ss_pred             CCCccch
Confidence            9986654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.77  E-value=4.9e-19  Score=130.83  Aligned_cols=81  Identities=21%  Similarity=0.271  Sum_probs=75.4

Q ss_pred             CCceEEecCCC------CCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCcc
Q psy4086         137 PTNLYIANLPL------NFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEP  209 (305)
Q Consensus       137 ~~~l~V~nlp~------~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~  209 (305)
                      .++|||+|||+      ++++++|+++|++||.|.+|+|+.++ +|+++|||||+|.+.++|++||+.|||..|.|. +.
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~-r~   84 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK-HR   84 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSS-CB
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCC-eE
Confidence            57899999999      99999999999999999999999998 699999999999999999999999999999982 45


Q ss_pred             EEEEeccCC
Q psy4086         210 LLVKFADSG  218 (305)
Q Consensus       210 l~v~~a~~~  218 (305)
                      |+|.++.+.
T Consensus        85 l~V~~a~~~   93 (100)
T 3ns6_A           85 LFLYTMKDV   93 (100)
T ss_dssp             CEEEESHHH
T ss_pred             EEEEECchh
Confidence            999998764

>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=99.77  E-value=1.3e-18  Score=125.05  Aligned_cols=75  Identities=20%  Similarity=0.511  Sum_probs=66.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      +...++|||+|||+++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++. ++..|.++.+
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~~g~~i   82 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDGRVI   82 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEEETTEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCEECCEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999975 5555555544

>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=99.77  E-value=1.9e-18  Score=124.62  Aligned_cols=80  Identities=19%  Similarity=0.319  Sum_probs=75.4

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      +.++|||+|||.++++++|+++|++||.|.+++++.++ ++.++|||||+|.+.++|++|+ .|||..|.|  +.|+|.+
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g--~~l~V~~   81 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRG--RQIKVIP   81 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETT--EECEEEE
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECC--cEEEEEE
Confidence            35789999999999999999999999999999999997 8899999999999999999999 999999999  7799999


Q ss_pred             ccCC
Q psy4086         215 ADSG  218 (305)
Q Consensus       215 a~~~  218 (305)
                      ++..
T Consensus        82 a~~~   85 (89)
T 3ucg_A           82 KRTN   85 (89)
T ss_dssp             TTTT
T ss_pred             ccCC
Confidence            8763

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.9e-18  Score=127.99  Aligned_cols=75  Identities=32%  Similarity=0.572  Sum_probs=69.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|++.||+..|.++.++
T Consensus        11 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 1x5s_A           11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIR   85 (102)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            457899999999999999999999999999999999999999999999999999999999999998887766554

>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=99.77  E-value=4.5e-18  Score=126.28  Aligned_cols=79  Identities=24%  Similarity=0.376  Sum_probs=72.4

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...++|||+|||+++++++|+++|++||.|..|+|+       ++||||+|.+.++|++|++.||+..|.+  +.|+|.+
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~   79 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMNGKDLEG--ENIEIVF   79 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESSHHHHHHHHHHHTTEEETT--EEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEeCCHHHHHHHHHHHCCCccCC--CEEEEEE
Confidence            346889999999999999999999999999999987       4599999999999999999999999999  7899999


Q ss_pred             ccCCCcCC
Q psy4086         215 ADSGLKKR  222 (305)
Q Consensus       215 a~~~~~~~  222 (305)
                      +..+..+.
T Consensus        80 a~~~~~~~   87 (103)
T 2dgu_A           80 AKPPDQKR   87 (103)
T ss_dssp             CCCCCCCC
T ss_pred             cCCCcccc
Confidence            99876654

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.77  E-value=2.3e-19  Score=130.17  Aligned_cols=73  Identities=22%  Similarity=0.296  Sum_probs=65.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccC-CeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHh-ccCcccceecc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYG-PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL-QDKGIHAQMAR  131 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G-~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l-~g~~i~~~~~~  131 (305)
                      .+|||+|||+++||++|+++|++|| +|.+|+|++|+.+|+++|||||+|.+.++|++|++.+ ++..+.++.++
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~   76 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVS   76 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEE
Confidence            5699999999999999999999999 8999999999999999999999999999999999876 34455555444

>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=99.77  E-value=1.1e-18  Score=131.42  Aligned_cols=85  Identities=9%  Similarity=0.157  Sum_probs=76.9

Q ss_pred             cCCCCceEEecCCCCCCHHHHH---HHHhhCCCeEEEEEeeCC-CC---CcccEEEEEecCHHHHHHHHHHhCCCCCCCC
Q psy4086         134 EQDPTNLYIANLPLNFKECDLE---SLLAKYVTVVSTRILRDN-NN---TSKGVGFARLESKDKCDQMIQLFNGSTLPGS  206 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~---~~F~~~g~v~~v~i~~~~-~g---~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  206 (305)
                      ....++|||+|||+++++++|+   ++|++||.|.+|.|+.++ ++   .++|||||+|.+.++|++||+.|||..|.| 
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~g-   90 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG-   90 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT-
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECC-
Confidence            3456899999999999999999   999999999999999887 33   566999999999999999999999999999 


Q ss_pred             CccEEEEeccCCCc
Q psy4086         207 KEPLLVKFADSGLK  220 (305)
Q Consensus       207 ~~~l~v~~a~~~~~  220 (305)
                       +.|+|.++..+..
T Consensus        91 -r~l~V~~a~~k~~  103 (111)
T 2cpi_A           91 -RTLKASLGTTKYC  103 (111)
T ss_dssp             -EEEEEESCCCCSC
T ss_pred             -EEEEEEecccccc
Confidence             7899999988653

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.77  E-value=9.9e-19  Score=129.36  Aligned_cols=83  Identities=25%  Similarity=0.334  Sum_probs=70.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc-----cc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR-----QQ  133 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~-----~~  133 (305)
                      ++|||+|||+++|+++|+++|++||+|.+|.++.+     ++|||||+|.+.++|++|++.|||..+.++.++     ..
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            57999999999999999999999999999999987     688999999999999999999887766655444     11


Q ss_pred             c------------CCCCceEEecCC
Q psy4086         134 E------------QDPTNLYIANLP  146 (305)
Q Consensus       134 ~------------~~~~~l~V~nlp  146 (305)
                      .            ....+||||||+
T Consensus        76 ~~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           76 PRRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             CCcccCCCCCccccCCCceecCCCC
Confidence            1            114679999986

>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=99.77  E-value=1.8e-18  Score=129.02  Aligned_cols=77  Identities=21%  Similarity=0.360  Sum_probs=69.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcc---cceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGI---HAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i---~~~~~~  131 (305)
                      +...++|||+|||+++++++|+++|++||+|.+|+|+.++.+++++|||||+|.+.++|++|++.|||..+   .++.++
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            34557899999999999999999999999999999999999999999999999999999999999998776   444443

>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=99.77  E-value=2.9e-18  Score=127.28  Aligned_cols=78  Identities=21%  Similarity=0.396  Sum_probs=68.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHH---hccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA---LQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~---l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++++++|+++|++||.|.+|+|+.++.+++++|||||+|.+.++|++|++.   |+|+.|.++++.
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~l~v~~a~   91 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPN   91 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHcCCeeCCeEEEEEecC
Confidence            34457799999999999999999999999999999999999999999999999999999999996   556666665554


Q ss_pred             c
Q psy4086         132 Q  132 (305)
Q Consensus       132 ~  132 (305)
                      .
T Consensus        92 ~   92 (103)
T 2cqg_A           92 S   92 (103)
T ss_dssp             T
T ss_pred             C
Confidence            3

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.77  E-value=1.7e-18  Score=122.38  Aligned_cols=82  Identities=21%  Similarity=0.314  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccccCCC
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDP  137 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~~~~  137 (305)
                      ...|||+||++.+||++|+++|.+||+|.+++++.      +||||||+|.++++|++|++.||+..+.++.++...   
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~---   77 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAES---   77 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC---
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEE---
Confidence            46699999999999999999999999999999865      689999999999999999999999998887654221   


Q ss_pred             CceEEecCCCCCCHHHHHHHHh
Q psy4086         138 TNLYIANLPLNFKECDLESLLA  159 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~  159 (305)
                                 .+|+++..+|+
T Consensus        78 -----------A~e~~~~~~~~   88 (89)
T 2wbr_A           78 -----------PSENEVQSIMQ   88 (89)
T ss_dssp             -----------CCHHHHHHHHC
T ss_pred             -----------CCHHHHHHHhh
Confidence                       26777777764

>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=99.76  E-value=2.1e-18  Score=126.00  Aligned_cols=76  Identities=17%  Similarity=0.288  Sum_probs=70.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +...++|||+|||+++++++|+++|++||+|.+|+|++++. ++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPIN   88 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEE
Confidence            34557899999999999999999999999999999999985 99999999999999999999999999988887665

>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=99.76  E-value=1.5e-18  Score=127.80  Aligned_cols=76  Identities=25%  Similarity=0.441  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++|+++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLH   81 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            3457899999999999999999999999999999999998999999999999999999999999998887776654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.3e-18  Score=128.44  Aligned_cols=76  Identities=25%  Similarity=0.442  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++++++|+++|++||.|.+|.|+.++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   96 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS   96 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEE
Confidence            3457899999999999999999999999999999999999999999999999999999999999999888776554

>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=99.76  E-value=2.2e-18  Score=122.67  Aligned_cols=73  Identities=29%  Similarity=0.491  Sum_probs=69.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ++|||+|||+++++++|+++|++||.|.++.+++++.+++++|||||+|.+.++|++|++.|||..+.++.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~   74 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR   74 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEE
Confidence            5799999999999999999999999999999999998999999999999999999999999999988877665

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.76  E-value=6.6e-18  Score=132.32  Aligned_cols=81  Identities=32%  Similarity=0.521  Sum_probs=73.3

Q ss_pred             CCCCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          51 TGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        51 ~~~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      ...+....++|||+|||+++++++|+++|+.||+|++|+|++++.+++++|||||+|.+.++|++|++.|||..|.++.+
T Consensus        35 ~~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  114 (139)
T 1u6f_A           35 MNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRL  114 (139)
T ss_dssp             SSCCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEE
T ss_pred             cCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            34455567889999999999999999999999999999999999999999999999999999999999999888777655


Q ss_pred             c
Q psy4086         131 R  131 (305)
Q Consensus       131 ~  131 (305)
                      +
T Consensus       115 ~  115 (139)
T 1u6f_A          115 K  115 (139)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=99.76  E-value=4.4e-18  Score=126.31  Aligned_cols=86  Identities=21%  Similarity=0.340  Sum_probs=77.2

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      .....++|||+|||+++++++|+++|++||.|..|+|+.++ ++.++|||||+|.+.++|++||+  ++..|.|  +.|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g--~~l~   86 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDG--RWCD   86 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETT--EEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCC--eEEE
Confidence            34456889999999999999999999999999999999997 79999999999999999999998  4678999  7799


Q ss_pred             EEeccCCCcCC
Q psy4086         212 VKFADSGLKKR  222 (305)
Q Consensus       212 v~~a~~~~~~~  222 (305)
                      |+++..+....
T Consensus        87 v~~a~~~~~~~   97 (103)
T 2cqg_A           87 CKLPNSKQSQD   97 (103)
T ss_dssp             EECCCTTCCCC
T ss_pred             EEecCCCCcCC
Confidence            99998865543

>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=99.76  E-value=5.7e-18  Score=125.72  Aligned_cols=81  Identities=16%  Similarity=0.213  Sum_probs=72.0

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCC--CCCCCCccEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGS--TLPGSKEPLLV  212 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~--~~~g~~~~l~v  212 (305)
                      ...++|||+|||+++++++|+++|++||.|.+|.|+.+     ||||||+|.+.++|.+|++.|++.  .|.|  ++|+|
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~G--r~l~V   85 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPVYIAG--QQAFF   85 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCBSSS--SBCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECC--EEEEE
Confidence            34578999999999999999999999999999998853     789999999999999999998765  4888  77999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      .|++.+..++
T Consensus        86 ~~a~~~~~~~   95 (104)
T 1wex_A           86 NYSTSKRITR   95 (104)
T ss_dssp             EECSSSSCCC
T ss_pred             EEccCccccC
Confidence            9998866554

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=2.6e-18  Score=125.55  Aligned_cols=75  Identities=24%  Similarity=0.433  Sum_probs=69.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||+|.+|++++++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   78 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMR   78 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Confidence            347799999999999999999999999999999999999999999999999999999999999998887776654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.76  E-value=8e-19  Score=133.64  Aligned_cols=80  Identities=28%  Similarity=0.487  Sum_probs=74.8

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++++++|+++|++||.|.+|+|+.++ ++.++|||||+|.+.++|++|++.|||..|.|  +.|+|+
T Consensus        38 ~~~~~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           38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGT--KRLKVQ  115 (118)
T ss_dssp             CCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETT--EECCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECC--EEEEEE
Confidence            345889999999999999999999999999999999997 78999999999999999999999999999999  779999


Q ss_pred             ecc
Q psy4086         214 FAD  216 (305)
Q Consensus       214 ~a~  216 (305)
                      |++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            974

>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=99.76  E-value=4.1e-18  Score=127.64  Aligned_cols=77  Identities=23%  Similarity=0.434  Sum_probs=71.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ...++|||+|||+++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus        24 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  100 (108)
T 2jrs_A           24 AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV  100 (108)
T ss_dssp             SSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34578999999999999999999999999999999999989999999999999999999999999998888776653

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.76  E-value=1.2e-18  Score=121.69  Aligned_cols=74  Identities=19%  Similarity=0.363  Sum_probs=70.3

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      +|||+|||+++++++|+++|++||.|.+++++.++ ++.++|||||+|.+.++|++|++ ||+..|.|  +.|+|++|
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-IHFHEINN--KMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSS--CCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECC--EEEEEEeC
Confidence            58999999999999999999999999999999998 88999999999999999999997 99999999  67999885

>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=1.8e-18  Score=128.26  Aligned_cols=77  Identities=18%  Similarity=0.229  Sum_probs=69.3

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        53 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .++...++|||+|||+++|+++|+++|++||+|.+|.|++++. |+++|||||+|.+.++|++|++ +|+..+.++.+.
T Consensus         6 ~~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~   82 (103)
T 1s79_A            6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLL   82 (103)
T ss_dssp             SSCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCE
T ss_pred             cccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEE
Confidence            4455668899999999999999999999999999999999987 9999999999999999999999 888777766543

>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=99.76  E-value=4e-18  Score=128.24  Aligned_cols=76  Identities=18%  Similarity=0.353  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhc------cCccccee
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ------DKGIHAQM  129 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~------g~~i~~~~  129 (305)
                      ...++|||+|||+++|+++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++.||      +..|.++.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~   92 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   92 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEE
Confidence            345779999999999999999999999999999999999999999999999999999999999999      88877766


Q ss_pred             cc
Q psy4086         130 AR  131 (305)
Q Consensus       130 ~~  131 (305)
                      ++
T Consensus        93 l~   94 (111)
T 1x4h_A           93 LK   94 (111)
T ss_dssp             EE
T ss_pred             EE
Confidence            55

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=3.9e-18  Score=127.03  Aligned_cols=76  Identities=28%  Similarity=0.462  Sum_probs=69.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +...++|||+|||+++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|++. |+..|.++.++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~   88 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNID   88 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999998 88777776655

>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=2.5e-18  Score=127.37  Aligned_cols=84  Identities=20%  Similarity=0.358  Sum_probs=75.0

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....++|||+|||.++++++|+++|+.|+   .|+++.++ ++.++|||||+|.+.++|++||+.||+..|.+  +.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~V   86 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDG--NKVTL   86 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT--EECEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECC--eEEEE
Confidence            44568999999999999999999999773   77888887 88999999999999999999999999999999  77999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      ++++.+..+.
T Consensus        87 ~~a~~~~~~~   96 (102)
T 2fc8_A           87 DWAKPKGEGG   96 (102)
T ss_dssp             EECCCCCSSS
T ss_pred             EEecCCCCCC
Confidence            9998865543

>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=99.76  E-value=4.3e-18  Score=127.51  Aligned_cols=83  Identities=16%  Similarity=0.244  Sum_probs=73.8

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCC---ccEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSK---EPLL  211 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~---~~l~  211 (305)
                      ...++|||+|||+++++++|+++|++||.|+.|+|+.+      +||||+|.+.++|++||+.||+..|.+..   +.|+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~   86 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   86 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEE
Confidence            45689999999999999999999999999999999865      79999999999999999999999998822   5599


Q ss_pred             EEeccCCCcCCC
Q psy4086         212 VKFADSGLKKRG  223 (305)
Q Consensus       212 v~~a~~~~~~~~  223 (305)
                      |+++..+...+.
T Consensus        87 V~~a~~~~~~~~   98 (108)
T 1x4c_A           87 VKVDGPRSPSYG   98 (108)
T ss_dssp             EEESSCCSCCCC
T ss_pred             EEeCCCCCCCCC
Confidence            999998665543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=3.5e-18  Score=126.82  Aligned_cols=75  Identities=27%  Similarity=0.472  Sum_probs=68.5

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++|+++|+++|++||.|.+|+|+.+  ++.++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   86 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLY   86 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            345678999999999999999999999999999999998  799999999999999999999999998887766554

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2.2e-18  Score=127.01  Aligned_cols=73  Identities=19%  Similarity=0.278  Sum_probs=68.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCee-EEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccccee
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPII-STKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQM  129 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~-~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~  129 (305)
                      ..++|||+|||+++++++|+++|++||+|. +|+|++++.+++++|||||+|.+.++|++|++.|||..+.++.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGAT   81 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCS
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCC
Confidence            347899999999999999999999999999 9999999999999999999999999999999999998887765

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.76  E-value=2.6e-18  Score=133.30  Aligned_cols=76  Identities=21%  Similarity=0.335  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeE--EEEeeCCCCCCccceEEEEecchhhHHHHHHHhccC----ccccee
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIIS--TKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDK----GIHAQM  129 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~--~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~----~i~~~~  129 (305)
                      ...++|||+|||+++|+++|+++|++||.|..  |+|++|+.+|+++|||||+|.+. +|.+|++.|||.    .|.++.
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            34577999999999999999999999999976  99999999999999999999999 999999999999    888776


Q ss_pred             ccc
Q psy4086         130 ARQ  132 (305)
Q Consensus       130 ~~~  132 (305)
                      ++.
T Consensus       100 l~V  102 (131)
T 2m2b_A          100 INV  102 (131)
T ss_dssp             CCC
T ss_pred             EEE
Confidence            653

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.9e-18  Score=130.13  Aligned_cols=77  Identities=31%  Similarity=0.437  Sum_probs=69.2

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ++...++|||+|||+++|+++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++.+++ .|.++.++
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~   89 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKAN   89 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEE
Confidence            344568899999999999999999999999999999999999999999999999999999999999886 56655544

>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=99.76  E-value=1.4e-18  Score=128.19  Aligned_cols=79  Identities=11%  Similarity=0.241  Sum_probs=70.9

Q ss_pred             CCCCceEEecCCC-CCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCC--CCCCCccEE
Q psy4086         135 QDPTNLYIANLPL-NFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGST--LPGSKEPLL  211 (305)
Q Consensus       135 ~~~~~l~V~nlp~-~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~--~~g~~~~l~  211 (305)
                      .+.++|||+|||+ ++++++|+++|++||.|.+|.|+++     ++||||+|++.++|++||+.||+..  |.|  ++|+
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G--r~l~   85 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFG--KPVR   85 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETT--EECE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCCCceECC--cEEE
Confidence            3567899999999 9999999999999999999999865     6899999999999999999998754  888  8899


Q ss_pred             EEeccCCCc
Q psy4086         212 VKFADSGLK  220 (305)
Q Consensus       212 v~~a~~~~~  220 (305)
                      |.|+.....
T Consensus        86 V~~a~~~~~   94 (102)
T 1x4d_A           86 VHLSQKYKR   94 (102)
T ss_dssp             EEEECCCTT
T ss_pred             EEECCCCCC
Confidence            999986443

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.8e-18  Score=128.14  Aligned_cols=75  Identities=32%  Similarity=0.522  Sum_probs=70.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        11 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2cqb_A           11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR   85 (102)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            457799999999999999999999999999999999998999999999999999999999999998888777665

>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=99.76  E-value=2.6e-18  Score=125.83  Aligned_cols=75  Identities=24%  Similarity=0.583  Sum_probs=70.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      .++|||+|||.++++++|+++|++||.|.+|+|+.++.+|+++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   76 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKC   76 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            467999999999999999999999999999999999989999999999999999999999999999888877653

>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=99.76  E-value=6.2e-18  Score=127.98  Aligned_cols=82  Identities=20%  Similarity=0.410  Sum_probs=73.6

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCC--CCCCCCCccEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNG--STLPGSKEPLL  211 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g--~~~~g~~~~l~  211 (305)
                      ....++|||+|||++++|++|+++|++||.|++|+|+.+     ||||||+|++.++|++|++.|++  ..|.|  ++|+
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~G--r~l~  100 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRG--QPIY  100 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTT--BCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECC--eEEE
Confidence            345688999999999999999999999999999999965     79999999999999999999874  68999  7899


Q ss_pred             EEeccCCCcCC
Q psy4086         212 VKFADSGLKKR  222 (305)
Q Consensus       212 v~~a~~~~~~~  222 (305)
                      |.|++.+..+.
T Consensus       101 V~~a~~k~~~~  111 (119)
T 2ad9_A          101 IQFSNHKELKT  111 (119)
T ss_dssp             EEECSSSSCCC
T ss_pred             EEEccCCCCCc
Confidence            99998876654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=3.4e-18  Score=123.97  Aligned_cols=81  Identities=21%  Similarity=0.322  Sum_probs=76.1

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||+++++++|+++|+.| .|.+|+|+.+.+|+++|||||+|.+.++|++|++ ||+..|.|  +.|+|.
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~g--r~i~v~   82 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGG--RYIEVF   82 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETT--EEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCC--cEEEEE
Confidence            3456899999999999999999999999 9999999999889999999999999999999999 99999999  779999


Q ss_pred             eccCC
Q psy4086         214 FADSG  218 (305)
Q Consensus       214 ~a~~~  218 (305)
                      ++..+
T Consensus        83 ~a~~~   87 (91)
T 2dgw_A           83 REKSG   87 (91)
T ss_dssp             EESSC
T ss_pred             ECCcC
Confidence            98875

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.76  E-value=4.4e-18  Score=125.85  Aligned_cols=78  Identities=18%  Similarity=0.369  Sum_probs=72.7

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      ++|||+|||.++++++|+++|++||.|.+|+++.+    ++|||||+|.+.++|++|++.|||..+.|  +.|+|+++..
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~V~~a~~   74 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICG--SRVRVELSTG   74 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSCSSS--CCCEEEESSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCeECC--cEEEEEEccC
Confidence            47999999999999999999999999999999976    68999999999999999999999999999  6699999998


Q ss_pred             CCcC
Q psy4086         218 GLKK  221 (305)
Q Consensus       218 ~~~~  221 (305)
                      ...+
T Consensus        75 ~~~~   78 (101)
T 2hvz_A           75 MPRR   78 (101)
T ss_dssp             CCCS
T ss_pred             CCCc
Confidence            6644

>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=99.75  E-value=1.6e-18  Score=127.44  Aligned_cols=75  Identities=20%  Similarity=0.250  Sum_probs=70.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||.|.+++++.++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   88 (98)
T 2cqp_A           14 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   88 (98)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            347799999999999999999999999999999999998999999999999999999999999999988887765

>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=99.75  E-value=4.9e-18  Score=126.32  Aligned_cols=83  Identities=10%  Similarity=0.158  Sum_probs=75.7

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEE-EEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVS-TRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~-v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++++++|+++|+.||.|.+ |+|+.+.+|+++|||||+|.+.++|++||+. |+..|.+  +.|+|.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~g--r~i~v~   89 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGH--RYIEIF   89 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSS--SCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCC--cEEEEE
Confidence            45688999999999999999999999999987 8898888899999999999999999999997 9999999  679999


Q ss_pred             eccCCCc
Q psy4086         214 FADSGLK  220 (305)
Q Consensus       214 ~a~~~~~  220 (305)
                      ++.....
T Consensus        90 ~~~~~~~   96 (104)
T 1wg5_A           90 KSSRAEV   96 (104)
T ss_dssp             EECTTTS
T ss_pred             ECCHHHH
Confidence            9876543

>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=99.75  E-value=1.4e-17  Score=125.84  Aligned_cols=77  Identities=30%  Similarity=0.452  Sum_probs=71.0

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ++...++|||+|||+++|+++|+++|+.||.|.+|+|++++ +++++|||||+|.+.++|++|++.|||+.|.++.+.
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~   97 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGV   97 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccc
Confidence            34456889999999999999999999999999999999999 899999999999999999999999999999776554

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.75  E-value=3.2e-18  Score=128.42  Aligned_cols=86  Identities=16%  Similarity=0.267  Sum_probs=75.1

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      .....++|||+|||.++++++|+++|+.||.|.+|+|+.++ +|.++|||||+|.+.++|++||+.+ +..|.|  +.|+
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g--~~l~   97 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDS--KTID   97 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETT--EEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCC--EEEE
Confidence            34456899999999999999999999999999999999998 7899999999999999999999976 488999  7799


Q ss_pred             EEeccCCCcC
Q psy4086         212 VKFADSGLKK  221 (305)
Q Consensus       212 v~~a~~~~~~  221 (305)
                      |+++..+..+
T Consensus        98 V~~a~~~~~~  107 (109)
T 2rs2_A           98 PKVAFPRRAQ  107 (109)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEccCCCCC
Confidence            9999875543

>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=99.75  E-value=6.3e-19  Score=133.41  Aligned_cols=82  Identities=21%  Similarity=0.384  Sum_probs=76.6

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||+++++++|+++|+.||.|..|+|+.++ ++.++|||||+|.+.++|++|| .||+..|.|  +.|+|+++
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g--~~l~V~~a  101 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLG--VPIIVQAS  101 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETT--EEEEEEEH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCC--eEEEEEec
Confidence            4789999999999999999999999999999999998 6899999999999999999999 999999999  77999999


Q ss_pred             cCCCcC
Q psy4086         216 DSGLKK  221 (305)
Q Consensus       216 ~~~~~~  221 (305)
                      ..+..+
T Consensus       102 ~~~~~~  107 (114)
T 2cq4_A          102 QAEKNR  107 (114)
T ss_dssp             HHHHHH
T ss_pred             CCCccC
Confidence            875544

>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=99.75  E-value=9.6e-19  Score=128.66  Aligned_cols=82  Identities=15%  Similarity=0.283  Sum_probs=75.6

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++++++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|++|++.|||..|.|  +.|+|+
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g--~~l~V~   90 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS--RKVKLV   90 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETT--EECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCC--eEEEEE
Confidence            345789999999999999999999999999988888876 88999999999999999999999999999999  779999


Q ss_pred             eccCC
Q psy4086         214 FADSG  218 (305)
Q Consensus       214 ~a~~~  218 (305)
                      ++..+
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98764

>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=99.75  E-value=3.6e-18  Score=122.73  Aligned_cols=80  Identities=23%  Similarity=0.391  Sum_probs=73.4

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      .....++|||+|||+++++++|+++|++||.|.+|+|+.++ ++.++|||||+|.+.++|++|++ +++..|.|  +.|+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g--~~i~   83 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDG--RVID   83 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETT--EEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECC--EEEE
Confidence            34567899999999999999999999999999999999997 79999999999999999999996 57888999  7799


Q ss_pred             EEec
Q psy4086         212 VKFA  215 (305)
Q Consensus       212 v~~a  215 (305)
                      |++|
T Consensus        84 v~~A   87 (87)
T 3s7r_A           84 PKKA   87 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            9886

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=4.5e-18  Score=128.45  Aligned_cols=78  Identities=28%  Similarity=0.389  Sum_probs=71.7

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCee--------EEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPII--------STKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGI  125 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~--------~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i  125 (305)
                      +....++|||+|||+++|+++|+++|++||.|.        .|+|+.++.+++++|||||+|.+.++|++|++.|||..|
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            344568899999999999999999999999999        699999988999999999999999999999999999988


Q ss_pred             cceecc
Q psy4086         126 HAQMAR  131 (305)
Q Consensus       126 ~~~~~~  131 (305)
                      .++.++
T Consensus        91 ~g~~l~   96 (113)
T 2cpe_A           91 QGSKLK   96 (113)
T ss_dssp             TTEECE
T ss_pred             CCCEEE
Confidence            877665

>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=99.75  E-value=6.6e-18  Score=124.63  Aligned_cols=81  Identities=19%  Similarity=0.334  Sum_probs=72.5

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhC--CCCCCCCCccEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN--GSTLPGSKEPLLV  212 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~--g~~~~g~~~~l~v  212 (305)
                      ...++|||+|||+++++++|+++|++||.|.+|.|+.+     ||||||+|.+.++|++|++.|+  +..|.|  ++|+|
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G--r~l~V   85 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRN--QPIYI   85 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETT--EECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECC--cEEEE
Confidence            45678999999999999999999999999999998854     8999999999999999999875  567899  88999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      .|++.+..+.
T Consensus        86 ~~a~~~~~~~   95 (101)
T 2cq1_A           86 QYSNHKELKT   95 (101)
T ss_dssp             EECSCSSCCC
T ss_pred             EEcCcccCcC
Confidence            9999866654

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=6.6e-18  Score=122.68  Aligned_cols=80  Identities=18%  Similarity=0.367  Sum_probs=72.6

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||.++++++|+++|++||.|.+|++++       +||||+|.+.++|++|++.||+..|.+  +.|+|+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~V~   77 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-------DYAFVHMERAEDAVEAIRGLDNTEFQG--KRMHVQ   77 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS-------SEEEEEESCHHHHHHHHHHHTTEEETT--EEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCeeCC--cEEEEE
Confidence            44568899999999999999999999999999999983       499999999999999999999999999  779999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      ++..+....
T Consensus        78 ~a~~~~~~~   86 (92)
T 2dgt_A           78 LSTSRLRTA   86 (92)
T ss_dssp             ESSCCCSCC
T ss_pred             EccCCCCCC
Confidence            998865544

>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=99.75  E-value=9.7e-18  Score=125.70  Aligned_cols=85  Identities=18%  Similarity=0.260  Sum_probs=76.7

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCC-eEEEEEe-eCC-CCCcccEEEEEecCHHHHHHHHHHhC--CCCCCCCCcc
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVT-VVSTRIL-RDN-NNTSKGVGFARLESKDKCDQMIQLFN--GSTLPGSKEP  209 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~-v~~v~i~-~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~--g~~~~g~~~~  209 (305)
                      ...++|||+|||+++++++|+++|++||. |.+|.++ .++ ++.++|||||+|.+.++|++|++.||  +..+.|  +.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g--~~   83 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWG--HQ   83 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTT--BC
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecC--Ce
Confidence            45688999999999999999999999998 9999998 666 67999999999999999999999996  589999  77


Q ss_pred             EEEEeccCCCcC
Q psy4086         210 LLVKFADSGLKK  221 (305)
Q Consensus       210 l~v~~a~~~~~~  221 (305)
                      |+|.|++++...
T Consensus        84 l~V~~a~~~~~~   95 (109)
T 2dis_A           84 IAVDWAEPEIDV   95 (109)
T ss_dssp             CEEEESCSSCST
T ss_pred             EEEEEcCCCCCc
Confidence            999999876543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.61  E-value=7.2e-20  Score=139.09  Aligned_cols=86  Identities=16%  Similarity=0.315  Sum_probs=79.0

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEE--------EEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCC
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVS--------TRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPG  205 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~--------v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  205 (305)
                      .+.++|||+|||.++++++|+++|++||.|..        |+|+.++ ++.++|||||+|.+.++|++|++.|||..|.|
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            45688999999999999999999999999998        8999986 78999999999999999999999999999999


Q ss_pred             CCccEEEEeccCCCcCC
Q psy4086         206 SKEPLLVKFADSGLKKR  222 (305)
Q Consensus       206 ~~~~l~v~~a~~~~~~~  222 (305)
                        +.|+|+++..+..+.
T Consensus        85 --~~l~V~~a~~~~~~~   99 (116)
T 2lcw_A           85 --NPIKVSFATRRADFN   99 (116)
Confidence              779999998865543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.75  E-value=5.2e-18  Score=130.29  Aligned_cols=85  Identities=19%  Similarity=0.386  Sum_probs=78.7

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...++|||+|||.++++++|+++|++||.|.+|+|+.+++|.++|||||+|.+.++|++|++.|||..|.|  +.|+|++
T Consensus        33 ~~~~~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           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDG--RPMDIQL  110 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSS--CEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECC--cEEEEEE
Confidence            34578999999999999999999999999999999999888999999999999999999999999999999  7799999


Q ss_pred             ccCCCcC
Q psy4086         215 ADSGLKK  221 (305)
Q Consensus       215 a~~~~~~  221 (305)
                      |......
T Consensus       111 a~~~~~~  117 (124)
T 2kt5_A          111 VASQIDL  117 (124)
T ss_dssp             ECCTTCC
T ss_pred             eCCCCCC
Confidence            9875443

>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=99.75  E-value=1.5e-18  Score=135.04  Aligned_cols=85  Identities=12%  Similarity=0.174  Sum_probs=77.7

Q ss_pred             cccCCCCceEEecCCCCCCHHHHHHHHhhCCC---eEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCc
Q psy4086         132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVT---VVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKE  208 (305)
Q Consensus       132 ~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~---v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~  208 (305)
                      ......++|||+|||+++|+++|+++|+.||.   |.+|+|+.+++|+++|||||+|.+.++|++||+ ||+..|.+  +
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~g--r  115 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGH--R  115 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSS--S
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECC--E
Confidence            44456788999999999999999999999999   899999999889999999999999999999999 99999999  7


Q ss_pred             cEEEEeccCCC
Q psy4086         209 PLLVKFADSGL  219 (305)
Q Consensus       209 ~l~v~~a~~~~  219 (305)
                      .|+|.++....
T Consensus       116 ~i~V~~a~~~e  126 (136)
T 2hgl_A          116 YIEVFKSHRTE  126 (136)
T ss_dssp             EEEEEECCHHH
T ss_pred             EEEEEECChHH
Confidence            79999986543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=2e-18  Score=121.01  Aligned_cols=75  Identities=19%  Similarity=0.351  Sum_probs=71.2

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ++|||+|||.++++++|+++|++||.|.++.++.++ ++.++|||||+|.+.++|++|++.++ ..+.|  +.|+|++|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g--~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDS--KTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSS--CCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCC--EEEEEEec
Confidence            579999999999999999999999999999999997 78999999999999999999999999 99999  67999986

>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=99.75  E-value=9.9e-18  Score=122.99  Aligned_cols=79  Identities=20%  Similarity=0.294  Sum_probs=72.2

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCC--CCCccEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLP--GSKEPLL  211 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~--g~~~~l~  211 (305)
                      ....++|||+|||.++++++|+++|++||.|++|.+..+     ++||||+|.+.++|++|++.||+..|.  +  +.|+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g--~~l~   86 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPD--RRLR   86 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSS--CBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCEeCCCC--cEEE
Confidence            345689999999999999999999999999999999854     789999999999999999999999999  7  7799


Q ss_pred             EEeccCCC
Q psy4086         212 VKFADSGL  219 (305)
Q Consensus       212 v~~a~~~~  219 (305)
                      |+|++++.
T Consensus        87 V~~a~~~~   94 (97)
T 1why_A           87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEECCCCC
Confidence            99998753

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.75  E-value=7e-18  Score=125.21  Aligned_cols=73  Identities=21%  Similarity=0.330  Sum_probs=68.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++|| |.+|+|++++.+++++|||||+|.+.++|++|+ .|||..|.++.++
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   86 (103)
T 2dng_A           14 PPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLR   86 (103)
T ss_dssp             SCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECE
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEE
Confidence            457899999999999999999999997 999999999999999999999999999999999 8999888777665

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.5e-18  Score=129.01  Aligned_cols=84  Identities=23%  Similarity=0.526  Sum_probs=76.7

Q ss_pred             cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       132 ~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      ......++|||+|||.++++++|+++|++||.|.+|+|+.++. .++|||||+|.+.++|++|++.|||..|.|  +.|+
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g--~~l~  100 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVVEG--RKIE  100 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEETT--EECE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEECC--EEEE
Confidence            3445678999999999999999999999999999999999864 489999999999999999999999999999  7799


Q ss_pred             EEeccCC
Q psy4086         212 VKFADSG  218 (305)
Q Consensus       212 v~~a~~~  218 (305)
                      |+++..+
T Consensus       101 V~~a~~~  107 (109)
T 2err_A          101 VNNATAR  107 (109)
T ss_dssp             EEECCCS
T ss_pred             EEECCCC
Confidence            9998764

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.75  E-value=5e-18  Score=130.37  Aligned_cols=80  Identities=16%  Similarity=0.336  Sum_probs=75.3

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||.++++++|+++|++||.|.+|+|+.++ ++.++|||||+|.+.++|++|+ .|||..|.|  +.|+|.++
T Consensus        36 ~~~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           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRG--RTIKVLPK  112 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETT--EECEEEES
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECC--eEEEEEEC
Confidence            4789999999999999999999999999999999997 8899999999999999999999 799999999  77999998


Q ss_pred             cCCC
Q psy4086         216 DSGL  219 (305)
Q Consensus       216 ~~~~  219 (305)
                      +...
T Consensus       113 ~~~~  116 (124)
T 2jwn_A          113 RTNM  116 (124)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8643

>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=99.75  E-value=6.4e-18  Score=125.65  Aligned_cols=73  Identities=16%  Similarity=0.381  Sum_probs=67.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCC-CCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTT-NKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~-g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|+.|| |.+|.|++++.+ ++++|||||+|.+.++|++|+ .||+..|.++.++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~   87 (104)
T 1wi8_A           14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIR   87 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEE
Confidence            447899999999999999999999999 999999999987 999999999999999999999 8998888777655

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=8.4e-19  Score=125.48  Aligned_cols=80  Identities=24%  Similarity=0.353  Sum_probs=73.8

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++++++|+++|++||.|.+++|+.++ ++.++|||||+|.+.++|++|++.|||..|.|  +.|+++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~~~~~   80 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQA--QMAKQS   80 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCE--ESCCSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEee--EEEeec
Confidence            356899999999999999999999999999999999997 78999999999999999999999999999999  668776


Q ss_pred             ecc
Q psy4086         214 FAD  216 (305)
Q Consensus       214 ~a~  216 (305)
                      ++.
T Consensus        81 ~~~   83 (85)
T 1x4e_A           81 GPS   83 (85)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>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=99.75  E-value=1.1e-18  Score=127.63  Aligned_cols=80  Identities=16%  Similarity=0.284  Sum_probs=73.7

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|++|++.||+..|.+  +.|+|++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g--r~l~v~~   91 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS--RKVKLSG   91 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETT--EECEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECC--cEEEEEe
Confidence            35789999999999999999999999999988888877 78999999999999999999999999999999  7799999


Q ss_pred             ccC
Q psy4086         215 ADS  217 (305)
Q Consensus       215 a~~  217 (305)
                      +..
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            764

>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=99.75  E-value=8.5e-18  Score=123.83  Aligned_cols=81  Identities=28%  Similarity=0.457  Sum_probs=73.6

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...++|||+|||.++++++|+++|++||.|.+|++..+     ++||||+|.+.++|++|++.|||..|.|  +.|+|++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~~~g--~~l~v~~   85 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRG--KQLRVRF   85 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTT--BCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEeCC--ceEEEEE
Confidence            45678999999999999999999999999999999844     7899999999999999999999999999  7799999


Q ss_pred             ccCCCcCC
Q psy4086         215 ADSGLKKR  222 (305)
Q Consensus       215 a~~~~~~~  222 (305)
                      +..+....
T Consensus        86 a~~~~~~~   93 (99)
T 2cpj_A           86 ACHSASLT   93 (99)
T ss_dssp             SSCCSCCC
T ss_pred             cCCCCCCC
Confidence            98865443

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=8.4e-18  Score=121.62  Aligned_cols=80  Identities=19%  Similarity=0.396  Sum_probs=72.8

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||+++++++|+++|++||.|.+|++++       +||||+|.+.++|++|++.|||..|.|  +.|+|+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~   76 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK-------DYAFVHMEKEADAKAAIAQLNGKEVKG--KRINVE   76 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS-------SCEEEEESCHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCEECC--cEEEEE
Confidence            45578999999999999999999999999999999983       499999999999999999999999999  779999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      ++.....+.
T Consensus        77 ~a~~~~~~~   85 (90)
T 2dnp_A           77 LSTKGQKKS   85 (90)
T ss_dssp             ESCCCCCCC
T ss_pred             ECCCCCCCC
Confidence            998875544

>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=99.75  E-value=5.2e-18  Score=127.44  Aligned_cols=76  Identities=25%  Similarity=0.435  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   99 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ   99 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            4557899999999999999999999999999999999999999999999999999999999999999888777654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=9.1e-18  Score=124.77  Aligned_cols=75  Identities=27%  Similarity=0.376  Sum_probs=69.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhc-cCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCc-ccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQ-YGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG-IHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~-~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~-i~~~~~~  131 (305)
                      ...++|||+|||+++|+++|+++|++ ||.|.+|+|++++ +++++|||||+|.+.++|++|++.|||.. |.++.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~   83 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVR   83 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEE
Confidence            34577999999999999999999999 9999999999999 89999999999999999999999999988 8777655

>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=99.75  E-value=9e-19  Score=126.73  Aligned_cols=80  Identities=19%  Similarity=0.420  Sum_probs=72.1

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      ++|||+|||.++++++|+++|++||.|.+++++.++ ++.++|||||+|.+.+ |.+|++.|||..+.|  +.|+|++|.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g--~~l~V~~a~   78 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMG--RTIRVTEAN   78 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSS--SSCSEEEC-
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECC--eEEEEEEcC
Confidence            579999999999999999999999999999999998 7899999999999999 999999999999999  779999998


Q ss_pred             CCCc
Q psy4086         217 SGLK  220 (305)
Q Consensus       217 ~~~~  220 (305)
                      ....
T Consensus        79 ~~~~   82 (90)
T 2ki2_A           79 PKKS   82 (90)
T ss_dssp             ----
T ss_pred             CCCC
Confidence            7543

>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=99.75  E-value=4.8e-18  Score=128.94  Aligned_cols=75  Identities=32%  Similarity=0.529  Sum_probs=69.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|+.++ +++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~   79 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIK   79 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            455789999999999999999999999999999999998 899999999999999999999999998887766554

>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=99.75  E-value=1.4e-18  Score=127.02  Aligned_cols=75  Identities=20%  Similarity=0.244  Sum_probs=70.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      .++|||+|||+++|+++|+++|++||.|.++.++.++.+++++|||||+|.+.++|++|++.||+..|.++.++.
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v   89 (95)
T 2ek1_A           15 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL   89 (95)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEE
Confidence            377999999999999999999999999999999999999999999999999999999999999999998877653

>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=99.74  E-value=1.7e-18  Score=127.90  Aligned_cols=81  Identities=22%  Similarity=0.398  Sum_probs=73.6

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC--CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN--NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~--~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ...++|||+|||+++++++|+++|+.|| |.+|+|+.++  +|+++|||||+|.+.++|.+|+ .|||..|.|  +.|+|
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g--~~l~V   92 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN--RRIRV   92 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTT--BCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECC--eEEEE
Confidence            4568999999999999999999999999 9999999986  7899999999999999999999 899999999  77999


Q ss_pred             EeccCCC
Q psy4086         213 KFADSGL  219 (305)
Q Consensus       213 ~~a~~~~  219 (305)
                      ++++.+.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9988753

>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=99.74  E-value=1.6e-18  Score=131.24  Aligned_cols=83  Identities=27%  Similarity=0.454  Sum_probs=73.7

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCe----EEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTV----VSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v----~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      ...++|||+|||.++++++|+++|+.||.|    ..+++.   ++.++|||||+|.+.++|++|++.|||..|.|  +.|
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~---~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g--~~l   97 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLYG--KIL   97 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE---CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSS--CBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC---CCccceEEEEEECCHHHHHHHHHHhCCCEeCC--cEE
Confidence            345899999999999999999999999999    455544   66889999999999999999999999999999  779


Q ss_pred             EEEeccCCCcCC
Q psy4086         211 LVKFADSGLKKR  222 (305)
Q Consensus       211 ~v~~a~~~~~~~  222 (305)
                      +|.|+..+..+.
T Consensus        98 ~v~~a~~~~~~~  109 (115)
T 2cpx_A           98 VIEFGKNKKQRS  109 (115)
T ss_dssp             EEEECCCCSCCC
T ss_pred             EEEEccCCCCCC
Confidence            999999876654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=4.8e-18  Score=124.87  Aligned_cols=75  Identities=27%  Similarity=0.399  Sum_probs=69.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCC---CCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT---TNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~---~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||+|.+|.|++++.   +++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLE   81 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            347799999999999999999999999999999999886   668999999999999999999999999888877665

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.74  E-value=2.7e-18  Score=128.79  Aligned_cols=80  Identities=16%  Similarity=0.180  Sum_probs=71.8

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCC-CeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYV-TVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g-~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++++++|+++|++|| .|..+.|..+   .++|||||+|.+.++|++||+.|||..|.|  +.|+|+
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~lng~~l~G--r~i~V~  100 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNNIEFRG--SVITVE  100 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTTEEETT--EEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCCCEECC--eEEEEE
Confidence            3457899999999999999999999999 8999998654   578999999999999999999999999999  779999


Q ss_pred             eccCCC
Q psy4086         214 FADSGL  219 (305)
Q Consensus       214 ~a~~~~  219 (305)
                      ++....
T Consensus       101 ~a~~~p  106 (111)
T 2jvr_A          101 RDDNPP  106 (111)
T ss_dssp             ESCC--
T ss_pred             ECCCCC
Confidence            987643

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=3e-18  Score=125.43  Aligned_cols=75  Identities=25%  Similarity=0.438  Sum_probs=69.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEE-EEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIIST-KAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~-~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||.|.++ +|++++.++.++|||||+|.+.++|++|++.|||..|.++.++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   79 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPIT   79 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34789999999999999999999999999999 9999988999999999999999999999999999888777655

>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=99.74  E-value=5e-18  Score=127.09  Aligned_cols=83  Identities=14%  Similarity=0.226  Sum_probs=72.6

Q ss_pred             ccCCCCceEEecCCCC-CCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCC--CCCCCCCcc
Q psy4086         133 QEQDPTNLYIANLPLN-FKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNG--STLPGSKEP  209 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~-~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g--~~~~g~~~~  209 (305)
                      .....++|||+|||++ +++++|+++|++||.|.+|.|+     ++||||||+|.+.++|++|++.|++  ..|.|  ++
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~-----~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~G--r~   93 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM-----RMKSQAFIEMETREDAMAMVDHCLKKALWFQG--RC   93 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE-----TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSS--SC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEe-----cCCCEEEEEECCHHHHHHHHHHhccCCceECC--EE
Confidence            3456789999999998 9999999999999999999998     3589999999999999999998864  56888  77


Q ss_pred             EEEEeccCCCcCC
Q psy4086         210 LLVKFADSGLKKR  222 (305)
Q Consensus       210 l~v~~a~~~~~~~  222 (305)
                      |+|.|+..+....
T Consensus        94 l~V~~a~~~~~~~  106 (112)
T 1x4f_A           94 VKVDLSEKYKKLV  106 (112)
T ss_dssp             CEEEEECSCSSSS
T ss_pred             EEEEECccccccc
Confidence            9999998765543

>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=99.74  E-value=1.5e-17  Score=123.38  Aligned_cols=76  Identities=24%  Similarity=0.406  Sum_probs=68.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ....++|||+|||+++|+++|+++|++||.|.+|+|++++.  .++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34557899999999999999999999999999999999874  38999999999999999999999998888776653

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=9.1e-18  Score=123.20  Aligned_cols=80  Identities=20%  Similarity=0.296  Sum_probs=72.3

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||+++++++|+++|++||.|. +.++.+   .++|||||+|.+.++|++|++.|||..|.|  +.|+|+
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~V~   89 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLRLGT--DTLRVA   89 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCCSSS--SCCEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCEECC--cEEEEE
Confidence            34468999999999999999999999999997 677765   678999999999999999999999999999  679999


Q ss_pred             eccCCC
Q psy4086         214 FADSGL  219 (305)
Q Consensus       214 ~a~~~~  219 (305)
                      ++..+.
T Consensus        90 ~a~~~~   95 (97)
T 2e5j_A           90 LARQQR   95 (97)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998754

>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=99.74  E-value=1.2e-17  Score=125.19  Aligned_cols=82  Identities=13%  Similarity=0.333  Sum_probs=74.8

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||.++++++|+++|++||.|.+|+|+.+     ++||||+|.+.++|++|++.|||..|.|  +.|+|.
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~   94 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEG--HVVKCY   94 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECC--cEEEEE
Confidence            345689999999999999999999999999999999965     7899999999999999999999999999  779999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      |++.....+
T Consensus        95 ~a~~~~~~~  103 (109)
T 1x4g_A           95 WGKESPDMT  103 (109)
T ss_dssp             CCCCCCSSC
T ss_pred             ecCCCCCCC
Confidence            998865543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.74  E-value=2.8e-18  Score=128.78  Aligned_cols=77  Identities=22%  Similarity=0.358  Sum_probs=63.9

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        53 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      .+....++|||+|||+++|+++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|++|++.++ ..|.++.+
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~g~~l   96 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTI   96 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC-EEETTEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC-CcCCCEEE
Confidence            334456789999999999999999999999999999999999999999999999999999999998643 44444443

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.74  E-value=1.1e-17  Score=131.02  Aligned_cols=76  Identities=32%  Similarity=0.509  Sum_probs=70.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++++++|+++|++||+|++++|++++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  136 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR  136 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEE
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3567899999999999999999999999999999999998999999999999999999999999999888877654

>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=99.74  E-value=1.3e-17  Score=123.71  Aligned_cols=75  Identities=29%  Similarity=0.419  Sum_probs=67.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++++++|+++|++||.|.+|+|++++.+  ++|||||+|.+.++|++|++.||+..|.++.++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVK   86 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEE
Confidence            345678999999999999999999999999999999998643  689999999999999999999998888777655

>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=99.74  E-value=9.5e-18  Score=125.33  Aligned_cols=75  Identities=19%  Similarity=0.305  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++|+++|+++|++||.|.+|+|+.++ +++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  101 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMN  101 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            356789999999999999999999999999999999999 899999999999999999999999999998887664

>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=99.74  E-value=3e-18  Score=145.44  Aligned_cols=74  Identities=26%  Similarity=0.400  Sum_probs=68.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccC--CeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYG--PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G--~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      ..++|||+||++++|+++|+++|++||  .|++|+|++|+.++++||||||+|.+.++|++||+.||++.|.++.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l  142 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNP  142 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEe
Confidence            567899999999999999999999999  99999999999999999999999999999999999999998887654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.7e-17  Score=125.45  Aligned_cols=74  Identities=22%  Similarity=0.302  Sum_probs=68.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||.|.+|+|+.++ +++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        14 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   87 (114)
T 2do0_A           14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMH   87 (114)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEE
Confidence            45779999999999999999999999999999999998 599999999999999999999999999888877665

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.74  E-value=1.3e-17  Score=128.24  Aligned_cols=83  Identities=13%  Similarity=0.358  Sum_probs=73.7

Q ss_pred             CCCCceEEecCCCCCCHHHHH----HHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         135 QDPTNLYIANLPLNFKECDLE----SLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~----~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      ...++|||+|||+.+++++|+    ++|++||.|.+|.+..  ++.++|||||+|.+.++|.+|++.|||..|.|  ++|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~--~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~g--r~l  102 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL--SDDNSGKAYIVFATQESAQAFVEAFQGYPFQG--NPL  102 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC--CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTT--SCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc--CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCC--CEE
Confidence            446789999999999999876    6999999999988754  56889999999999999999999999999999  779


Q ss_pred             EEEeccCCCcC
Q psy4086         211 LVKFADSGLKK  221 (305)
Q Consensus       211 ~v~~a~~~~~~  221 (305)
                      +|.|+..+...
T Consensus       103 ~V~~a~~~~~~  113 (127)
T 2a3j_A          103 VITFSETPQSQ  113 (127)
T ss_dssp             EEEECCCCCHH
T ss_pred             EEEEccCcchh
Confidence            99999876543

>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=99.74  E-value=7.7e-18  Score=121.44  Aligned_cols=75  Identities=13%  Similarity=0.315  Sum_probs=70.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      +.++|||+|||+++++++|+++|++||.|.+++++.++.+++++|||||+|.+.++|++|+ .|||..+.++.++.
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V   79 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKV   79 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEE
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEE
Confidence            4578999999999999999999999999999999999989999999999999999999999 89999888877653

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.74  E-value=4.5e-18  Score=126.77  Aligned_cols=82  Identities=12%  Similarity=0.133  Sum_probs=74.5

Q ss_pred             CCCCceEEecCCCCC------CHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCc
Q psy4086         135 QDPTNLYIANLPLNF------KECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKE  208 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~------te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~  208 (305)
                      ...++|||+|||+.+      ++++|+++|++||.|.+|.|+ ..+|.++|||||+|.+.++|.+||+.|||..|.|  +
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g--~   89 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK--Q   89 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECST--T
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCC--C
Confidence            346789999999999      789999999999999999988 3478999999999999999999999999999999  6


Q ss_pred             -cEEEEeccCCC
Q psy4086         209 -PLLVKFADSGL  219 (305)
Q Consensus       209 -~l~v~~a~~~~  219 (305)
                       +|+|.++....
T Consensus        90 ~~l~V~~a~~~~  101 (105)
T 2nlw_A           90 HTFRVNLFTDFD  101 (105)
T ss_dssp             CEEEEECSCCCC
T ss_pred             ceEEEEEcchHh
Confidence             79999998643

>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=7.8e-19  Score=132.90  Aligned_cols=84  Identities=18%  Similarity=0.266  Sum_probs=77.4

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCe-EEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTV-VSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v-~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....++|||+|||+++++++|+++|+.||.| ..|+|+.+++++++|||||+|.+.++|++||+. |+..|.+  +.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~g--r~i~v   88 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNG--REAFV   88 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETT--EEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCC--eEEEE
Confidence            3456889999999999999999999999999 899999999999999999999999999999987 9999999  77999


Q ss_pred             EeccCCCc
Q psy4086         213 KFADSGLK  220 (305)
Q Consensus       213 ~~a~~~~~  220 (305)
                      .++..+..
T Consensus        89 ~~a~~~~~   96 (114)
T 2cpy_A           89 HVVTLEDM   96 (114)
T ss_dssp             EEECHHHH
T ss_pred             EECCHHHH
Confidence            99987653

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=5.6e-18  Score=128.52  Aligned_cols=76  Identities=29%  Similarity=0.484  Sum_probs=68.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++|+++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++|++. ++..|.++.++
T Consensus        24 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~   99 (116)
T 1x4b_A           24 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVE   99 (116)
T ss_dssp             HHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEE
Confidence            34558899999999999999999999999999999999999999999999999999999999997 77777666554

>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=129.21  Aligned_cols=84  Identities=19%  Similarity=0.323  Sum_probs=74.8

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++++++|+++|+.||.|.. .++.+. ++.++|||||+|.+.++|++||+ |||..|.|  +.|+|.
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g--~~l~V~   90 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFG--NEIKLE   90 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTT--BCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECC--cEEEEE
Confidence            35678999999999999999999999999888 566665 78899999999999999999998 99999999  779999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      ++..+..++
T Consensus        91 ~a~~~~~~~   99 (101)
T 1fj7_A           91 KPKGRDGTR   99 (101)
T ss_dssp             CCSCCCCSS
T ss_pred             EcCCCCCCC
Confidence            998765543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=8.2e-18  Score=126.21  Aligned_cols=81  Identities=22%  Similarity=0.386  Sum_probs=71.2

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        53 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      .+....++|||+|||.++++++|+++|++||+|.+|+|++++  +.++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            334456889999999999999999999999999999999986  358999999999999999999999999988877664


Q ss_pred             ccC
Q psy4086         133 QEQ  135 (305)
Q Consensus       133 ~~~  135 (305)
                      ...
T Consensus       102 ~~a  104 (109)
T 2err_A          102 NNA  104 (109)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            433

>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=99.73  E-value=5.7e-18  Score=121.81  Aligned_cols=75  Identities=25%  Similarity=0.418  Sum_probs=69.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCC-ccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNK-CRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~-~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++||.|.++.|+.++.++. ++|||||+|.+.++|++|++.|||..+.++.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   78 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEIT   78 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEE
Confidence            357899999999999999999999999999999999987766 999999999999999999999999998887765

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.73  E-value=4.1e-18  Score=120.80  Aligned_cols=70  Identities=20%  Similarity=0.288  Sum_probs=64.8

Q ss_pred             CeEEEcCCCCCC------cHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccce-ec
Q psy4086          59 TNLYIRGLTQDT------TDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ-MA  130 (305)
Q Consensus        59 ~~l~V~~Lp~~~------t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~-~~  130 (305)
                      ++|||+|||+.+      ++++|+++|++||+|.+|.|+  +.+|+++|||||+|.+.++|++|++.|||..+.++ .+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            679999999999      789999999999999999987  45799999999999999999999999999999887 54

>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=99.73  E-value=9e-18  Score=129.27  Aligned_cols=76  Identities=25%  Similarity=0.442  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++|+++|+++|++||.|.+|.|+.++.++.++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   95 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS   95 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            3467899999999999999999999999999999999998999999999999999999999999999887766554

>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=99.73  E-value=4.5e-17  Score=122.12  Aligned_cols=74  Identities=22%  Similarity=0.265  Sum_probs=66.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++|+++|+++|++||.|.+|+|..+   ++++|||||+|.+.++|++|++.||+..|.++.++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   92 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLR   92 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            335578999999999999999999999999999999654   56899999999999999999999999888777665

>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=8.4e-18  Score=125.05  Aligned_cols=74  Identities=19%  Similarity=0.271  Sum_probs=66.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeE-EEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIIS-TKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~-~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++|+++|+++|+.||.|.+ |.|+.+ .+|+++|||||+|.+.++|++|++. |+..|.++.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~   87 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIE   87 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEE
Confidence            34578999999999999999999999999987 888888 6899999999999999999999997 88887776654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=2.3e-17  Score=121.50  Aligned_cols=78  Identities=22%  Similarity=0.341  Sum_probs=70.9

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhC--CCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKY--VTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~--g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ...++|||+|||+++++++|+++|++|  |.|..|++.       ++||||+|.+.++|++|++.|||..|.+  +.|+|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v   83 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDG--SPIEV   83 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETT--EEEEE
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCC--cEEEE
Confidence            346789999999999999999999999  999998875       6699999999999999999999999999  77999


Q ss_pred             EeccCCCcC
Q psy4086         213 KFADSGLKK  221 (305)
Q Consensus       213 ~~a~~~~~~  221 (305)
                      .+++.+...
T Consensus        84 ~~a~~~~~~   92 (99)
T 2cpd_A           84 TLAKPVDKD   92 (99)
T ss_dssp             ECCCCCCCC
T ss_pred             EECCCCCCC
Confidence            999876543

>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=99.73  E-value=2.9e-18  Score=127.47  Aligned_cols=75  Identities=25%  Similarity=0.574  Sum_probs=69.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|++|++.|||..+.++.++
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALR   81 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBE
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Confidence            457899999999999999999999999999999999998999999999999999999999999999888776554

>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=99.73  E-value=1.3e-17  Score=125.21  Aligned_cols=77  Identities=25%  Similarity=0.426  Sum_probs=70.6

Q ss_pred             CCceEEecCCCC-CCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLN-FKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~-~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||++ +++++|+++|++||.|.+|.|       +++||||+|.+.++|++|++.||+..|.|  +.|+|.++
T Consensus        27 ~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~V~~a   97 (110)
T 1wf1_A           27 NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVLAG--QTLDINMA   97 (110)
T ss_dssp             SSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCEETT--EECCEEES
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEECC--eEEEEEEC
Confidence            479999999999 999999999999999999998       47899999999999999999999999999  77999999


Q ss_pred             cCCCcCC
Q psy4086         216 DSGLKKR  222 (305)
Q Consensus       216 ~~~~~~~  222 (305)
                      ......+
T Consensus        98 ~~~~~~~  104 (110)
T 1wf1_A           98 GEPKPDR  104 (110)
T ss_dssp             CCCCSCC
T ss_pred             CCCCCCC
Confidence            8654443

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.6e-17  Score=122.75  Aligned_cols=69  Identities=16%  Similarity=0.247  Sum_probs=61.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhcc--Ccccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQD--KGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g--~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++||+|.+|+|+++      ||||||+|.+.++|++|++.|++  ..|.++.++
T Consensus        15 ~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            4578999999999999999999999999999999875      68999999999999999998763  566666555

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.73  E-value=1.2e-17  Score=122.39  Aligned_cols=79  Identities=22%  Similarity=0.382  Sum_probs=70.4

Q ss_pred             cCCCCceEEecCCC-CCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPL-NFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~-~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ..+.++|||+|||+ ++++++|+++|++||.|.+|+|.       +|||||+|.+.++|++|++.|||..+.|  +.|+|
T Consensus         7 ~~~~~~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            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFG--KKLIL   77 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBT--TTBCE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCC--cEEEE
Confidence            34568999999998 99999999999999999999985       7899999999999999999999999999  67999


Q ss_pred             EeccCCCcC
Q psy4086         213 KFADSGLKK  221 (305)
Q Consensus       213 ~~a~~~~~~  221 (305)
                      .++......
T Consensus        78 ~~a~~~~~~   86 (96)
T 2kvi_A           78 EVSSSNARP   86 (96)
T ss_dssp             EEEECCCC-
T ss_pred             EEcCcCCCC
Confidence            999875443

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.73  E-value=4.2e-18  Score=120.73  Aligned_cols=72  Identities=14%  Similarity=0.214  Sum_probs=66.3

Q ss_pred             CceEEecCCCCC------CHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCc-cE
Q psy4086         138 TNLYIANLPLNF------KECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKE-PL  210 (305)
Q Consensus       138 ~~l~V~nlp~~~------te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~-~l  210 (305)
                      ++|||+|||..+      ++++|+++|++||.|.+|.|. ..+|.++|||||+|.+.++|++|++.|||..|.|  + +|
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g--~~~l   78 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK--QHTF   78 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSS--SSCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCC--ceeE
Confidence            689999999999      779999999999999999988 3478999999999999999999999999999999  5 57


Q ss_pred             EE
Q psy4086         211 LV  212 (305)
Q Consensus       211 ~v  212 (305)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            65

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.73  E-value=2.6e-17  Score=119.41  Aligned_cols=73  Identities=22%  Similarity=0.339  Sum_probs=67.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||+|.+|+|+++  +++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~   79 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREID   79 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            4578999999999999999999999999999999984  789999999999999999999999999888877655

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.73  E-value=4.2e-18  Score=129.63  Aligned_cols=83  Identities=14%  Similarity=0.199  Sum_probs=76.8

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCC---eEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVT---VVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~---v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      ....++|||+|||+++|+++|+++|+.||.   |..|+|+.+++|+++|||||+|.+.++|++||+ ||+..|.+  +.|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~g--r~i   90 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGH--RYI   90 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETT--EEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECC--eEE
Confidence            345688999999999999999999999999   899999999889999999999999999999999 99999999  779


Q ss_pred             EEEeccCCC
Q psy4086         211 LVKFADSGL  219 (305)
Q Consensus       211 ~v~~a~~~~  219 (305)
                      +|.++....
T Consensus        91 ~V~~a~~~~   99 (118)
T 2db1_A           91 EVFKSHRTE   99 (118)
T ss_dssp             EEEEECHHH
T ss_pred             EEEECCHHH
Confidence            999987644

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.73  E-value=4.3e-18  Score=118.77  Aligned_cols=71  Identities=31%  Similarity=0.561  Sum_probs=66.5

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +|||+|||+++++++|+++|++||.|.++.++.++.+++++|||||+|.+.++|++|++ +|+..+.++.++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~   71 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVE   71 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCE
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEE
Confidence            49999999999999999999999999999999999899999999999999999999998 898888776654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=3.9e-18  Score=119.51  Aligned_cols=71  Identities=23%  Similarity=0.411  Sum_probs=64.9

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      ++|||+|||+++++++|+++|++||+|.++.+++++.+++++|||||+|.+.++|++|++.++ ..+.++.+
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l   71 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTI   71 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEE
Confidence            469999999999999999999999999999999999899999999999999999999999776 66555543

>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=99.72  E-value=6.8e-18  Score=129.65  Aligned_cols=74  Identities=19%  Similarity=0.306  Sum_probs=67.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|+.||.|.++.++.+..+|+++|||||+|.+.++|++||+ |||..|.++.++
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   97 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQ   97 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEE
Confidence            45789999999999999999999999999987777777799999999999999999999999 999988877553

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.72  E-value=6.9e-17  Score=123.99  Aligned_cols=77  Identities=18%  Similarity=0.284  Sum_probs=70.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ....++|||+|||+++++++|+++|++||.|.+|+|+.++ +|+++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  108 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI  108 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            3456789999999999999999999999999999999999 8999999999999999999999999998887776653

>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=99.72  E-value=1.1e-17  Score=123.98  Aligned_cols=72  Identities=19%  Similarity=0.326  Sum_probs=65.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|+.||. .+|+|++++ +++++|||||+|.+.++|++||+ +|+..|..+.++
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (102)
T 1wez_A           14 TGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVE   85 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEE
Confidence            4477999999999999999999999995 599999998 89999999999999999999995 788888777654

>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=99.72  E-value=1.4e-17  Score=121.24  Aligned_cols=79  Identities=22%  Similarity=0.318  Sum_probs=70.0

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCC-eEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCC-CCCCCCCccEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVT-VVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNG-STLPGSKEPLLV  212 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~-v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g-~~~~g~~~~l~v  212 (305)
                      ...++|||+|||.++++++|+++|++||. |..+.+.      +++||||+|.+.++|++|++.||| ..|.|  +.|+|
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g--~~l~v   77 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHG--KIMEV   77 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETT--EECEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECC--EEEEE
Confidence            45689999999999999999999999999 6665553      478999999999999999999999 99999  77999


Q ss_pred             EeccCCCcC
Q psy4086         213 KFADSGLKK  221 (305)
Q Consensus       213 ~~a~~~~~~  221 (305)
                      +++..+..+
T Consensus        78 ~~a~~~~~~   86 (93)
T 2cqh_A           78 DYSVSKKLR   86 (93)
T ss_dssp             EECCCCCCC
T ss_pred             EEccCcccc
Confidence            999876544

>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=99.72  E-value=2.2e-17  Score=131.98  Aligned_cols=75  Identities=23%  Similarity=0.341  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      ...++|||+|||+++|+++|+++|++||+|.+|+|+.++.++.++|||||+|.+.++|++||+.||+..|.++.+
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l  111 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRII  111 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            456789999999999999999999999999999999999999999999999999999999999999988877654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.72  E-value=8.5e-18  Score=127.95  Aligned_cols=73  Identities=19%  Similarity=0.239  Sum_probs=67.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCC---eeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGP---IISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~---i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|+.||.   |..|+|++++. |+++|||||+|.+.++|++|++ +|+..|.++.++
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   91 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIE   91 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEE
Confidence            4578999999999999999999999999   89999999986 9999999999999999999999 999988887654

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.72  E-value=1.1e-17  Score=130.96  Aligned_cols=80  Identities=20%  Similarity=0.319  Sum_probs=74.5

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....++|||+|||.++++++|+++|++||.|.+++|+.++ ++.++|||||+|.+.++|++|++.|||..|.|  +.|+|
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v  137 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG--RTIRV  137 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETT--EEEEE
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECC--EEEEE
Confidence            3456899999999999999999999999999999999997 78999999999999999999999999999999  77999


Q ss_pred             Eec
Q psy4086         213 KFA  215 (305)
Q Consensus       213 ~~a  215 (305)
                      ++|
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            986

>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=99.72  E-value=7.7e-18  Score=127.40  Aligned_cols=73  Identities=15%  Similarity=0.175  Sum_probs=67.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCe-eEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPI-ISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i-~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|+.||.| ..|+|++++ +|+++|||||+|.+.++|++||+. |+..|.++.++
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~   87 (114)
T 2cpy_A           14 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAF   87 (114)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEE
T ss_pred             CccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEE
Confidence            45779999999999999999999999999 899999999 899999999999999999999996 88887776553

>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=99.72  E-value=6.8e-18  Score=124.62  Aligned_cols=76  Identities=16%  Similarity=0.350  Sum_probs=67.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCC-CCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDK-TTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~-~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ....++|||+|||+++++++|+++|++|| |.+|+|++++ .+|+++|||||+|.+.++|++|+ .|||..|.++.++.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            34558899999999999999999999999 9999999998 68999999999999999999999 89999888776653

>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=99.72  E-value=1e-17  Score=126.15  Aligned_cols=79  Identities=14%  Similarity=0.265  Sum_probs=70.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHH---HHHhccCCeeEEEEeeCCCCC---CccceEEEEecchhhHHHHHHHhccCcccce
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLI---NMCSQYGPIISTKAILDKTTN---KCRGYGFVDFESGGYALAAVKALQDKGIHAQ  128 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~---~~f~~~G~i~~~~i~~~~~~g---~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~  128 (305)
                      ....++|||+|||+++++++|+   ++|++||+|.+|.|++++.++   +++|||||+|.+.++|++|++.|||..|.++
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3456779999999999999999   999999999999999988654   5669999999999999999999999998887


Q ss_pred             ecccc
Q psy4086         129 MARQQ  133 (305)
Q Consensus       129 ~~~~~  133 (305)
                      .++..
T Consensus        92 ~l~V~   96 (111)
T 2cpi_A           92 TLKAS   96 (111)
T ss_dssp             EEEEE
T ss_pred             EEEEE
Confidence            76643

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1e-17  Score=125.41  Aligned_cols=72  Identities=13%  Similarity=0.208  Sum_probs=66.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +.++|||+|||+++|+++|+++|+.| .|.+|+|++|+. |+++|||||+|.+.++|++|+ .+|+..|.++.+.
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~   86 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVE   86 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEE
Confidence            34689999999999999999999999 899999999985 999999999999999999999 5999888887654

>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=99.72  E-value=2.9e-17  Score=124.42  Aligned_cols=80  Identities=15%  Similarity=0.234  Sum_probs=67.0

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCcc-----
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEP-----  209 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~-----  209 (305)
                      ...++|||+|||+++++++|+++|++||.|++|.|+.+      |||||+|.+.++|++||+.|||..|.|  +.     
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g--r~~~~~~   85 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRS--HEGETAY   85 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCC--TTSCCCB
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECC--cEeeeEE
Confidence            34588999999999999999999999999999999865      899999999999999999999999999  55     


Q ss_pred             EEEEeccCCCcCC
Q psy4086         210 LLVKFADSGLKKR  222 (305)
Q Consensus       210 l~v~~a~~~~~~~  222 (305)
                      |+|..+......+
T Consensus        86 i~v~~~~~~~~~~   98 (115)
T 3beg_B           86 IRVKVDGPRSPSY   98 (115)
T ss_dssp             CEEEECC----CC
T ss_pred             EEeccCCCCCCCC
Confidence            7777776654443

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.2e-17  Score=124.95  Aligned_cols=78  Identities=15%  Similarity=0.197  Sum_probs=72.9

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      ..+|||+|||+++++++|+++|+.| .|.+|+|+.+++|+++|||||+|.+.++|++|| .||+..|.+  +.|.|..+.
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~g--r~i~V~~a~   91 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQ--RYVEVSPAT   91 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETT--EEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECC--eEEEEEECC
Confidence            3689999999999999999999999 899999999998999999999999999999999 699999999  779998887


Q ss_pred             CC
Q psy4086         217 SG  218 (305)
Q Consensus       217 ~~  218 (305)
                      ..
T Consensus        92 ~~   93 (109)
T 2dnn_A           92 ER   93 (109)
T ss_dssp             HH
T ss_pred             cc
Confidence            54

>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=2.4e-17  Score=117.78  Aligned_cols=76  Identities=17%  Similarity=0.323  Sum_probs=70.1

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHh-CCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF-NGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l-~g~~~~g~~~~l~v  212 (305)
                      ....++|||+|||.++++++|+++|++||.|.+|+++.     ++|||||+|.+.++|++|++.| ++..+.|  ++|+|
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~-----~kg~afV~f~~~~~A~~a~~~l~~~~~~~g--~~l~v   81 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ-----RQQCAFIQFATRQAAEVAAEKSFNKLIVNG--RRLNV   81 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG-----GGTEEEEEESSHHHHHHHHHTTTTTCEETT--EECCE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC-----CCCEEEEEECCHHHHHHHHHHhcCCeeECC--CEEEE
Confidence            34568999999999999999999999999999999995     4789999999999999999998 9999999  77999


Q ss_pred             Eecc
Q psy4086         213 KFAD  216 (305)
Q Consensus       213 ~~a~  216 (305)
                      +|++
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9974

>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=99.72  E-value=6.6e-18  Score=117.77  Aligned_cols=74  Identities=15%  Similarity=0.274  Sum_probs=69.3

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      +|||+|||.++++++|+++|++||.|.++.++.++ ++.++|||||+|.+.++|++|++. ++..+.|  +.|+|++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g--~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGL--SKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTT--BCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECC--EEEEEEEC
Confidence            68999999999999999999999999999999987 789999999999999999999985 8899999  66998875

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=3e-17  Score=118.92  Aligned_cols=73  Identities=16%  Similarity=0.290  Sum_probs=67.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++++++|+++|+.| .|.+|+|+++ .+|+++|||||+|.+.++|++|++ |||..|.++.++
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~   80 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIE   80 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEE
Confidence            345789999999999999999999999 9999999999 689999999999999999999999 999988887665

>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=99.71  E-value=2.9e-17  Score=120.27  Aligned_cols=73  Identities=15%  Similarity=0.141  Sum_probs=67.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHH----HHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLI----NMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~----~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      +.++|||+|||+++++++|+    ++|++||+|.+|+|++++.+   +|||||+|.+.++|++|++.|||..|.++.++.
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            44789999999999999999    99999999999999999865   899999999999999999999999888877653

>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=99.71  E-value=1.7e-17  Score=124.89  Aligned_cols=76  Identities=12%  Similarity=0.184  Sum_probs=70.4

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ..++|||+|||+++++++|+++|++||.|..|.|..     +++||||+|.+.++|++||+.|||..|.+  ++|.|.|+
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~l~V~~a   81 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHH--VPLYLEWA   81 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSS--SBCEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhCCCEECC--eEEEEEEC
Confidence            457899999999999999999999999999999873     57899999999999999999999999999  77999998


Q ss_pred             cCC
Q psy4086         216 DSG  218 (305)
Q Consensus       216 ~~~  218 (305)
                      ...
T Consensus        82 ~~~   84 (111)
T 1whx_A           82 PIG   84 (111)
T ss_dssp             ETT
T ss_pred             CCC
Confidence            764

>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=99.71  E-value=9.8e-18  Score=130.41  Aligned_cols=75  Identities=17%  Similarity=0.177  Sum_probs=68.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCC---eeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGP---IISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~---i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++|+++|+++|+.||.   |.+|+|++|+. |+++|||||+|.+.++|++|++ ||+..|.++.++
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~  118 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE  118 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEE
Confidence            345678999999999999999999999999   89999999997 9999999999999999999999 999888877553

>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=2.3e-17  Score=123.55  Aligned_cols=81  Identities=22%  Similarity=0.502  Sum_probs=72.0

Q ss_pred             cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       132 ~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      ......++|||+|||.++++++|+++|++||.|.+|++.       +|||||+|.+.++|++|++.|||..|.|  +.|+
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g--~~l~   96 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFAN--QPLE   96 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETT--EECE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECC--eEEE
Confidence            344566899999999999999999999999999999988       7899999999999999999999999999  7799


Q ss_pred             EEeccCCCcC
Q psy4086         212 VKFADSGLKK  221 (305)
Q Consensus       212 v~~a~~~~~~  221 (305)
                      |.|++....+
T Consensus        97 V~~a~~~~~r  106 (108)
T 2jvo_A           97 VVYSKLPAKR  106 (108)
T ss_dssp             EESCSCCC--
T ss_pred             EEEecCCCCC
Confidence            9999876543

>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=99.71  E-value=6.8e-17  Score=128.42  Aligned_cols=79  Identities=11%  Similarity=0.122  Sum_probs=71.2

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      .+|||+||++.+|+++|+++|++||.|++|.|..+   ..++||||+|.+.++|++|++.|||..|.+..+.|+|.|++.
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k---~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~  123 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL  123 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES---SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSS
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC---CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecC
Confidence            56899999999999999999999999999999765   357899999999999999999999999966336799999987


Q ss_pred             CC
Q psy4086         218 GL  219 (305)
Q Consensus       218 ~~  219 (305)
                      +.
T Consensus       124 ~~  125 (164)
T 1sjr_A          124 TS  125 (164)
T ss_dssp             SS
T ss_pred             Cc
Confidence            53

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.71  E-value=1.5e-17  Score=122.86  Aligned_cols=76  Identities=20%  Similarity=0.340  Sum_probs=70.8

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...++|||+|||.++++++|+++|++||.|.++++.     +++|||||+|.+.++|++|++.|||..|.|  +.|+|+|
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-----~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~l~V~~   97 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-----PEKGCCFIKYDTHEQAAVCIVALANFPFQG--RNLRTGW   97 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-----TTTTEEEEECSSHHHHHHHHHHHTTCEETT--EECCCCB
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-----cCCCEEEEEECCHHHHHHHHHHhCCCeECC--eEEEEEe
Confidence            346789999999999999999999999999999998     468999999999999999999999999999  7799999


Q ss_pred             ccC
Q psy4086         215 ADS  217 (305)
Q Consensus       215 a~~  217 (305)
                      +++
T Consensus        98 a~~  100 (101)
T 2la4_A           98 GKE  100 (101)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            875

>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=99.71  E-value=7.6e-18  Score=125.95  Aligned_cols=83  Identities=11%  Similarity=0.104  Sum_probs=76.3

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCC---eEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVT---VVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~---v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      ....++|||+|||+++|+++|+++|+.||.   |.+|+|+.++.|+++|||||+|.+.++|++||+ +|+..|.+  +.|
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~g--r~i   84 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQ--RYV   84 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSS--SCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCC--eEE
Confidence            345688999999999999999999999998   899999999889999999999999999999999 99999999  679


Q ss_pred             EEEeccCCC
Q psy4086         211 LVKFADSGL  219 (305)
Q Consensus       211 ~v~~a~~~~  219 (305)
                      +|.++....
T Consensus        85 ~V~~a~~~~   93 (107)
T 2lmi_A           85 EVYEINNED   93 (107)
T ss_dssp             CCEECCHHH
T ss_pred             EEEECCHHH
Confidence            999987643

>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=99.71  E-value=4.5e-18  Score=123.03  Aligned_cols=73  Identities=26%  Similarity=0.531  Sum_probs=68.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ++|||+|||+++++++|+++|++||+|.+|++++++.+++++|||||+|.+.+ |++|++.|||..+.++.++.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V   74 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRV   74 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSE
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEE
Confidence            57999999999999999999999999999999999999999999999999999 99999999998888776653

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.71  E-value=6.9e-18  Score=123.55  Aligned_cols=82  Identities=16%  Similarity=0.344  Sum_probs=72.6

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...++|||+|||.++++++|+++|+.||.|..+    ..++.++|||||+|.+.++|++|++.|||..|.|  +.|+|.+
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~l~v~~   87 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG--RSVSLYY   87 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETT--EEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC--eEEEEEE
Confidence            346789999999999999999999999987765    3367889999999999999999999999999999  7799999


Q ss_pred             ccCCCcCC
Q psy4086         215 ADSGLKKR  222 (305)
Q Consensus       215 a~~~~~~~  222 (305)
                      +..+...+
T Consensus        88 a~~~~~~~   95 (96)
T 1fjc_A           88 TGEKGGTR   95 (96)
T ss_dssp             CSSSCCCC
T ss_pred             cCCCCCCC
Confidence            98765543

>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=6.4e-17  Score=118.67  Aligned_cols=77  Identities=22%  Similarity=0.397  Sum_probs=70.2

Q ss_pred             ccCCCCceEEecCCC-CCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         133 QEQDPTNLYIANLPL-NFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~-~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      .....++|||+|||+ ++++++|+++|++||.|.++++.       +|||||+|.+.++|++|++.|||..+.|  +.|+
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~~g--~~l~   88 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFG--KKLI   88 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEETT--EECE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEECC--EEEE
Confidence            334568999999998 99999999999999999999984       7899999999999999999999999999  7799


Q ss_pred             EEeccCC
Q psy4086         212 VKFADSG  218 (305)
Q Consensus       212 v~~a~~~  218 (305)
                      |++++.+
T Consensus        89 V~~a~~~   95 (97)
T 2xnq_A           89 LEVSSSN   95 (97)
T ss_dssp             EEECCCC
T ss_pred             EEecCCC
Confidence            9998764

>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=99.70  E-value=1.5e-17  Score=121.95  Aligned_cols=83  Identities=14%  Similarity=0.366  Sum_probs=74.5

Q ss_pred             cCCCCceEEecCCCCCCHHHHH----HHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCcc
Q psy4086         134 EQDPTNLYIANLPLNFKECDLE----SLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEP  209 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~----~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~  209 (305)
                      ....++|||+|||.++++++|+    ++|++||.|.+|.+..  ++.++|||||+|.+.++|++|++.|||..+.|  +.
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~   80 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYD--KP   80 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETT--EE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECC--cE
Confidence            3456899999999999999999    9999999999999874  45678999999999999999999999999999  78


Q ss_pred             EEEEeccCCCc
Q psy4086         210 LLVKFADSGLK  220 (305)
Q Consensus       210 l~v~~a~~~~~  220 (305)
                      |+|.|+.....
T Consensus        81 l~v~~a~~~~~   91 (97)
T 1nu4_A           81 MRIQYAKTDSD   91 (97)
T ss_dssp             CEEEECSSCCT
T ss_pred             EEEEEccCCCc
Confidence            99999987543

>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=8.8e-17  Score=121.67  Aligned_cols=82  Identities=17%  Similarity=0.318  Sum_probs=74.7

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...++|||+|||.++++++|+++|+.||.|.+|.|+.+.  .++|||||+|.+.++|.+|++.|||..+.|  +.|+|.|
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~--~~~g~afV~f~~~~~A~~A~~~l~g~~~~g--~~l~v~~   81 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--ETRGTAYVVYEDIFDAKNAVDHLSGFNVSN--RYLVVLY   81 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECST--TTTTCEEEEESSHHHHHHHHHHHTTCBSSS--CBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCC--CCCcEEEEEECCHHHHHHHHHHcCCCEECC--eEEEEEE
Confidence            456899999999999999999999999999999998764  568999999999999999999999999999  7799999


Q ss_pred             ccCCCc
Q psy4086         215 ADSGLK  220 (305)
Q Consensus       215 a~~~~~  220 (305)
                      +.....
T Consensus        82 a~~~~~   87 (115)
T 3lqv_A           82 YNANRA   87 (115)
T ss_dssp             CCHHHH
T ss_pred             ecCChh
Confidence            986443

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.70  E-value=3.1e-17  Score=122.16  Aligned_cols=73  Identities=21%  Similarity=0.291  Sum_probs=66.5

Q ss_pred             CCCeEEEcCCCCCC------cHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccce-e
Q psy4086          57 SKTNLYIRGLTQDT------TDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ-M  129 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~------t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~-~  129 (305)
                      ..++|||+|||+.+      |+++|+++|++||.|.+|.|+  +.+|+++|||||+|.+.++|++|++.|||..|.++ .
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            35789999999999      789999999999999999988  45799999999999999999999999999988876 5


Q ss_pred             cc
Q psy4086         130 AR  131 (305)
Q Consensus       130 ~~  131 (305)
                      ++
T Consensus        92 l~   93 (105)
T 2nlw_A           92 FR   93 (105)
T ss_dssp             EE
T ss_pred             EE
Confidence            54

>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=99.70  E-value=3.7e-17  Score=122.50  Aligned_cols=85  Identities=19%  Similarity=0.210  Sum_probs=72.0

Q ss_pred             ccCCCCceEE--ecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCC---CCCC
Q psy4086         133 QEQDPTNLYI--ANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTL---PGSK  207 (305)
Q Consensus       133 ~~~~~~~l~V--~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~---~g~~  207 (305)
                      .....++|||  +||++++++++|+++|++||.|.+|.|+.     .||||||+|.+.++|++|++.|||..|   .+..
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~-----~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-----TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            3345678999  77999999999999999999999998874     378999999999999999999999977   2223


Q ss_pred             ccEEEEeccCCCcCC
Q psy4086         208 EPLLVKFADSGLKKR  222 (305)
Q Consensus       208 ~~l~v~~a~~~~~~~  222 (305)
                      ++|.|.|+.......
T Consensus        96 ~~l~v~~a~~~p~~~  110 (114)
T 2cq2_A           96 ITLYLNFVEKVQWSG  110 (114)
T ss_dssp             EECEEEEESCCCCSS
T ss_pred             cEEEEEecccCcccC
Confidence            889999998755443

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.70  E-value=1.4e-17  Score=129.75  Aligned_cols=78  Identities=24%  Similarity=0.329  Sum_probs=71.0

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +....++|||+|||+++|+++|+++|++||+|..|+|+.++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        43 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~  120 (135)
T 2lea_A           43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR  120 (135)
T ss_dssp             SGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            344567899999999999999999999999999999999998999999999999999999999999998887766554

>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=99.70  E-value=7.4e-18  Score=129.46  Aligned_cols=83  Identities=12%  Similarity=0.160  Sum_probs=73.6

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeC-CCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~-~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ....++|||+|||+++++++|+++|+.||.|..+.++.+ .+|.++|||||+|.+.++|++||+ ||+..|.|  +.|.|
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~g--r~i~V   98 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGN--RFIQV   98 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTT--SCBEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECC--cEEEE
Confidence            345689999999999999999999999999988555554 489999999999999999999999 99999999  77999


Q ss_pred             EeccCCC
Q psy4086         213 KFADSGL  219 (305)
Q Consensus       213 ~~a~~~~  219 (305)
                      .++..+.
T Consensus        99 ~~a~~~~  105 (124)
T 1wel_A           99 HPITKKG  105 (124)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9987643

>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=99.70  E-value=7.8e-17  Score=118.61  Aligned_cols=72  Identities=21%  Similarity=0.407  Sum_probs=64.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ  133 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~  133 (305)
                      ...++|||+|||+++|+++|+++|++||+|.+|++.++      +|||||+|.+.++|++|++.|||..|.++.++..
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   84 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            34578999999999999999999999999999999854      6899999999999999999999998888776643

>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=99.70  E-value=1.6e-17  Score=124.14  Aligned_cols=74  Identities=18%  Similarity=0.172  Sum_probs=67.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCC---eeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGP---IISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~---i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++|+++|+++|+.||.   |.+|+|++++. |+++|||||+|.+.++|++|++ +|+..|.++.++
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            45678999999999999999999999988   89999999987 9999999999999999999999 998888776553

>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=99.70  E-value=4.9e-17  Score=130.13  Aligned_cols=77  Identities=25%  Similarity=0.321  Sum_probs=70.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++|+++|+++|+.||.|.+|+|++++.+|+++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  143 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR  143 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            34567899999999999999999999999999999999998999999999999999999999999998887776554

>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=1.2e-16  Score=117.23  Aligned_cols=80  Identities=15%  Similarity=0.257  Sum_probs=71.6

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+||  ++++++|+++|++||.|.+|.|.     .++|||||+|.+.++|++||+.|||..|.+  +.|+|.
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g--~~l~v~   82 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVES--VQLKVN   82 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEEETT--EEEEEE
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCeECC--eEEEEE
Confidence            345689999996  89999999999999999999985     568999999999999999999999999999  789999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      |+..+..+.
T Consensus        83 ~a~~~~~~~   91 (97)
T 1x5p_A           83 IARKQPMLD   91 (97)
T ss_dssp             CCSSCCCCC
T ss_pred             ECCCCCCCC
Confidence            998765543

>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=1.5e-17  Score=115.93  Aligned_cols=70  Identities=20%  Similarity=0.417  Sum_probs=64.7

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      +|||+|||+++++++|+++|++||+|.++.+++++.+++++|||||+|.+.++|++|++. ++..+.++.+
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l   70 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKC   70 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEE
Confidence            599999999999999999999999999999999999999999999999999999999994 7777766654

>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=99.70  E-value=1.1e-16  Score=119.82  Aligned_cols=64  Identities=22%  Similarity=0.318  Sum_probs=60.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      ..++|||+|||+++|+++|+++|++||+|.+|+|+.+       |||||+|.+.++|++||+.|||+.|.+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g   77 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRS   77 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccC
Confidence            4578999999999999999999999999999999876       799999999999999999999988877

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.70  E-value=5.5e-17  Score=132.23  Aligned_cols=83  Identities=19%  Similarity=0.401  Sum_probs=77.6

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...++|||+|||+.+++++|+++|++||.|++|.|+.++++.++|||||+|.+.++|++||+.|||..|.|  +.|+|.|
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~G--r~l~V~~  163 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDG--RPMDIQL  163 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSS--SBCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECC--EEEEEEE
Confidence            34579999999999999999999999999999999999888999999999999999999999999999999  7799999


Q ss_pred             ccCCC
Q psy4086         215 ADSGL  219 (305)
Q Consensus       215 a~~~~  219 (305)
                      +....
T Consensus       164 a~~~~  168 (177)
T 2f3j_A          164 VASQI  168 (177)
T ss_dssp             ESSGG
T ss_pred             ecCCC
Confidence            88643

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.70  E-value=3e-17  Score=126.00  Aligned_cols=76  Identities=22%  Similarity=0.395  Sum_probs=70.4

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ...++|||+|||+++|+++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|+ .|||..|.++.++.
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V  109 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKV  109 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEE
Confidence            34678999999999999999999999999999999999989999999999999999999999 79999888877653

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.69  E-value=1.3e-17  Score=123.57  Aligned_cols=74  Identities=22%  Similarity=0.451  Sum_probs=66.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHH---HhccCcccceec
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK---ALQDKGIHAQMA  130 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~---~l~g~~i~~~~~  130 (305)
                      ...++|||+|||+++++++|+++|++||.|.+|+|++++ +++++|||||+|.+.++|++|++   .|+|+.|.+...
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-TGVSKGYGFVSFYNDVDVQKIVESQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTTCCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHhCCCeECCEEEEEEEC
Confidence            355789999999999999999999999999999999999 89999999999999999999999   566666654443

>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=99.69  E-value=3.8e-17  Score=122.47  Aligned_cols=75  Identities=17%  Similarity=0.307  Sum_probs=67.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCC-eeEEEEe-eCCCCCCccceEEEEecchhhHHHHHHHhc--cCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGP-IISTKAI-LDKTTNKCRGYGFVDFESGGYALAAVKALQ--DKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~-i~~~~i~-~~~~~g~~~G~afV~f~~~~~A~~a~~~l~--g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++||. |.+|.++ .++.+++++|||||+|.+.++|++|++.||  +..+.++.++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            4578999999999999999999999998 9999999 888889999999999999999999999996  4777666554

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=1.3e-16  Score=116.63  Aligned_cols=79  Identities=29%  Similarity=0.326  Sum_probs=71.0

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEE-EEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVST-RILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v-~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++++++|+++|++||.|.+| .|+.++   ..+.|||+|.+.++|++|++.|||..|.|  +.|+|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~---~~~~afV~f~~~~~a~~Ai~~l~g~~~~g--~~l~V~   87 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS---ETAVVNVTYSSKDQARQALDKLNGFQLEN--FTLKVA   87 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSS---SSEEEEEEESSHHHHHHHHHHHTTCBCSS--CBCEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEECCHHHHHHHHHHhCCCEECC--cEEEEE
Confidence            446889999999999999999999999999999 488774   23349999999999999999999999999  779999


Q ss_pred             eccCC
Q psy4086         214 FADSG  218 (305)
Q Consensus       214 ~a~~~  218 (305)
                      ++.++
T Consensus        88 ~a~~~   92 (96)
T 2e44_A           88 YIPDE   92 (96)
T ss_dssp             ECCCC
T ss_pred             EcCcc
Confidence            99876

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=6.2e-17  Score=119.36  Aligned_cols=69  Identities=14%  Similarity=0.224  Sum_probs=60.3

Q ss_pred             CCCeEEEcCCCC-CCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCc--ccceecc
Q psy4086          57 SKTNLYIRGLTQ-DTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG--IHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~--i~~~~~~  131 (305)
                      ..++|||+|||+ ++|+++|+++|++||.|.+|.|+++      +|||||+|.+.++|++|++.||+..  |.++.+.
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            357799999999 9999999999999999999999865      4799999999999999999988653  5665544

>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=99.69  E-value=1.4e-16  Score=117.51  Aligned_cols=69  Identities=16%  Similarity=0.274  Sum_probs=59.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhc--cCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ--DKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~--g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||.|.+|.|+++      ||||||+|.+.++|++|++.|+  +..|.++.+.
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           14 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   84 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEE
Confidence            3467999999999999999999999999999998864      7899999999999999999764  3445555444

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=1.4e-16  Score=118.22  Aligned_cols=68  Identities=24%  Similarity=0.291  Sum_probs=58.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCc--ccceecc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG--IHAQMAR  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~--i~~~~~~  131 (305)
                      .++|||+|||+++++++|+++|++||.|.+|.|+++      ||||||+|.+.++|++|++.|++..  |.++.++
T Consensus        15 ~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~   84 (104)
T 1wex_A           15 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            467999999999999999999999999999998863      6899999999999999999876543  4444433

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.69  E-value=8.5e-17  Score=123.25  Aligned_cols=78  Identities=12%  Similarity=0.143  Sum_probs=70.5

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccE-EEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGV-GFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~-afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      -.|||+||++.+|+++|+++|++||.|.+|+|..+    .++| |||+|.+.++|++|++.|||..|.+..+.|+|.|++
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak  104 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  104 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECS
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecC
Confidence            45889999999999999999999999999998864    3677 999999999999999999999998855779999998


Q ss_pred             CCC
Q psy4086         217 SGL  219 (305)
Q Consensus       217 ~~~  219 (305)
                      ...
T Consensus       105 ~~~  107 (130)
T 3zzy_A          105 LTS  107 (130)
T ss_dssp             CSS
T ss_pred             CCc
Confidence            754

>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=99.69  E-value=1e-16  Score=129.27  Aligned_cols=76  Identities=25%  Similarity=0.435  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|++||+.|||..|.++.+.
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  145 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ  145 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            4467899999999999999999999999999999999999999999999999999999999999999888776654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.3e-16  Score=118.07  Aligned_cols=73  Identities=30%  Similarity=0.539  Sum_probs=65.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++|+++|+++|+.|   ..|+++.++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   85 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVT   85 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            345779999999999999999999977   4788999988999999999999999999999999999888777655

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=2.3e-17  Score=126.09  Aligned_cols=82  Identities=6%  Similarity=0.124  Sum_probs=73.9

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCe----EEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTV----VSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v----~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      ....+|||+|||+++|+++|+++|+.||.|    ..|.|+.+++|+++|||||+|.+.++|++||+. |+..|.+  +.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~g--R~i   97 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGK--RYI   97 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSS--CEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCC--eEE
Confidence            456899999999999999999999999875    689999998999999999999999999999986 9999999  679


Q ss_pred             EEEeccCCC
Q psy4086         211 LVKFADSGL  219 (305)
Q Consensus       211 ~v~~a~~~~  219 (305)
                      .|..+....
T Consensus        98 ~V~~a~~~e  106 (123)
T 2dha_A           98 ELFRSTAAE  106 (123)
T ss_dssp             CCEEECHHH
T ss_pred             EEEECCHHH
Confidence            998876543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.69  E-value=1.7e-16  Score=120.97  Aligned_cols=76  Identities=17%  Similarity=0.132  Sum_probs=68.4

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccE-EEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGV-GFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~-afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      .|||+||++.+++++|+++|++||.|++|.|+..     .|| |||+|.+.++|++|++.|||..|.+..+.|+|.||+.
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~  101 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP  101 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSC
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecC
Confidence            3689999999999999999999999999999753     376 9999999999999999999999988546799999987


Q ss_pred             CC
Q psy4086         218 GL  219 (305)
Q Consensus       218 ~~  219 (305)
                      +.
T Consensus       102 ~~  103 (124)
T 2e5i_A          102 TR  103 (124)
T ss_dssp             SC
T ss_pred             Cc
Confidence            54

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=6.9e-17  Score=119.34  Aligned_cols=71  Identities=23%  Similarity=0.351  Sum_probs=63.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++||.|   +++.+ .+++++|||||+|.+.++|++|++.||+..|.++.++
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   84 (101)
T 2fc9_A           14 ESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIR   84 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEE
Confidence            45789999999999999999999999976   56666 5799999999999999999999999998888777655

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.68  E-value=1.7e-16  Score=116.02  Aligned_cols=69  Identities=26%  Similarity=0.322  Sum_probs=60.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCc--ccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG--IHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~--i~~~~~~  131 (305)
                      .+++|||+|||+++|+++|+++|++||.|.++++++      .||||||+|.+.++|.+|++.|++..  |.++.+.
T Consensus        20 ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~   90 (100)
T 3r27_A           20 ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAF   90 (100)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEE
Confidence            346799999999999999999999999999999985      46899999999999999999998775  4455443

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.68  E-value=9.5e-17  Score=123.39  Aligned_cols=73  Identities=18%  Similarity=0.237  Sum_probs=64.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHH----HHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLI----NMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~----~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ..++|||+|||+++++++|+    ++|++||+|.+|.+.+   +++++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus        28 p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V  104 (127)
T 2a3j_A           28 PSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI  104 (127)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEE
Confidence            35779999999999999876    6999999999988753   6789999999999999999999999999888876653

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=2.8e-16  Score=115.17  Aligned_cols=69  Identities=20%  Similarity=0.341  Sum_probs=61.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccc--ceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH--AQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~--~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++||.|.+|.++++      +|||||+|.+.++|++|++.|||..|.  ++.++
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~   86 (97)
T 1why_A           16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEE
Confidence            3467999999999999999999999999999998754      679999999999999999999998887  65554

>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=99.68  E-value=1.2e-16  Score=119.56  Aligned_cols=70  Identities=16%  Similarity=0.259  Sum_probs=59.4

Q ss_pred             CCCCeEEEcCCCCC-CcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccC--cccceecc
Q psy4086          56 LSKTNLYIRGLTQD-TTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDK--GIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~-~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~--~i~~~~~~  131 (305)
                      ...++|||+|||++ +++++|+++|++||+|.+|.|++      +||||||+|.+.++|++|++.||+.  .|.++.++
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            34678999999998 99999999999999999999974      4789999999999999999987643  35554443

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.68  E-value=1.4e-16  Score=133.84  Aligned_cols=82  Identities=17%  Similarity=0.333  Sum_probs=76.5

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      +.++|||+|||+++||++|+++|++||.|++|+|++|+ +++++|||||+|.+.++|++||+.||+..+.+  +.|++.+
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g--~~i~~~~   91 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKG--KPVRIMW   91 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT--EECEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCC--ccccccc
Confidence            45789999999999999999999999999999999998 89999999999999999999999999999999  7799999


Q ss_pred             ccCCC
Q psy4086         215 ADSGL  219 (305)
Q Consensus       215 a~~~~  219 (305)
                      +....
T Consensus        92 ~~~~~   96 (213)
T 4f02_A           92 SQRDP   96 (213)
T ss_dssp             CCCCT
T ss_pred             ccccc
Confidence            87644

>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=99.68  E-value=7.8e-17  Score=123.44  Aligned_cols=73  Identities=22%  Similarity=0.308  Sum_probs=64.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCee--EEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPII--STKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~--~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++|+++|+++|+.| .|.  +|+|++|+. |+++|||||+|.+.++|++|++. ++..|.++.++
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~  114 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIE  114 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEE
Confidence            455779999999999999999999999 677  899999986 99999999999999999999984 66777766543

>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=99.68  E-value=4.9e-17  Score=124.54  Aligned_cols=80  Identities=10%  Similarity=0.193  Sum_probs=72.2

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeE--EEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVV--STRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~--~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ...++|||+|||+++|+++|+++|+.| .|+  +|+|+.|++|+++|||||+|.+.++|++||+. ++..|.+  +.|+|
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~g--R~I~V  115 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGH--RYIEV  115 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTT--BCCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECC--EEEEE
Confidence            456789999999999999999999999 677  99999998899999999999999999999985 7799999  77999


Q ss_pred             EeccCC
Q psy4086         213 KFADSG  218 (305)
Q Consensus       213 ~~a~~~  218 (305)
                      ..+..+
T Consensus       116 ~~a~~~  121 (126)
T 2hgm_A          116 FKSSQE  121 (126)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            887653

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=2.6e-16  Score=115.39  Aligned_cols=71  Identities=20%  Similarity=0.280  Sum_probs=62.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++++++|+++|++||.|. ++++.+    +++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   87 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLR   87 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            3457899999999999999999999999997 777754    5789999999999999999999999888776654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=4.9e-17  Score=122.95  Aligned_cols=71  Identities=17%  Similarity=0.346  Sum_probs=63.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCC---CCccceEEEEecchhhHHHHHHHh---ccCcccce
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTT---NKCRGYGFVDFESGGYALAAVKAL---QDKGIHAQ  128 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~---g~~~G~afV~f~~~~~A~~a~~~l---~g~~i~~~  128 (305)
                      ..++|||+|||+++|+++|+++|++||+|. +.++.++.+   |+++|||||+|.+.++|++|++.|   ||+.+.+.
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~~~~   83 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCV   83 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEEEec
Confidence            347799999999999999999999999999 888888877   799999999999999999999998   66655443

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.68  E-value=5.6e-17  Score=122.25  Aligned_cols=77  Identities=17%  Similarity=0.098  Sum_probs=67.8

Q ss_pred             CeEEEcCC----CCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecc----hhh----HHHHHH--HhccCc
Q psy4086          59 TNLYIRGL----TQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES----GGY----ALAAVK--ALQDKG  124 (305)
Q Consensus        59 ~~l~V~~L----p~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~----~~~----A~~a~~--~l~g~~  124 (305)
                      +.|||+||    |+.+++++|+++|+.||+|.+|.++.|+.||+++|||||+|.+    +++    |.+|+.  .|||..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            57999999    9999999999999999999999999999999999999999996    444    788888  689999


Q ss_pred             ccceecccccC
Q psy4086         125 IHAQMARQQEQ  135 (305)
Q Consensus       125 i~~~~~~~~~~  135 (305)
                      |.++.++..-.
T Consensus        83 I~Gr~irV~ln   93 (136)
T 2j8a_A           83 IMGFKFEVILN   93 (136)
T ss_dssp             ETTEEEEEEEC
T ss_pred             ecCcEEEEEEC
Confidence            99987764433

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=1.7e-16  Score=115.62  Aligned_cols=79  Identities=11%  Similarity=0.233  Sum_probs=68.6

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++++++|+++|++||.|.+|  +.++ ++.   ||||+|.+.++|++||+ |||..|.|  +.|+|+
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g--~~l~V~   77 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGG--HRLRVR   77 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETT--EECCCB
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECC--EEEEEE
Confidence            345789999999999999999999999999987  4444 443   99999999999999999 99999999  779999


Q ss_pred             eccCCCcC
Q psy4086         214 FADSGLKK  221 (305)
Q Consensus       214 ~a~~~~~~  221 (305)
                      ++..+...
T Consensus        78 ~a~~~~~~   85 (94)
T 2e5g_A           78 PREQKEFQ   85 (94)
T ss_dssp             CSCCSCCC
T ss_pred             ECCcCCCC
Confidence            88765443

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.67  E-value=2.2e-17  Score=122.05  Aligned_cols=73  Identities=25%  Similarity=0.314  Sum_probs=66.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++||.|.. .++.++.+++++|||||+|.+.++|++|++ |||..|.++.++
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~   88 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIK   88 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEE
Confidence            4578999999999999999999999999988 777777789999999999999999999999 999988877655

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.5e-16  Score=112.27  Aligned_cols=73  Identities=21%  Similarity=0.301  Sum_probs=65.1

Q ss_pred             CCc-eEEecCCCCCCHHH----HHHHHhhC-CCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         137 PTN-LYIANLPLNFKECD----LESLLAKY-VTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       137 ~~~-l~V~nlp~~~te~~----l~~~F~~~-g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      ..+ |||+|||+.+++++    |+++|++| |+|.+|      ++   |+|||+|.+.++|++|++.|||..+.|  |+|
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------tg---G~AfV~F~~~esA~~A~~~l~G~~l~g--r~i   76 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------TG---CSAILRFINQDSAERAQKRMENEDVFG--NRI   76 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------CT---TCEEEEESSHHHHHHHHHHHTTCCSSS--SCC
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------ec---CEEEEEECCHHHHHHHHHHhcCCccCC--ceE
Confidence            445 99999999999987    55899999 599998      22   899999999999999999999999999  789


Q ss_pred             EEEeccCCCc
Q psy4086         211 LVKFADSGLK  220 (305)
Q Consensus       211 ~v~~a~~~~~  220 (305)
                      +|.||..+..
T Consensus        77 ~v~~A~~~sd   86 (96)
T 2diu_A           77 IVSFTPKNRE   86 (96)
T ss_dssp             EEESSCCSCC
T ss_pred             EEEecCCCcc
Confidence            9999998654

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.67  E-value=1.5e-16  Score=119.00  Aligned_cols=71  Identities=27%  Similarity=0.532  Sum_probs=63.6

Q ss_pred             CCCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        53 ~~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..+...++|||+|||+++|+++|+++|++||.|.+|.++        +|||||+|.+.++|++|++.|||..|.++.++
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   96 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLE   96 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            334556889999999999999999999999999999997        68999999999999999999999988887665

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.67  E-value=2.9e-17  Score=121.62  Aligned_cols=81  Identities=20%  Similarity=0.415  Sum_probs=74.5

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ..++|||+|||+++++++|+++|+.||.|.+|+|+.++++.++|||||+|.+.++|++|++  ++..+.|  +.|.|.++
T Consensus         8 ~~~~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            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHG--KKLKLGPA   83 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETT--EECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECC--EEEEEEEC
Confidence            4578999999999999999999999999999999999988999999999999999999998  8999999  77999998


Q ss_pred             cCCCc
Q psy4086         216 DSGLK  220 (305)
Q Consensus       216 ~~~~~  220 (305)
                      ..+..
T Consensus        84 ~~~~~   88 (102)
T 2xs2_A           84 IRKQN   88 (102)
T ss_dssp             EECC-
T ss_pred             CcCcc
Confidence            76543

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=2.2e-16  Score=119.47  Aligned_cols=69  Identities=16%  Similarity=0.247  Sum_probs=59.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhcc--Ccccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQD--KGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g--~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|+++      ||||||+|.+.++|++|++.|++  ..|.++.++
T Consensus        30 ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           30 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            4577999999999999999999999999999999875      68999999999999999998763  345554443

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.67  E-value=5.3e-16  Score=116.39  Aligned_cols=67  Identities=22%  Similarity=0.393  Sum_probs=61.5

Q ss_pred             CCCeEEEcCCCCC-CcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQD-TTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~-~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||++ +++++|+++|++||.|.+|.|        ++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   93 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLD   93 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            4578999999999 999999999999999999998        578999999999999999999999888877665

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.67  E-value=7.3e-17  Score=120.98  Aligned_cols=72  Identities=13%  Similarity=0.219  Sum_probs=64.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccC-CeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYG-PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G-~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ..++|||+|||+++++++|+++|++|| +|..+.|..    ++++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V   99 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV   99 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            457899999999999999999999999 899999864    347899999999999999999999999998887653

>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=99.67  E-value=2.7e-16  Score=112.28  Aligned_cols=70  Identities=23%  Similarity=0.317  Sum_probs=62.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHh-ccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL-QDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l-~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++++++|+++|++||.|.+|++++      ++|||||+|.+.++|++|++.| |+..+.++.++
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~------~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~   80 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ------RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLN   80 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECC
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC------CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEE
Confidence            4457799999999999999999999999999999986      3689999999999999999998 88888776654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=5.8e-17  Score=123.82  Aligned_cols=72  Identities=19%  Similarity=0.273  Sum_probs=64.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCe----eEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPI----ISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i----~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      ..++|||+|||+++|+++|+++|++||+|    ..|.|++++ +|+++|||||+|.+.++|++|++. |++.|..+.+
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i   97 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYI   97 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEE
Confidence            45789999999999999999999999975    689999995 899999999999999999999995 8877776654

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.67  E-value=3.1e-16  Score=115.79  Aligned_cols=71  Identities=23%  Similarity=0.358  Sum_probs=64.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ  133 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~  133 (305)
                      ..++|||+|||.++++++|+++|++||.|.++++.      +++|||||+|.+.++|++|++.|||..|.++.++..
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   96 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG   96 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            35789999999999999999999999999999997      357899999999999999999999999888776543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.67  E-value=8.9e-17  Score=121.17  Aligned_cols=80  Identities=11%  Similarity=0.150  Sum_probs=71.4

Q ss_pred             CCceEEecC----CCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecC----HHH----HHHHHH--HhCCC
Q psy4086         137 PTNLYIANL----PLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLES----KDK----CDQMIQ--LFNGS  201 (305)
Q Consensus       137 ~~~l~V~nl----p~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~----~~~----A~~Ai~--~l~g~  201 (305)
                      +.+|||+||    ++.+++++|+++|+.||+|.+|+++.|+ +|.++|||||+|.+    .++    |.+|+.  .|||.
T Consensus         2 p~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~   81 (136)
T 2j8a_A            2 SCEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGC   81 (136)
T ss_dssp             CCEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCE
T ss_pred             CcEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCC
Confidence            368999999    9999999999999999999999999999 99999999999996    333    889988  78999


Q ss_pred             CCCCCCccEEEEeccCC
Q psy4086         202 TLPGSKEPLLVKFADSG  218 (305)
Q Consensus       202 ~~~g~~~~l~v~~a~~~  218 (305)
                      .|+|  +.|+|.+.+..
T Consensus        82 ~I~G--r~irV~ln~~g   96 (136)
T 2j8a_A           82 FIMG--FKFEVILNKHS   96 (136)
T ss_dssp             EETT--EEEEEEECCTT
T ss_pred             eecC--cEEEEEECccc
Confidence            9999  77999996653

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=4e-16  Score=112.68  Aligned_cols=67  Identities=25%  Similarity=0.516  Sum_probs=61.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||+|.+|+++        +|||||+|.+.++|++|++.||+..|.++.++
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   73 (90)
T 2dnq_A            7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNIN   73 (90)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCE
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEE
Confidence            45789999999999999999999999999999987        57999999999999999999998887776655

>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=99.67  E-value=1.1e-16  Score=115.18  Aligned_cols=75  Identities=20%  Similarity=0.395  Sum_probs=69.7

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ..++|||+|||+++++++|+++|++| .|.++++.     +++|||||+|.+.++|++|++.|||..+.|  +.|+|+++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g--~~l~V~~a   75 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRG--KDLIVQLQ   75 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETT--EEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECC--cEEEEEEc
Confidence            46789999999999999999999999 99999985     578999999999999999999999999999  77999998


Q ss_pred             cCC
Q psy4086         216 DSG  218 (305)
Q Consensus       216 ~~~  218 (305)
                      ...
T Consensus        76 ~~~   78 (88)
T 1wg1_A           76 PTD   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.67  E-value=1.5e-15  Score=123.74  Aligned_cols=76  Identities=18%  Similarity=0.296  Sum_probs=70.2

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++++++|+++|++||+|++|.|+.++ ++.++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~  160 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMD  160 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence            3456789999999999999999999999999999999999 899999999999999999999999999888776655

>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=99.67  E-value=1.5e-16  Score=114.76  Aligned_cols=79  Identities=11%  Similarity=0.222  Sum_probs=63.7

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      .....+|||+|||+++|+++|+++|++||.|.+|+|+.+    ++|||||+|.+.++|++    |++..+.+..+.|.|+
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEE
Confidence            345789999999999999999999999999999999875    78999999999999883    5677665433889999


Q ss_pred             eccCCCc
Q psy4086         214 FADSGLK  220 (305)
Q Consensus       214 ~a~~~~~  220 (305)
                      ++.++..
T Consensus        80 ~a~~k~~   86 (89)
T 3d2w_A           80 NAEPKHN   86 (89)
T ss_dssp             ECC----
T ss_pred             EcCCCCc
Confidence            9987543

>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=99.66  E-value=3.5e-17  Score=127.70  Aligned_cols=72  Identities=18%  Similarity=0.285  Sum_probs=65.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++|| |++|+|++|+. ++++|||||+|.+.++|++|| .+|+..|..+.++
T Consensus        45 ~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~  116 (139)
T 2hgn_A           45 TGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIE  116 (139)
T ss_dssp             CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEE
Confidence            446799999999999999999999999 77999999986 999999999999999999999 6898888877665

>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=99.66  E-value=7.1e-17  Score=127.07  Aligned_cols=86  Identities=28%  Similarity=0.439  Sum_probs=73.6

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEE------EEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCC
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVST------RILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSK  207 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v------~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~  207 (305)
                      ....++|||+|||+++|+++|+++|+.||.|..+      .+....++.++|||||+|.+.++|.+||+.|||..|.|  
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g--  119 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFG--  119 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETT--
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCC--
Confidence            3456889999999999999999999999998774      12222367899999999999999999999999999999  


Q ss_pred             ccEEEEeccCCCcC
Q psy4086         208 EPLLVKFADSGLKK  221 (305)
Q Consensus       208 ~~l~v~~a~~~~~~  221 (305)
                      ++|+|.|+.....+
T Consensus       120 ~~l~V~~a~~~~~~  133 (143)
T 3egn_A          120 KPMVVQFARSARPK  133 (143)
T ss_dssp             EECEEEECCCSCC-
T ss_pred             cEEEEEECCCCCCc
Confidence            78999999875544

>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=99.66  E-value=4.3e-16  Score=125.06  Aligned_cols=82  Identities=26%  Similarity=0.427  Sum_probs=77.1

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||.++++++|+++|+.||.|.+++++.++ +|.++|||||+|.+.++|.+|++.|||..+.+  ++|+|.++
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g--~~l~v~~~   79 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQT--KTIKVSYA   79 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT--EECEEEEC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCC--ceEEEEec
Confidence            5789999999999999999999999999999999998 89999999999999999999999999999999  77999998


Q ss_pred             cCCCc
Q psy4086         216 DSGLK  220 (305)
Q Consensus       216 ~~~~~  220 (305)
                      .+...
T Consensus        80 ~~~~~   84 (167)
T 1fxl_A           80 RPSSA   84 (167)
T ss_dssp             CCCCG
T ss_pred             CCCcc
Confidence            86543

>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=99.66  E-value=7.4e-17  Score=122.07  Aligned_cols=75  Identities=17%  Similarity=0.354  Sum_probs=62.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++||.|..+.+..+..+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   98 (115)
T 2cpx_A           24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILV   98 (115)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            457899999999999999999999999984333322222788999999999999999999999998887766554

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.47  E-value=8.2e-18  Score=127.63  Aligned_cols=76  Identities=21%  Similarity=0.322  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeE--------EEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIIS--------TKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~--------~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      ...++|||+|||+++++++|+++|++||.|..        |+|+.++.+++++|||||+|.+.++|++|++.|||..|.+
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            35577999999999999999999999999998        9999998899999999999999999999999999888777


Q ss_pred             eecc
Q psy4086         128 QMAR  131 (305)
Q Consensus       128 ~~~~  131 (305)
                      +.++
T Consensus        85 ~~l~   88 (116)
T 2lcw_A           85 NPIK   88 (116)
Confidence            6554

>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=99.65  E-value=4.1e-16  Score=116.82  Aligned_cols=71  Identities=21%  Similarity=0.438  Sum_probs=64.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||.++++++|+++|++||.|.+|+|+++      +|||||+|.+.++|++|++.|||..|.++.++
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   92 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVK   92 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            345678999999999999999999999999999999876      68999999999999999999999888877665

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.65  E-value=5.9e-16  Score=113.47  Aligned_cols=69  Identities=20%  Similarity=0.372  Sum_probs=62.4

Q ss_pred             CCCCCeEEEcCCCC-CCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQ-DTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+ ++++++|+++|++||.|.++++.        +|||||+|.+.++|++|++.|||..+.++.++
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   88 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLI   88 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34567899999998 99999999999999999999983        78999999999999999999999988877655

>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=99.65  E-value=3.9e-16  Score=125.62  Aligned_cols=82  Identities=28%  Similarity=0.433  Sum_probs=76.9

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ..++|||+|||.++++++|+++|+.||.|.+++++.++ ++.++|||||+|.+.++|.+|++.|+|..+.+  +.|.|.+
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g--~~l~v~~   79 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN--KRLKVSY   79 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETT--EECEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCC--cEEEEEe
Confidence            45789999999999999999999999999999999987 88899999999999999999999999999999  7799999


Q ss_pred             ccCCC
Q psy4086         215 ADSGL  219 (305)
Q Consensus       215 a~~~~  219 (305)
                      +....
T Consensus        80 ~~~~~   84 (168)
T 1b7f_A           80 ARPGG   84 (168)
T ss_dssp             CCCCS
T ss_pred             cCCCc
Confidence            88654

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.65  E-value=5.7e-16  Score=124.19  Aligned_cols=81  Identities=19%  Similarity=0.285  Sum_probs=75.2

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      ++|||+|||.++++++|+++|++||.|.+++++.++++.++|||||+|.+.++|.+|++.|||..+.+  +.|.|.++..
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g--~~i~v~~~~~   78 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIEN--NIVKINWAFQ   78 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETT--EECEEEECCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCC--CeeEEEEcCC
Confidence            58999999999999999999999999999999999988899999999999999999999999999999  7799999876


Q ss_pred             CCc
Q psy4086         218 GLK  220 (305)
Q Consensus       218 ~~~  220 (305)
                      ...
T Consensus        79 ~~~   81 (166)
T 3md3_A           79 SQQ   81 (166)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=2.2e-16  Score=118.74  Aligned_cols=69  Identities=19%  Similarity=0.104  Sum_probs=62.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||.|.+|.|++      ++|||||+|.+.++|++|++.|||..|.++.+.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   77 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLY   77 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEE
Confidence            467899999999999999999999999999999874      568999999999999999999999988877655

>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=99.64  E-value=4.6e-16  Score=116.51  Aligned_cols=62  Identities=16%  Similarity=0.258  Sum_probs=57.1

Q ss_pred             CCeEEE--cCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcc
Q psy4086          58 KTNLYI--RGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGI  125 (305)
Q Consensus        58 ~~~l~V--~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i  125 (305)
                      .++|||  |||++++++++|+++|++||+|.+|.|+.      .||||||+|.+.++|++|++.|||+.|
T Consensus        25 t~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~   88 (114)
T 2cq2_A           25 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEV   88 (114)
T ss_dssp             CSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEE
Confidence            467999  77999999999999999999999998763      378999999999999999999999987

>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=99.64  E-value=6.8e-16  Score=114.41  Aligned_cols=67  Identities=22%  Similarity=0.443  Sum_probs=60.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|+        +|||||+|.+.++|++|++.||+..|.++.++
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   76 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIE   76 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEE
Confidence            34779999999999999999999999999999987        45999999999999999999998887776654

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.64  E-value=2.1e-16  Score=115.73  Aligned_cols=73  Identities=23%  Similarity=0.347  Sum_probs=65.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHH----HHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLI----NMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~----~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++++++|+    ++|++||.|.+|.+++   ++.++|||||+|.+.++|++|++.|||..+.++.++
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            345789999999999999999    9999999999999874   578899999999999999999999999988777655

>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=99.64  E-value=2.7e-16  Score=119.06  Aligned_cols=66  Identities=21%  Similarity=0.305  Sum_probs=60.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccccee
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQM  129 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~  129 (305)
                      ..++|||+|||+++++++|+++|++||+|.+|.|+.+       |||||+|.+.++|++||+.|||+.|.++.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~   80 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHE   80 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            3477999999999999999999999999999999876       79999999999999999999999888765

>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=99.64  E-value=1.8e-16  Score=114.09  Aligned_cols=78  Identities=13%  Similarity=0.287  Sum_probs=66.0

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCC--CCCCccEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTL--PGSKEPLLV  212 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~~~l~v  212 (305)
                      ...++|||+|||+++++++|+++|++||.|.+|+|+.+    ++|||||+|.+.++|++|    ++..+  .+  +.|+|
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~----~~~~~~~~g--~~l~v   72 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSL----CGEDLIIKG--ISVHI   72 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHT----TTCEEEETT--EEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHH----hcCCceeCC--EEEEE
Confidence            35689999999999999999999999999999999865    689999999999999754    44444  55  78999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      .++.++....
T Consensus        73 ~~a~~~~~~~   82 (88)
T 1wf0_A           73 SNAEPKHNSN   82 (88)
T ss_dssp             ECCCCCCCCC
T ss_pred             EecCCCCCCC
Confidence            9988765543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=9e-16  Score=111.29  Aligned_cols=69  Identities=22%  Similarity=0.443  Sum_probs=62.1

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++++++|+++|++||.|.+|.+++        +||||+|.+.++|++|++.|||..|.++.++
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   75 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMH   75 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEE
Confidence            34567899999999999999999999999999999973        3999999999999999999999888777665

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=2.1e-15  Score=110.85  Aligned_cols=68  Identities=29%  Similarity=0.407  Sum_probs=61.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhcc--CCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQY--GPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~--G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++|+++|+++|++|  |.|.+|++.        +|||||+|.+.++|++|++.|||..|.++.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIE   82 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEE
Confidence            345789999999999999999999999  999988864        56999999999999999999999888777655

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=7.6e-16  Score=112.54  Aligned_cols=71  Identities=21%  Similarity=0.164  Sum_probs=63.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEE-EEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIIST-KAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~-~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||.|.+| .|+.++.++    .|||+|.+.++|++|++.|||..|.++.++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   85 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLK   85 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCE
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            34779999999999999999999999999999 588887654    399999999999999999999988877654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=1.1e-15  Score=115.38  Aligned_cols=75  Identities=13%  Similarity=0.262  Sum_probs=63.6

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-C---CCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-N---NTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~---g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      ...++|||+|||+++++++|+++|++||.|. +.++.++ +   |+++|||||+|.+.++|++||+.|++  ++|  +.|
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~--~~G--~~~   80 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLE--EDG--KLY   80 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEE--ETT--EEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhh--cCC--cEE
Confidence            4568999999999999999999999999999 8888776 4   78999999999999999999999832  444  334


Q ss_pred             EEEe
Q psy4086         211 LVKF  214 (305)
Q Consensus       211 ~v~~  214 (305)
                      .+..
T Consensus        81 ~~~~   84 (114)
T 2dnl_A           81 LCVS   84 (114)
T ss_dssp             EEEC
T ss_pred             Eecc
Confidence            4443

>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=99.63  E-value=5e-15  Score=129.49  Aligned_cols=82  Identities=15%  Similarity=0.364  Sum_probs=74.8

Q ss_pred             cCCCCceEEecCCCCCCHHHHH----HHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCcc
Q psy4086         134 EQDPTNLYIANLPLNFKECDLE----SLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEP  209 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~----~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~  209 (305)
                      ....++|||+|||+++++++|+    ++|+.||.|.+|+|++  +++++|||||+|.+.++|++||+.|||..|.|  +.
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--~~   81 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYD--KP   81 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCeeCC--cE
Confidence            4567899999999999999977    8999999999999886  56889999999999999999999999999999  77


Q ss_pred             EEEEeccCCC
Q psy4086         210 LLVKFADSGL  219 (305)
Q Consensus       210 l~v~~a~~~~  219 (305)
                      |+|.|+....
T Consensus        82 l~v~~a~~~~   91 (282)
T 3pgw_A           82 MRIQYAKTDS   91 (282)
T ss_pred             EEEEEeccCc
Confidence            9999997654

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1.2e-15  Score=110.15  Aligned_cols=68  Identities=19%  Similarity=0.354  Sum_probs=61.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++|+++|+++|++||.|.+|++++        +||||+|.+.++|++|++.|||..|.++.++
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   74 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRIN   74 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            3457799999999999999999999999999999973        3999999999999999999999888877665

>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=99.62  E-value=1.5e-15  Score=120.46  Aligned_cols=72  Identities=24%  Similarity=0.369  Sum_probs=65.4

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++|+++|+++|++||.|.+|+|+++     ++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  141 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVR  141 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            345688999999999999999999999999999999876     588999999999999999999999888777655

>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=1e-15  Score=127.70  Aligned_cols=78  Identities=14%  Similarity=0.215  Sum_probs=72.1

Q ss_pred             CCCceEEecCC-CCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLP-LNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp-~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      +.++|||+||+ +.+++++|+++|++||.|.+|+|+.+    .+|||||+|.+.++|++||+.|||..+.|  ++|+|.+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~lng~~~~g--~~l~v~~   76 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHLNNNFMFG--QKMNVCV   76 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT----STTCEEEEESSHHHHHHHHHHHTTCEETT--EECEEEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC----CCCEEEEEECCHHHHHHHHHHhCCCEECC--ceEEEEE
Confidence            46899999999 89999999999999999999999876    37899999999999999999999999999  7899999


Q ss_pred             ccCCC
Q psy4086         215 ADSGL  219 (305)
Q Consensus       215 a~~~~  219 (305)
                      ++...
T Consensus        77 s~~~~   81 (205)
T 3tyt_A           77 SKQPA   81 (205)
T ss_dssp             CSCSC
T ss_pred             ccCCc
Confidence            87543

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.62  E-value=1.1e-15  Score=111.82  Aligned_cols=68  Identities=21%  Similarity=0.388  Sum_probs=60.4

Q ss_pred             CCCCeEEEcCCCC-CCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQ-DTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+ ++++++|+++|++||.|.+|.|.        +|||||+|.+.++|++|++.|||..+.++.++
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   76 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLI   76 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            3457899999998 99999999999999999999984        68999999999999999999998877765544

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.62  E-value=1.7e-15  Score=127.02  Aligned_cols=81  Identities=16%  Similarity=0.241  Sum_probs=73.4

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||.++++++|+++|+.||.|.+|+|+.++ ++.++|||||+|.+.++|.+|++.||+..|.+  +.|+|.++
T Consensus        28 ~~~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           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGG--RNIKVGRP  105 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC---CCCEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCC--eeEEEecC
Confidence            4789999999999999999999999999999999998 88999999999999999999999999999999  67999987


Q ss_pred             cCCC
Q psy4086         216 DSGL  219 (305)
Q Consensus       216 ~~~~  219 (305)
                      ....
T Consensus       106 ~~~~  109 (216)
T 2qfj_A          106 SNIG  109 (216)
T ss_dssp             SCCG
T ss_pred             CCcc
Confidence            7654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=2.6e-15  Score=109.34  Aligned_cols=71  Identities=15%  Similarity=0.367  Sum_probs=62.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ  133 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~  133 (305)
                      ..++|||+|||+++|+++|+++|++||.|.+|  +.++.+++   ||||+|.+.++|++|++ |||..|.++.++..
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~   77 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVR   77 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCB
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEE
Confidence            34679999999999999999999999999987  66666665   99999999999999999 99999888877644

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.62  E-value=3.8e-16  Score=114.19  Aligned_cols=72  Identities=17%  Similarity=0.238  Sum_probs=63.3

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++++++|+++|++||.|..+     ..+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   84 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVS   84 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            3456789999999999999999999999988765     33688999999999999999999999999888777655

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.62  E-value=6.9e-16  Score=110.97  Aligned_cols=74  Identities=15%  Similarity=0.236  Sum_probs=65.6

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccccCC
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQD  136 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~~~  136 (305)
                      ..++|||+|||+++++++|+++|++| .|.++++.      +++|||||+|.+.++|++|++.|||..+.++.++.....
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            34779999999999999999999999 99999984      578999999999999999999999999988887754443


Q ss_pred             C
Q psy4086         137 P  137 (305)
Q Consensus       137 ~  137 (305)
                      .
T Consensus        77 ~   77 (88)
T 1wg1_A           77 T   77 (88)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=2.1e-15  Score=110.46  Aligned_cols=67  Identities=27%  Similarity=0.302  Sum_probs=60.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+||  ++|+++|+++|++||+|.+|.|.      +++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        14 ~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   80 (97)
T 1x5p_A           14 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLK   80 (97)
T ss_dssp             CCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEE
T ss_pred             CCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            4578999996  89999999999999999999984      4688999999999999999999999888777655

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.61  E-value=2.9e-15  Score=111.23  Aligned_cols=81  Identities=15%  Similarity=0.084  Sum_probs=72.0

Q ss_pred             CCCCceEEecCCC-----CCCHHHHHHHHhhCCCeEEEEEeeCC--CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCC
Q psy4086         135 QDPTNLYIANLPL-----NFKECDLESLLAKYVTVVSTRILRDN--NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSK  207 (305)
Q Consensus       135 ~~~~~l~V~nlp~-----~~te~~l~~~F~~~g~v~~v~i~~~~--~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~  207 (305)
                      ..+++|+|.||..     +-++++|+++|++||.|++|.|+.++  ++.++|||||+|.+.++|.+|++.|||..+.|  
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~G--   83 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGG--   83 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETT--
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECC--
Confidence            4568899999963     23789999999999999999999986  36889999999999999999999999999999  


Q ss_pred             ccEEEEeccC
Q psy4086         208 EPLLVKFADS  217 (305)
Q Consensus       208 ~~l~v~~a~~  217 (305)
                      +.|+|.|+..
T Consensus        84 r~i~v~~a~~   93 (105)
T 2pe8_A           84 RVVKACFYNL   93 (105)
T ss_dssp             EECEEEECCH
T ss_pred             cEEEEEEcCH
Confidence            8899999875

>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=99.61  E-value=1.1e-15  Score=109.46  Aligned_cols=72  Identities=24%  Similarity=0.457  Sum_probs=65.9

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhC----C-------CeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCC
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKY----V-------TVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTL  203 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~----g-------~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~  203 (305)
                      ...++|||+|||+++++++|+++|++|    |       .|.++++..+     +|||||+|.+.++|++|+ .|||..+
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            346789999999999999999999999    8       8999998854     899999999999999999 9999999


Q ss_pred             CCCCccEEEEe
Q psy4086         204 PGSKEPLLVKF  214 (305)
Q Consensus       204 ~g~~~~l~v~~  214 (305)
                      .|  +.|+|+.
T Consensus        78 ~g--~~l~V~r   86 (87)
T 2hzc_A           78 QG--QSLKIRR   86 (87)
T ss_dssp             TT--EECEEEC
T ss_pred             CC--eEEEEeC
Confidence            99  7798874

>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=99.61  E-value=2.9e-15  Score=120.98  Aligned_cols=74  Identities=19%  Similarity=0.377  Sum_probs=70.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .++|||+|||+++|+++|+++|++||.|..+.+++++.+|+++|||||+|.+.++|++|++.|||..+.++.++
T Consensus        94 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~  167 (172)
T 2g4b_A           94 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL  167 (172)
T ss_dssp             TTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECE
T ss_pred             CCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEE
Confidence            57799999999999999999999999999999999998999999999999999999999999999998887654

>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=99.61  E-value=1.8e-15  Score=120.22  Aligned_cols=70  Identities=14%  Similarity=0.139  Sum_probs=62.0

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccc--eecc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA--QMAR  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~--~~~~  131 (305)
                      -.+|||+||++.+|+++|+++|++||+|++|+|+.+.    ++|||||+|.+.++|++|++.|||+.|.+  +.++
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~  117 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR  117 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEE
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEE
Confidence            4569999999999999999999999999999987543    57899999999999999999999998854  4444

>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=99.61  E-value=1.9e-15  Score=124.76  Aligned_cols=83  Identities=20%  Similarity=0.332  Sum_probs=74.6

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++|+++|+++|+.||.|.+|+|+.++ ++.++|||||+|.+.++|++|++. ++..+.|  +.|.|.
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g--~~l~v~   87 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDG--RVVEPK   87 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETT--EECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECC--EEeeee
Confidence            345789999999999999999999999999999999998 789999999999999999999976 8899999  779999


Q ss_pred             eccCCCc
Q psy4086         214 FADSGLK  220 (305)
Q Consensus       214 ~a~~~~~  220 (305)
                      ++.....
T Consensus        88 ~~~~~~~   94 (196)
T 1l3k_A           88 RAVSRED   94 (196)
T ss_dssp             ECCC---
T ss_pred             cccCccc
Confidence            9876543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.61  E-value=9.3e-15  Score=111.37  Aligned_cols=76  Identities=26%  Similarity=0.237  Sum_probs=62.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccce-EEEEecchhhHHHHHHHhccCcccc--eecccccC
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY-GFVDFESGGYALAAVKALQDKGIHA--QMARQQEQ  135 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~-afV~f~~~~~A~~a~~~l~g~~i~~--~~~~~~~~  135 (305)
                      ..|||+||++.+|+++|+++|++||.|.+|+|+..      .|| |||+|.+.++|++|++.|||..|.+  +.++....
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 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            45789999999999999999999999999999752      276 9999999999999999999999976  34444333


Q ss_pred             CCCce
Q psy4086         136 DPTNL  140 (305)
Q Consensus       136 ~~~~l  140 (305)
                      ....|
T Consensus       100 k~~~l  104 (124)
T 2e5i_A          100 RPTRL  104 (124)
T ss_dssp             SCSCC
T ss_pred             cCCcc
Confidence            33333

>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=99.60  E-value=1.8e-15  Score=139.92  Aligned_cols=77  Identities=26%  Similarity=0.389  Sum_probs=71.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ...++|||+|||+++|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||+.|||..|.++.+..
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V  176 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  176 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEE
Confidence            34578999999999999999999999999999999999999999999999999999999999999999888777663

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1e-15  Score=111.16  Aligned_cols=68  Identities=24%  Similarity=0.456  Sum_probs=59.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCC-eeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhcc-Ccccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGP-IISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQD-KGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~-i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g-~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++||. |..+.+.       ++|||||+|.+.++|++|++.||| ..|.++.++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~   76 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIME   76 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEE
Confidence            3467999999999999999999999999 6666552       478999999999999999999999 888777665

>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=99.60  E-value=7.8e-16  Score=110.95  Aligned_cols=55  Identities=22%  Similarity=0.396  Sum_probs=49.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHH
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA  115 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~  115 (305)
                      ...++|||+|||+++|+++|+++|++||.|.+|+|+++     +||||||+|.+.++|++
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~   63 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS   63 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH
Confidence            35578999999999999999999999999999999874     78999999999999984

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.60  E-value=2.9e-15  Score=114.69  Aligned_cols=71  Identities=14%  Similarity=0.164  Sum_probs=62.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccce-EEEEecchhhHHHHHHHhccCcccc--eeccccc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY-GFVDFESGGYALAAVKALQDKGIHA--QMARQQE  134 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~-afV~f~~~~~A~~a~~~l~g~~i~~--~~~~~~~  134 (305)
                      .+|||+||++.+|+++|+++|++||+|.+|+|+.+     .+|| |||+|.+.++|++|++.|||+.|.+  +.++...
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~  102 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  102 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEE
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEe
Confidence            56899999999999999999999999999998864     3677 9999999999999999999999876  5554333

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.60  E-value=2.5e-15  Score=127.16  Aligned_cols=79  Identities=20%  Similarity=0.370  Sum_probs=70.0

Q ss_pred             cCCCCceEEecCCCCC---------CHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCC-
Q psy4086         134 EQDPTNLYIANLPLNF---------KECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTL-  203 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~---------te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~-  203 (305)
                      ....++|||+||+..+         +|++|+++|++||.|++|+|+.     ++|||||+|.+.++|+.|+++|+|..| 
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~-----~kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG-----GGTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC-----CCCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            3456899999999998         7999999999999999999994     589999999999999999999999999 


Q ss_pred             -----------CCCCccEEEEeccCCC
Q psy4086         204 -----------PGSKEPLLVKFADSGL  219 (305)
Q Consensus       204 -----------~g~~~~l~v~~a~~~~  219 (305)
                                 .|  +.|.|+||....
T Consensus       206 ~~~~~e~~~~~~g--r~L~V~wA~~~p  230 (240)
T 3u1l_A          206 LPSDKEWDDRREG--TGLLVKWANEDP  230 (240)
T ss_dssp             CTTSTTGGGGGGS--CCCEEEECC---
T ss_pred             ccccccccccCCC--CEEEEEEccCCC
Confidence                       66  779999998753

>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=99.59  E-value=4.4e-15  Score=120.12  Aligned_cols=85  Identities=26%  Similarity=0.454  Sum_probs=75.1

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CC--CcccEEEEEecCHHHHHHHHHHhCCCCCC-CCCccEE
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NN--TSKGVGFARLESKDKCDQMIQLFNGSTLP-GSKEPLL  211 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~-g~~~~l~  211 (305)
                      +.++|||+|||+++++++|+++|++||.|.+|+|++++ ++  .++|||||+|.+.++|++|++.||+..+. +..+.+.
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            46789999999999999999999999999999999998 43  79999999999999999999999998764 4347899


Q ss_pred             EEeccCCCc
Q psy4086         212 VKFADSGLK  220 (305)
Q Consensus       212 v~~a~~~~~  220 (305)
                      +.++.....
T Consensus        82 ~~~~~~~~~   90 (175)
T 3nmr_A           82 MKPADSEKN   90 (175)
T ss_dssp             EEECGGGCC
T ss_pred             Ecccccccc
Confidence            998876543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.59  E-value=7.7e-15  Score=121.24  Aligned_cols=77  Identities=19%  Similarity=0.348  Sum_probs=71.7

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ...++|||+|||+++++++|+++|++||.|.++++++++.++.++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  188 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV  188 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            45678999999999999999999999999999999999989999999999999999999999999999888776653

>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=2.4e-15  Score=107.75  Aligned_cols=68  Identities=19%  Similarity=0.408  Sum_probs=62.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcc----C-------CeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQY----G-------PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGI  125 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~----G-------~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i  125 (305)
                      ..++|||+|||+++++++|+++|++|    |       .|.++.+.++      +|||||+|.+.++|++|+ .|||..+
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            45789999999999999999999999    8       8999998754      689999999999999999 9999999


Q ss_pred             cceecc
Q psy4086         126 HAQMAR  131 (305)
Q Consensus       126 ~~~~~~  131 (305)
                      .++.++
T Consensus        78 ~g~~l~   83 (87)
T 2hzc_A           78 QGQSLK   83 (87)
T ss_dssp             TTEECE
T ss_pred             CCeEEE
Confidence            887764

>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=99.59  E-value=4e-15  Score=122.91  Aligned_cols=80  Identities=19%  Similarity=0.293  Sum_probs=73.0

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      .++|||+|||+++++++|+++|++||.|..|+|+++.++.++|||||+|.+.++|++|++.++ ..+.|  +.|.|.++.
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~G--r~l~V~~~~  185 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG-QKYKE--TDLLILFKD  185 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTT-CEETT--EECEEEETT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCC-CeECC--EEEEEEEhH
Confidence            378999999999999999999999999999999999888999999999999999999998665 68999  779999987


Q ss_pred             CCC
Q psy4086         217 SGL  219 (305)
Q Consensus       217 ~~~  219 (305)
                      .-.
T Consensus       186 ~y~  188 (193)
T 2voo_A          186 DYF  188 (193)
T ss_dssp             TC-
T ss_pred             HHH
Confidence            643

>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=99.58  E-value=6.2e-16  Score=121.62  Aligned_cols=76  Identities=17%  Similarity=0.255  Sum_probs=64.0

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEE--E---eeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTK--A---ILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~--i---~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      ...++|||+|||+++|+++|+++|+.||.|..+.  +   +....+++++|||||+|.+.++|.+|++.|||..|.++.+
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            3457899999999999999999999999987641  1   1112368899999999999999999999999998887765


Q ss_pred             c
Q psy4086         131 R  131 (305)
Q Consensus       131 ~  131 (305)
                      +
T Consensus       123 ~  123 (143)
T 3egn_A          123 V  123 (143)
T ss_dssp             E
T ss_pred             E
Confidence            5

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=1.8e-15  Score=108.71  Aligned_cols=57  Identities=23%  Similarity=0.395  Sum_probs=51.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHH
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK  118 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~  118 (305)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|+++     ++|||||+|.+.++|++|+.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~   60 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG   60 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhc
Confidence            3478999999999999999999999999999999864     68999999999999976543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.55  E-value=2.4e-14  Score=106.20  Aligned_cols=75  Identities=15%  Similarity=0.224  Sum_probs=65.6

Q ss_pred             CCCeEEEcCCCC-----CCcHHHHHHHHhccCCeeEEEEeeCCCC-CCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          57 SKTNLYIRGLTQ-----DTTDKDLINMCSQYGPIISTKAILDKTT-NKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        57 ~~~~l~V~~Lp~-----~~t~~~L~~~f~~~G~i~~~~i~~~~~~-g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      .+++|+|.||..     +-++++|+++|++||.|.+|.|++++.+ ++++|||||+|.+.++|.+|++.|||+.+.++.+
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i   86 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV   86 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEE
Confidence            346799999962     2378999999999999999999998754 6899999999999999999999999999988876


Q ss_pred             c
Q psy4086         131 R  131 (305)
Q Consensus       131 ~  131 (305)
                      +
T Consensus        87 ~   87 (105)
T 2pe8_A           87 K   87 (105)
T ss_dssp             E
T ss_pred             E
Confidence            5

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=2.3e-14  Score=102.14  Aligned_cols=69  Identities=19%  Similarity=0.251  Sum_probs=59.0

Q ss_pred             CCCeEEEcCCCCCCcHHH----HHHHHhcc-CCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKD----LINMCSQY-GPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~----L~~~f~~~-G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..|.|||+|||+++++++    |+++|++| |+|.+|       ++   |+|||+|.+.++|++|++.|||..+.++.++
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            345599999999999988    55899999 499888       33   8999999999999999999999999988877


Q ss_pred             cccC
Q psy4086         132 QQEQ  135 (305)
Q Consensus       132 ~~~~  135 (305)
                      ....
T Consensus        78 v~~A   81 (96)
T 2diu_A           78 VSFT   81 (96)
T ss_dssp             EESS
T ss_pred             EEec
Confidence            4433

>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=99.54  E-value=2e-14  Score=121.96  Aligned_cols=80  Identities=19%  Similarity=0.314  Sum_probs=73.6

Q ss_pred             ccCCCCceEEecCCC-CCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         133 QEQDPTNLYIANLPL-NFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~-~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      .....++|||+|||. ++++++|+++|++||.|.+|+|+.++    +|||||+|.+.++|++|++.|||..|.|  +.|.
T Consensus        30 ~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----~g~afV~F~~~~~A~~Ai~~l~g~~~~g--~~l~  103 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHG--KPIR  103 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSS--SBCE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCeECC--eEEE
Confidence            344568999999999 99999999999999999999999874    7899999999999999999999999999  7799


Q ss_pred             EEeccCC
Q psy4086         212 VKFADSG  218 (305)
Q Consensus       212 v~~a~~~  218 (305)
                      |.++...
T Consensus       104 v~~a~~~  110 (229)
T 2adc_A          104 ITLSKHQ  110 (229)
T ss_dssp             EECCSCC
T ss_pred             EEEecCc
Confidence            9999865

>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=99.54  E-value=5.7e-15  Score=118.68  Aligned_cols=74  Identities=24%  Similarity=0.472  Sum_probs=67.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.+.++|++|++ +++..+.++.++
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~  159 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIE  159 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEE
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEE
Confidence            34679999999999999999999999999999999999899999999999999999999998 787777666554

>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=99.53  E-value=4.2e-14  Score=106.36  Aligned_cols=83  Identities=17%  Similarity=0.211  Sum_probs=70.1

Q ss_pred             ccCCCCceEEecCCCCCC-----------HHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCC
Q psy4086         133 QEQDPTNLYIANLPLNFK-----------ECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGS  201 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~t-----------e~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~  201 (305)
                      .....++|+|.||.....           +++|+++|++||.|.+|.| .++  .++|||||+|.+.++|++|++.|||.
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCCC
Confidence            334568899999944332           5899999999999999966 444  47999999999999999999999999


Q ss_pred             CCCCCCccEEEEeccCCCc
Q psy4086         202 TLPGSKEPLLVKFADSGLK  220 (305)
Q Consensus       202 ~~~g~~~~l~v~~a~~~~~  220 (305)
                      .|.|  ++|+|.++..+..
T Consensus        88 ~~~g--r~l~v~~a~~~~~  104 (112)
T 2dit_A           88 WFGG--RQITAQAWDGTTD  104 (112)
T ss_dssp             EETT--EECEEEECCSCCC
T ss_pred             EECC--cEEEEEEeCCCCC
Confidence            9999  8899999987544

>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=99.53  E-value=4.4e-15  Score=110.11  Aligned_cols=72  Identities=11%  Similarity=0.270  Sum_probs=63.4

Q ss_pred             EecCCCCCCHHHHHHHH------------hhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCcc
Q psy4086         142 IANLPLNFKECDLESLL------------AKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEP  209 (305)
Q Consensus       142 V~nlp~~~te~~l~~~F------------~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~  209 (305)
                      +.+|++.+++++|++.|            ++||.|++|.|++++++.++|||||+|.+.++|.+|++.|||..+.|  ++
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~G--r~   97 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNG--QP   97 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETT--EE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECC--EE
Confidence            45677777777666655            99999999999998888899999999999999999999999999999  78


Q ss_pred             EEEEec
Q psy4086         210 LLVKFA  215 (305)
Q Consensus       210 l~v~~a  215 (305)
                      |+|.|+
T Consensus        98 i~v~~s  103 (104)
T 1jmt_A           98 IHAELS  103 (104)
T ss_dssp             CCEEEC
T ss_pred             EEEEEc
Confidence            999986

>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=99.52  E-value=3.7e-14  Score=105.24  Aligned_cols=81  Identities=22%  Similarity=0.309  Sum_probs=70.0

Q ss_pred             CCCCceEEecC--CCCCC--------HHHHHHHHhhCCCeEEEEEeeCCC---CCcccEEEEEecCHHHHHHHHHHhCCC
Q psy4086         135 QDPTNLYIANL--PLNFK--------ECDLESLLAKYVTVVSTRILRDNN---NTSKGVGFARLESKDKCDQMIQLFNGS  201 (305)
Q Consensus       135 ~~~~~l~V~nl--p~~~t--------e~~l~~~F~~~g~v~~v~i~~~~~---g~~~g~afV~f~~~~~A~~Ai~~l~g~  201 (305)
                      .+++.|.+.|+  +..+.        +++|++.|++||.|++|.|++++.   +.++|+|||+|.+.++|.+|++.|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            35677889998  44443        368999999999999999998873   367999999999999999999999999


Q ss_pred             CCCCCCccEEEEeccC
Q psy4086         202 TLPGSKEPLLVKFADS  217 (305)
Q Consensus       202 ~~~g~~~~l~v~~a~~  217 (305)
                      .+.|  |.|+|.|++.
T Consensus        83 ~f~G--R~i~v~~~~~   96 (105)
T 3v4m_A           83 KFAN--RVVVTKYCDP   96 (105)
T ss_dssp             EETT--EECEEEEECH
T ss_pred             EeCC--CEEEEEEeCH
Confidence            9999  8899999865

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.51  E-value=2.3e-14  Score=118.58  Aligned_cols=78  Identities=19%  Similarity=0.314  Sum_probs=72.1

Q ss_pred             CCCceEEecCCC-CCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPL-NFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~-~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ..++|||+|||. ++++++|+++|++||.|.+|+++.++    +|||||+|.+.++|++|++.|||..+.|  +.|+|.+
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~----~g~afV~f~~~~~a~~A~~~l~~~~~~g--~~l~v~~   75 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHG--KPIRITL   75 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC----SSCCEEECTTTHHHHHHHHHHTTCCCSS--CCCEEEE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCeecC--eEEEEEE
Confidence            357899999999 99999999999999999999999874    7899999999999999999999999999  7799999


Q ss_pred             ccCCC
Q psy4086         215 ADSGL  219 (305)
Q Consensus       215 a~~~~  219 (305)
                      +....
T Consensus        76 a~~~~   80 (198)
T 1qm9_A           76 SKHQN   80 (198)
T ss_dssp             CCCCS
T ss_pred             ecCCC
Confidence            88653

>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=99.51  E-value=3.8e-14  Score=116.97  Aligned_cols=73  Identities=19%  Similarity=0.222  Sum_probs=64.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++||.|..|+|+++. +++++|||||+|.+.++|++|++.++ ..+.++.+.
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~  180 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLL  180 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECE
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEE
Confidence            45789999999999999999999999999999999987 59999999999999999999998643 355555443

>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=99.48  E-value=7.9e-15  Score=118.88  Aligned_cols=85  Identities=16%  Similarity=0.298  Sum_probs=72.2

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      .....++|||+|||.++++++|+++|+.||.+..+.+....++.++|||||+|.+.++|.+|+ .|||..|.|  +.|+|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g--~~l~v   85 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFG--NEIKL   85 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETT--EEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCC--eEEEE
Confidence            345578999999999999999999999999876633333336789999999999999999999 599999999  77999


Q ss_pred             EeccCCCc
Q psy4086         213 KFADSGLK  220 (305)
Q Consensus       213 ~~a~~~~~  220 (305)
                      .++.....
T Consensus        86 ~~~~~~~~   93 (175)
T 1fje_B           86 EKPKGRDS   93 (175)
T ss_dssp             ECCCCSSC
T ss_pred             ecCCCccc
Confidence            99887543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.48  E-value=8.1e-14  Score=117.93  Aligned_cols=65  Identities=20%  Similarity=0.340  Sum_probs=60.0

Q ss_pred             CCCCCeEEEcCCCCCC---------cHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcc
Q psy4086          55 QLSKTNLYIRGLTQDT---------TDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGI  125 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~---------t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i  125 (305)
                      ....++|||+||+.++         +|++|+++|++||+|++|+|+.      ++|||||+|.+.++|+.|++.|+|+.|
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            4456889999999998         7999999999999999999985      478999999999999999999999988

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=2.4e-13  Score=99.64  Aligned_cols=68  Identities=18%  Similarity=0.241  Sum_probs=58.8

Q ss_pred             CCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCCCcCC
Q psy4086         147 LNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKR  222 (305)
Q Consensus       147 ~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~~~~~  222 (305)
                      ..+++++|+++|++||.|.+|.|+.    .++|||||+|.+.++|++|++.+++  +.+  ++|+|+|+..+..+.
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~----~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g--~~l~V~~a~~~~~~~   94 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSS----KKPGTAVVEFATVKAAELAVQNEVG--LVD--NPLKISWLEGQPQDA   94 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEES----SSSSEEEEEESCHHHHHHHHHTCCB--CSS--SBCEEECSSCCCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEcc----CCCCEEEEEECCHHHHHHHHHhcCC--CCC--CeEEEEEccCCCCCC
Confidence            4689999999999999999999983    6799999999999999999998554  567  779999998765544

>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=99.46  E-value=1.2e-13  Score=119.47  Aligned_cols=75  Identities=31%  Similarity=0.555  Sum_probs=69.8

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ..++|||+|||+++|+++|+++|+.||.|.+|.|.+     ++|||||+|.+.++|.+|+..|||..|.|  +.|.|.++
T Consensus        21 ~~~~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           21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR-----DRGFGFIRLESRTLAEIAKAELDGTILKS--RPLRIRFA   93 (261)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETT--EECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCcEEEEEECCHHHHHHHHHHcCCcEECC--ceeEeeec
Confidence            347899999999999999999999999999999974     48999999999999999999999999999  78999998


Q ss_pred             cC
Q psy4086         216 DS  217 (305)
Q Consensus       216 ~~  217 (305)
                      ..
T Consensus        94 ~~   95 (261)
T 3sde_A           94 TH   95 (261)
T ss_dssp             CC
T ss_pred             cc
Confidence            75

>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=99.45  E-value=1.4e-13  Score=122.52  Aligned_cols=80  Identities=23%  Similarity=0.286  Sum_probs=68.7

Q ss_pred             ccCCCCceEEec--CCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCC---CCC
Q psy4086         133 QEQDPTNLYIAN--LPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLP---GSK  207 (305)
Q Consensus       133 ~~~~~~~l~V~n--lp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~---g~~  207 (305)
                      .....++|||+|  |++.+||++|+++|++||+|.+|.+..     +||||||+|++.++|++||+.|||+.+.   |++
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            355678999999  578999999999999999999987763     5799999999999999999999999873   443


Q ss_pred             ccEEEEeccC
Q psy4086         208 EPLLVKFADS  217 (305)
Q Consensus       208 ~~l~v~~a~~  217 (305)
                      .+|.|.|+..
T Consensus        89 ~~ly~~~~~~   98 (345)
T 3tht_A           89 ITLYLNFVEK   98 (345)
T ss_dssp             EECEEEECSS
T ss_pred             eEEEEEEeec
Confidence            4789999864

>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=99.45  E-value=1.4e-13  Score=104.06  Aligned_cols=80  Identities=16%  Similarity=0.227  Sum_probs=69.6

Q ss_pred             CCCceEEecCC--CCC---CHHHHHHHHhhCCCeEEEEEeeCCC-----CCcccEEEEEecCHHHHHHHHHHhCCCCCCC
Q psy4086         136 DPTNLYIANLP--LNF---KECDLESLLAKYVTVVSTRILRDNN-----NTSKGVGFARLESKDKCDQMIQLFNGSTLPG  205 (305)
Q Consensus       136 ~~~~l~V~nlp--~~~---te~~l~~~F~~~g~v~~v~i~~~~~-----g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  205 (305)
                      .+++|+|.|+-  .++   -+++|++.|++||.|.+|.|++++.     +.++|++||+|.+.++|.+|++.|||..+.|
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            56789999983  223   3689999999999999999999862     4578999999999999999999999999999


Q ss_pred             CCccEEEEeccC
Q psy4086         206 SKEPLLVKFADS  217 (305)
Q Consensus       206 ~~~~l~v~~a~~  217 (305)
                        |.|+|.|+..
T Consensus        99 --R~i~v~~~~~  108 (118)
T 3ue2_A           99 --RKVVAEVYDQ  108 (118)
T ss_dssp             --EECEEEEECH
T ss_pred             --cEEEEEEcCh
Confidence              8899999864

>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=99.43  E-value=8.2e-13  Score=99.21  Aligned_cols=74  Identities=19%  Similarity=0.264  Sum_probs=61.6

Q ss_pred             CCCeEEEcCCCCCCc-----------HHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcc
Q psy4086          57 SKTNLYIRGLTQDTT-----------DKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGI  125 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t-----------~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i  125 (305)
                      ..++|+|.||-...+           +++|+++|++||.|.+|.| .++   .++|||||+|.+.++|++|++.|||+.+
T Consensus        14 ~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~~~   89 (112)
T 2dit_A           14 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGRWF   89 (112)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCCEE
Confidence            457799999944332           6899999999999999965 554   3799999999999999999999999998


Q ss_pred             cceeccccc
Q psy4086         126 HAQMARQQE  134 (305)
Q Consensus       126 ~~~~~~~~~  134 (305)
                      .++.++...
T Consensus        90 ~gr~l~v~~   98 (112)
T 2dit_A           90 GGRQITAQA   98 (112)
T ss_dssp             TTEECEEEE
T ss_pred             CCcEEEEEE
Confidence            888766433

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.41  E-value=4.8e-13  Score=99.19  Aligned_cols=74  Identities=19%  Similarity=0.215  Sum_probs=63.8

Q ss_pred             CCeEEEcCC--CCCCc--------HHHHHHHHhccCCeeEEEEeeCCCC--CCccceEEEEecchhhHHHHHHHhccCcc
Q psy4086          58 KTNLYIRGL--TQDTT--------DKDLINMCSQYGPIISTKAILDKTT--NKCRGYGFVDFESGGYALAAVKALQDKGI  125 (305)
Q Consensus        58 ~~~l~V~~L--p~~~t--------~~~L~~~f~~~G~i~~~~i~~~~~~--g~~~G~afV~f~~~~~A~~a~~~l~g~~i  125 (305)
                      ++.|.|.|+  +.++.        +++|++.|++||.|.+|+|++++.+  ++++|++||+|.+.++|.+|++.|||+.+
T Consensus         5 s~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f   84 (105)
T 3v4m_A            5 TEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF   84 (105)
T ss_dssp             CSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEe
Confidence            467999998  43443        3689999999999999999998754  46899999999999999999999999999


Q ss_pred             cceecc
Q psy4086         126 HAQMAR  131 (305)
Q Consensus       126 ~~~~~~  131 (305)
                      .++.++
T Consensus        85 ~GR~i~   90 (105)
T 3v4m_A           85 ANRVVV   90 (105)
T ss_dssp             TTEECE
T ss_pred             CCCEEE
Confidence            988765

>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=99.41  E-value=9.4e-14  Score=102.88  Aligned_cols=68  Identities=19%  Similarity=0.251  Sum_probs=59.8

Q ss_pred             EcCCCCCCcHHHHHHHH------------hccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          63 IRGLTQDTTDKDLINMC------------SQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        63 V~~Lp~~~t~~~L~~~f------------~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      +.+|+.++++++|++.|            ++||+|.+|+|+++.. ++++|||||+|.+.++|++|++.|||+.+.++.+
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 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56777888888777666            9999999999999874 7899999999999999999999999999998876


Q ss_pred             c
Q psy4086         131 R  131 (305)
Q Consensus       131 ~  131 (305)
                      +
T Consensus        99 ~   99 (104)
T 1jmt_A           99 H   99 (104)
T ss_dssp             C
T ss_pred             E
Confidence            4

>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=99.37  E-value=1.1e-12  Score=99.09  Aligned_cols=74  Identities=16%  Similarity=0.281  Sum_probs=64.1

Q ss_pred             CCeEEEcCCC--CCC---cHHHHHHHHhccCCeeEEEEeeCCC----CCCccceEEEEecchhhHHHHHHHhccCcccce
Q psy4086          58 KTNLYIRGLT--QDT---TDKDLINMCSQYGPIISTKAILDKT----TNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ  128 (305)
Q Consensus        58 ~~~l~V~~Lp--~~~---t~~~L~~~f~~~G~i~~~~i~~~~~----~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~  128 (305)
                      +++|+|.|+-  .++   -++||++.|++||+|.+|+|++++.    +++++|++||+|.+.++|.+|++.|||+.+.++
T Consensus        20 s~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR   99 (118)
T 3ue2_A           20 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR   99 (118)
T ss_dssp             CCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            4679999983  222   3689999999999999999999864    467889999999999999999999999999988


Q ss_pred             ecc
Q psy4086         129 MAR  131 (305)
Q Consensus       129 ~~~  131 (305)
                      .++
T Consensus       100 ~i~  102 (118)
T 3ue2_A          100 KVV  102 (118)
T ss_dssp             ECE
T ss_pred             EEE
Confidence            765

>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=99.37  E-value=5.9e-13  Score=118.52  Aligned_cols=62  Identities=15%  Similarity=0.227  Sum_probs=56.3

Q ss_pred             CCeEEEcC--CCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcc
Q psy4086          58 KTNLYIRG--LTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGI  125 (305)
Q Consensus        58 ~~~l~V~~--Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i  125 (305)
                      ..+|||+|  |++.+||++|+++|++||+|++|.+..      +||||||+|.+.++|++|++.|||+.+
T Consensus        18 s~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~   81 (345)
T 3tht_A           18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEV   81 (345)
T ss_dssp             CSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCcc
Confidence            46799999  588999999999999999999887753      478999999999999999999999987

>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=99.32  E-value=2e-12  Score=97.05  Aligned_cols=77  Identities=10%  Similarity=0.109  Sum_probs=64.9

Q ss_pred             CCCceEEecCCC--CC--------CHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCC
Q psy4086         136 DPTNLYIANLPL--NF--------KECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPG  205 (305)
Q Consensus       136 ~~~~l~V~nlp~--~~--------te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  205 (305)
                      .++.|.+.|+=.  ..        -+++|++.|++||.|++|.|.++   ..+|++||+|.+.++|.+|++.|||..+.|
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~---~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKN---SAQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTT---CTTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecC---CCcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            456678888732  21        13589999999999999999766   368999999999999999999999999999


Q ss_pred             CCccEEEEeccC
Q psy4086         206 SKEPLLVKFADS  217 (305)
Q Consensus       206 ~~~~l~v~~a~~  217 (305)
                        +.|+|.|+..
T Consensus        83 --R~i~v~~~~~   92 (114)
T 3s6e_A           83 --KMITAAYVPL   92 (114)
T ss_dssp             --EECEEEEECH
T ss_pred             --EEEEEEEEcH
Confidence              7899999864

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.28  E-value=3.5e-11  Score=88.04  Aligned_cols=59  Identities=19%  Similarity=0.235  Sum_probs=49.8

Q ss_pred             CCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhc---cCcccceecc
Q psy4086          68 QDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ---DKGIHAQMAR  131 (305)
Q Consensus        68 ~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~---g~~i~~~~~~  131 (305)
                      .++++++|+++|++||+|.+|.|+     ++++|||||+|.+.++|++|++.++   ++.|.+.+++
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~~~g~~l~V~~a~   88 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKISWLE   88 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCBCSSSBCEEECSS
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCCCCCCeEEEEEcc
Confidence            468999999999999999999998     4689999999999999999999855   3455555544

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.16  E-value=1.2e-10  Score=87.24  Aligned_cols=70  Identities=21%  Similarity=0.302  Sum_probs=57.7

Q ss_pred             CCeEEEcCCCCCC----------cHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          58 KTNLYIRGLTQDT----------TDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        58 ~~~l~V~~Lp~~~----------t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      ++.|.|.|+=..-          -++||++.|++||.|.+|.|.++.    .+|++||+|.+.++|++|++.|||+.+.+
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            4568888873221          245789999999999999987653    58999999999999999999999999998


Q ss_pred             eecc
Q psy4086         128 QMAR  131 (305)
Q Consensus       128 ~~~~  131 (305)
                      +.++
T Consensus        83 R~i~   86 (114)
T 3s6e_A           83 KMIT   86 (114)
T ss_dssp             EECE
T ss_pred             EEEE
Confidence            8764

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.11  E-value=2.2e-10  Score=80.85  Aligned_cols=74  Identities=14%  Similarity=0.243  Sum_probs=61.9

Q ss_pred             CCCCceEEecCCC----CCCH----HHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCC
Q psy4086         135 QDPTNLYIANLPL----NFKE----CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGS  206 (305)
Q Consensus       135 ~~~~~l~V~nlp~----~~te----~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  206 (305)
                      ....||+|...+.    +.-.    .+|.+.|++||.|..++++.++       +||+|.+.++|.+||+ |||..+.| 
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~-------~fVtF~d~~sAlaAi~-mnG~~v~G-   75 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK-------MWVTFLEGSSALNVLS-LNGKELLN-   75 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS-------EEEEESSHHHHHHGGG-GTTCEETT-
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC-------EEEEECChHHHHHHHh-cCCeEeCC-
Confidence            3456788877662    3333    5799999999999999999873       8999999999999998 99999999 


Q ss_pred             CccEEEEeccCC
Q psy4086         207 KEPLLVKFADSG  218 (305)
Q Consensus       207 ~~~l~v~~a~~~  218 (305)
                       |.|+|+++.+.
T Consensus        76 -r~LkV~lkt~d   86 (91)
T 2dnr_A           76 -RTITIALKSPS   86 (91)
T ss_dssp             -EEEEEEECCCS
T ss_pred             -eEEEEEeCCCC
Confidence             77999998764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.10  E-value=1.7e-10  Score=86.79  Aligned_cols=60  Identities=23%  Similarity=0.177  Sum_probs=55.4

Q ss_pred             CCCCeEEEcCCCCC-CcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecc-hhhHHHHHHHhc
Q psy4086          56 LSKTNLYIRGLTQD-TTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES-GGYALAAVKALQ  121 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~-~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~-~~~A~~a~~~l~  121 (305)
                      ...+.|||+||+.+ +++++|+++|++||+|..|.++++..      .|||+|.+ .++|..|++.||
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln   77 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDAN   77 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTT
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhh
Confidence            45688999999999 99999999999999999999998875      59999999 899999999985

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.08  E-value=4.9e-10  Score=84.27  Aligned_cols=76  Identities=11%  Similarity=-0.008  Sum_probs=65.2

Q ss_pred             CCCCceEEecCCCC-CCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecC-HHHHHHHHHHhC--CCCCCCCCccE
Q psy4086         135 QDPTNLYIANLPLN-FKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLES-KDKCDQMIQLFN--GSTLPGSKEPL  210 (305)
Q Consensus       135 ~~~~~l~V~nlp~~-~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~-~~~A~~Ai~~l~--g~~~~g~~~~l  210 (305)
                      ...+.|||+||++. +++++|+++|+.||.|..|.+..+.     ..|||+|.+ .++|..|++.||  +..|.+  ..+
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~-----~tgfVrf~~~~~~A~~av~~ln~~~~~i~g--~~~   88 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA-----KEGIILFKEKAKEALGKAKDANNGNLQLRN--KEV   88 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTC-----SEEEEEESSCHHHHHHHHHHTTTSCBCTTS--SSE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-----CEEEEEECCChHHHHHHHHHhhcCCcEEeC--cEE
Confidence            45678999999999 9999999999999999999999774     269999999 899999999995  667888  557


Q ss_pred             EEEeccC
Q psy4086         211 LVKFADS  217 (305)
Q Consensus       211 ~v~~a~~  217 (305)
                      +++....
T Consensus        89 ~~evL~G   95 (121)
T 1owx_A           89 TWEVLEG   95 (121)
T ss_dssp             EEEECCH
T ss_pred             EEEECCC
Confidence            7776543

>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=98.96  E-value=1.4e-09  Score=91.45  Aligned_cols=67  Identities=16%  Similarity=0.190  Sum_probs=60.4

Q ss_pred             CCHHHHHHHHhhCCCeEEEEEeeCC-----CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         149 FKECDLESLLAKYVTVVSTRILRDN-----NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       149 ~te~~l~~~F~~~g~v~~v~i~~~~-----~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      -.+++|++.|++||.|.++.|+++.     ++.++|++||+|.+.++|.+|++.|||..+.|  |+|++.|...
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~g--r~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG--RKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSS--SBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECC--eEEEEEEcCH
Confidence            3568999999999999999998664     34889999999999999999999999999999  7799999864

>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=98.93  E-value=9.3e-10  Score=78.05  Aligned_cols=74  Identities=14%  Similarity=0.149  Sum_probs=62.0

Q ss_pred             cCCCCceEEecCCCC-----CCH----HHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCC
Q psy4086         134 EQDPTNLYIANLPLN-----FKE----CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLP  204 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~-----~te----~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~  204 (305)
                      ..+..||+|..++.+     +-.    .+|.+.|++||+|..+++..++       +||+|.+.++|.+||+ |||..+.
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-------~fVtF~d~~sAl~AI~-ldG~~v~   83 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-------MLVTFADSHSALSVLD-VDGMKVK   83 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-------EEEECSCSHHHHHHHH-GGGSEET
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-------EEEEEcChHHHHHHHh-cCCeeeC
Confidence            445678999887643     222    4689999999999999999873       9999999999999998 9999999


Q ss_pred             CCCccEEEEeccC
Q psy4086         205 GSKEPLLVKFADS  217 (305)
Q Consensus       205 g~~~~l~v~~a~~  217 (305)
                      |  |.|+|++..+
T Consensus        84 G--r~L~V~~k~~   94 (95)
T 1ufw_A           84 G--RAVKISGPSS   94 (95)
T ss_dssp             T--EEEEEECCCC
T ss_pred             C--eEEEEeccCC
Confidence            9  7799998543

>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=98.79  E-value=9.9e-09  Score=86.20  Aligned_cols=62  Identities=15%  Similarity=0.236  Sum_probs=55.1

Q ss_pred             CcHHHHHHHHhccCCeeEEEEeeCCC----CCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          70 TTDKDLINMCSQYGPIISTKAILDKT----TNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        70 ~t~~~L~~~f~~~G~i~~~~i~~~~~----~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      -.+++|++.|++||.|.++.|+++..    +++++|++||+|.+.++|.+|++.|||+.+.++.+.
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~  206 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVV  206 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEE
Confidence            35688999999999999999996543    458999999999999999999999999999888764

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.77  E-value=1e-08  Score=72.37  Aligned_cols=69  Identities=19%  Similarity=0.301  Sum_probs=56.6

Q ss_pred             CeEEEcCCCC----CCcH----HHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          59 TNLYIRGLTQ----DTTD----KDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        59 ~~l~V~~Lp~----~~t~----~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      .||+|.-.+.    +.-.    .+|.+.|.+||+|..++++.++        +||+|.+.++|.+|++ |||..+.++.+
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            5688887662    2333    5789999999999999999875        8999999999999999 99999999887


Q ss_pred             ccccCC
Q psy4086         131 RQQEQD  136 (305)
Q Consensus       131 ~~~~~~  136 (305)
                      +.....
T Consensus        79 kV~lkt   84 (91)
T 2dnr_A           79 TIALKS   84 (91)
T ss_dssp             EEEECC
T ss_pred             EEEeCC
Confidence            754443

>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=98.69  E-value=1.5e-08  Score=71.84  Aligned_cols=67  Identities=12%  Similarity=0.251  Sum_probs=56.4

Q ss_pred             CeEEEcCCCCC------CcH---HHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccccee
Q psy4086          59 TNLYIRGLTQD------TTD---KDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQM  129 (305)
Q Consensus        59 ~~l~V~~Lp~~------~t~---~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~  129 (305)
                      .||+|.-++..      ..+   .+|.+.|+.||+|..++++.|+        +||+|.+.++|.+||+ |||..|.++.
T Consensus        16 ~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~Gr~   86 (95)
T 1ufw_A           16 ATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVKGRA   86 (95)
T ss_dssp             CEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEETTEE
T ss_pred             CeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeCCeE
Confidence            56999988642      232   5688999999999999999875        9999999999999999 9999999998


Q ss_pred             ccccc
Q psy4086         130 ARQQE  134 (305)
Q Consensus       130 ~~~~~  134 (305)
                      ++...
T Consensus        87 L~V~~   91 (95)
T 1ufw_A           87 VKISG   91 (95)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            76443

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.49  E-value=5.3e-07  Score=65.22  Aligned_cols=74  Identities=12%  Similarity=0.130  Sum_probs=66.3

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhC-----CCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCc
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKY-----VTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKE  208 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~-----g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~  208 (305)
                      ....++|-+-|||..+++..|+.+.+++     |.|+.+.+..|     .+-|+|+|.|...|-+|..+|+|.+|.|  +
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD-----H~GAivef~d~~~AgKasLaL~G~ef~g--r   90 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-----FNGAIIIFRDSKFAAKMLMILNGSQFQG--K   90 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-----TTEEEEECSCHHHHHHHHHHHSSEEETT--E
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC-----CCceEEEEccchhhHHHHhhcCCeeecC--e
Confidence            3447889999999999999999999999     99999999877     4569999999999999999999999998  7


Q ss_pred             cEEEEe
Q psy4086         209 PLLVKF  214 (305)
Q Consensus       209 ~l~v~~  214 (305)
                      .|++.-
T Consensus        91 ~Lr~gT   96 (117)
T 2l9w_A           91 VIRSGT   96 (117)
T ss_dssp             EEEEEC
T ss_pred             EEEecC
Confidence            788764

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.24  E-value=4.8e-06  Score=60.21  Aligned_cols=69  Identities=12%  Similarity=0.126  Sum_probs=62.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhcc-----CCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQY-----GPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~-----G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +.++|-+-+||-.+++..|+.+++.+     |.|+++.+..|..      =|+|+|.|...|.+|.=.|||..|.++.++
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~------GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN------GAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT------EEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC------ceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            34679999999999999999999999     9999999998874      599999999999999988999999976544

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.12  E-value=1.7e-05  Score=56.89  Aligned_cols=83  Identities=19%  Similarity=0.277  Sum_probs=67.5

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhcc-----CCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHH----hccCcccce
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQY-----GPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA----LQDKGIHAQ  128 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~-----G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~----l~g~~i~~~  128 (305)
                      ..+|.|.|||+++.++.|.-+|+.-     |+|..+....        +-|+|+|.+.+.|++.++.    |++..|.+.
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~LsV~   79 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLSLR   79 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCEEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEEEE
Confidence            3669999999999999999999872     4788887654        2699999999999999986    777777665


Q ss_pred             ecccccCCCCceEEecCCCCCC
Q psy4086         129 MARQQEQDPTNLYIANLPLNFK  150 (305)
Q Consensus       129 ~~~~~~~~~~~l~V~nlp~~~t  150 (305)
                      .  .....+.+|++.+|++.++
T Consensus        80 P--~~~~~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           80 P--APPRAPARLLLQGLPPGTS   99 (104)
T ss_dssp             E--CCCCCCCCCCCCSCCCCCC
T ss_pred             c--CCCCCcceEeeecCCCCCC
Confidence            5  3455678899999998775

>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=97.83  E-value=4.1e-05  Score=55.12  Aligned_cols=76  Identities=11%  Similarity=0.087  Sum_probs=63.3

Q ss_pred             CCCceEEecCCCCC-C----HHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         136 DPTNLYIANLPLNF-K----ECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       136 ~~~~l~V~nlp~~~-t----e~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      -+++|+|.||+.++ .    .+.++++|..|+.+......+.     -.-..|.|.+.++|.+|...||+..+.|  +.|
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A~~AR~~Lh~~~f~g--~~~   76 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLG--KEM   76 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETT--EEC
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHHHHHHHHhccceecC--cee
Confidence            46889999998865 2    2578999999999888777743     3347999999999999999999999999  669


Q ss_pred             EEEeccCC
Q psy4086         211 LVKFADSG  218 (305)
Q Consensus       211 ~v~~a~~~  218 (305)
                      +|=|+...
T Consensus        77 r~YFgq~~   84 (104)
T 1wey_A           77 KLYFAQTL   84 (104)
T ss_dssp             EEECCCCS
T ss_pred             EEEecCCC
Confidence            99998843

>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=97.82  E-value=9.6e-05  Score=52.28  Aligned_cols=69  Identities=10%  Similarity=0.050  Sum_probs=57.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCC--ccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNK--CRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~--~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      ++|.|++||+.+||+++.+.+..+.++.....+..+.+..  .-.-|+|.|.+.+++....+.++|+.+..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            5699999999999999999999988887777766654322  22459999999999999999999987654

>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=97.80  E-value=0.00015  Score=51.33  Aligned_cols=54  Identities=22%  Similarity=0.265  Sum_probs=45.5

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ  121 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~  121 (305)
                      +.++| ++|++....||.++|+.||.|. |+.+-|-       .|||.|.+++.|..|+..+.
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            43555 9999999999999999999654 6666664       79999999999999999774

>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=97.69  E-value=0.00024  Score=50.19  Aligned_cols=80  Identities=14%  Similarity=0.219  Sum_probs=62.1

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CC--CcccEEEEEecCHHHHHHHHHHhCCCCCCCC---CccEE
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NN--TSKGVGFARLESKDKCDQMIQLFNGSTLPGS---KEPLL  211 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g--~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~---~~~l~  211 (305)
                      ++|.|++||+.+||+++.+.+.....+........+ +.  ..-.-|+|.|.+.+++..-.+.++|+.+.+.   ..+..
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            578999999999999999999998887777666655 21  1234599999999999999999999977443   23455


Q ss_pred             EEeccC
Q psy4086         212 VKFADS  217 (305)
Q Consensus       212 v~~a~~  217 (305)
                      |++|--
T Consensus        82 VE~AP~   87 (91)
T 1uw4_A           82 VEFAPF   87 (91)
T ss_dssp             EEECSS
T ss_pred             EEEcCC
Confidence            777653

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.53  E-value=0.00099  Score=47.72  Aligned_cols=75  Identities=15%  Similarity=0.124  Sum_probs=59.8

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhh-----CCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAK-----YVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~-----~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      .++|.|.|||..+.++.|+-+|+.     -|.|..++...       +-|+|+|.+.+.|++.++. ..+.|.+  .+|.
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~rVL~k-~~H~L~~--~~Ls   77 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAERVLAQ-ADHELHG--AQLS   77 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHHHHHTC-SCCBSSS--SBCE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHHHHhcC-CcceecC--eEEE
Confidence            578999999999999999999987     26688887753       4799999999999999863 3578888  6688


Q ss_pred             EEeccCCCcC
Q psy4086         212 VKFADSGLKK  221 (305)
Q Consensus       212 v~~a~~~~~~  221 (305)
                      |.-.......
T Consensus        78 V~P~~~~~~~   87 (104)
T 2dhx_A           78 LRPAPPRAPA   87 (104)
T ss_dssp             EEECCCCCCC
T ss_pred             EEcCCCCCcc
Confidence            8775554443

>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=97.25  E-value=0.001  Score=47.08  Aligned_cols=54  Identities=17%  Similarity=0.340  Sum_probs=45.0

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhC
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN  199 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~  199 (305)
                      ..++| .+|.++...||.++|+.||. ..|+++.|.      -|||.|.+++.|..|+..+.
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT------EEEEECSCHHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            34555 99999999999999999994 456666663      69999999999999998764

>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=97.24  E-value=0.00087  Score=49.56  Aligned_cols=66  Identities=17%  Similarity=0.204  Sum_probs=51.8

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      +..+.+.|.|-+.|+.. .+.|...|++||+|.+......      .-+-.|.|.+..+|++||. .||..|..
T Consensus        20 ~~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~------~NWihI~Y~s~~~A~rAL~-kNG~ii~g   85 (119)
T 1wwh_A           20 DHLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGE   85 (119)
T ss_dssp             -CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHT-TTTCEETT
T ss_pred             CCCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCC------CCeEEEEeCCHHHHHHHHH-hCCeEecC
Confidence            34567889999999885 5666677999999998886211      2389999999999999999 58877654

>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=97.20  E-value=0.00077  Score=48.48  Aligned_cols=67  Identities=10%  Similarity=0.051  Sum_probs=55.5

Q ss_pred             CeEEEcCCCCCC-cH----HHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          59 TNLYIRGLTQDT-TD----KDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        59 ~~l~V~~Lp~~~-t~----~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ++|+|.||+.++ +.    +.++++|..|+++......+.-.      -..|.|.+.++|.+|-..||+..+.++.++
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR------Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK------RVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT------EEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce------EEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            569999999876 32    56788999999988887776532      478999999999999999999999888654

>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=97.10  E-value=0.0021  Score=47.54  Aligned_cols=72  Identities=15%  Similarity=0.089  Sum_probs=57.0

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      .+.|.|-+.|... .+.+.+.|++||+|++....     ....+-.|+|.+..+|++||. .||..|.+. ..|-|....
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~-----~~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~-~mIGV~p~~   95 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS-----NTGNWMHIRYQSKLQARKALS-KDGRIFGES-IMIGVKPCI   95 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC-----SSSSEEEEEESSHHHHHHHHT-TTTCEETTT-EECEEEECC
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC-----CCCCeEEEEeCCHHHHHHHHH-hCCeEecCC-EEEEEEECC
Confidence            4668888888875 56777899999999988762     235699999999999999997 599998753 456677754

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.10  E-value=0.0012  Score=46.91  Aligned_cols=54  Identities=20%  Similarity=0.253  Sum_probs=45.1

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhc
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ  121 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~  121 (305)
                      .||+-++|++....||.++|+.||.| .|+.+-|-       .|||.|.+++.|..|+..+.
T Consensus         7 HV~~l~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEEeCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            34544999999999999999999943 46666654       79999999999999999764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.90  E-value=0.0011  Score=47.05  Aligned_cols=80  Identities=16%  Similarity=0.191  Sum_probs=56.5

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-C-C-CcccEEEEEecCHHHHHHHHHHhCCCCCCC---CCccE
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-N-N-TSKGVGFARLESKDKCDQMIQLFNGSTLPG---SKEPL  210 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~-g-~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g---~~~~l  210 (305)
                      .-+|.|+.||+.+||+++.+.+...-.+........+ + + ..-.-|+|.|.+.++...-.+.++|+.+.+   ..-+-
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            4579999999999999998888776554333322222 1 1 112348999999999999999999987743   23456


Q ss_pred             EEEecc
Q psy4086         211 LVKFAD  216 (305)
Q Consensus       211 ~v~~a~  216 (305)
                      .|+||-
T Consensus        89 ~VE~AP   94 (97)
T 2l08_A           89 VVEFAP   94 (97)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            677764

>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=96.89  E-value=0.0014  Score=46.45  Aligned_cols=53  Identities=17%  Similarity=0.329  Sum_probs=44.8

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhC
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN  199 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~  199 (305)
                      .++| ++|.++...||.++|+.|| -..|+++.|.      -|||.|.+++.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC------eEEEEecCHHHHHHHHHhcc
Confidence            3555 9999999999999999999 4566777663      69999999999999998775

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.88  E-value=0.00082  Score=47.79  Aligned_cols=70  Identities=10%  Similarity=-0.003  Sum_probs=49.7

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCC--ccceEEEEecchhhHHHHHHHhccCcccce
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNK--CRGYGFVDFESGGYALAAVKALQDKGIHAQ  128 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~--~~G~afV~f~~~~~A~~a~~~l~g~~i~~~  128 (305)
                      -+|.|+.||+.+||+++.+.+..+-++.....+..+.+-.  .-.-|+|.|.+.++.....+.++|+.+...
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~   81 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDS   81 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECT
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeC
Confidence            4599999999999999888877654443322222221111  223589999999999999999998866543

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.59  E-value=0.0012  Score=60.80  Aligned_cols=56  Identities=16%  Similarity=0.218  Sum_probs=42.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHH
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK  118 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~  118 (305)
                      ..+.|||. .+..+++++|.++|++||+|.++.+.+++.     -||.|+|.+.+++..++.
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g-----~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFG-----LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSS-----EEEEEECC---CCHHHHS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCC-----eEEEEEeCCHHHHHHHHh
Confidence            45779998 799999999999999999999998876653     499999999999987754

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=94.92  E-value=0.014  Score=53.64  Aligned_cols=57  Identities=11%  Similarity=0.121  Sum_probs=42.2

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ  196 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~  196 (305)
                      ...++|+|. .+..+++.+|.+.|++||.|.++.+-.++    .-||.|+|.+.+++..++.
T Consensus        51 qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~----g~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           51 QAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF----GLYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS----SEEEEEECC---CCHHHHS
T ss_pred             HhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC----CeEEEEEeCCHHHHHHHHh
Confidence            345789997 79999999999999999999998877542    3599999999999887754

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.86  E-value=0.023  Score=42.57  Aligned_cols=69  Identities=9%  Similarity=0.236  Sum_probs=45.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeE-EEEeeCC--------CCC-----CccceEEEEecchhhHHHHHHHhccC
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIIS-TKAILDK--------TTN-----KCRGYGFVDFESGGYALAAVKALQDK  123 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~-~~i~~~~--------~~g-----~~~G~afV~f~~~~~A~~a~~~l~g~  123 (305)
                      .+.|.|-+.|++.+.. +.+.|++||.|.+ ..+.+..        ...     .....-.|+|.+..+|++|+. .||+
T Consensus         7 e~~VtVFGFp~~~~~~-VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMANQ-VIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGHHH-HHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHHHH-HHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            3568888998766555 4557999999866 2211100        000     124577999999999999999 6777


Q ss_pred             cccce
Q psy4086         124 GIHAQ  128 (305)
Q Consensus       124 ~i~~~  128 (305)
                      .|.+.
T Consensus        85 ii~G~   89 (132)
T 3p3d_A           85 VFNGV   89 (132)
T ss_dssp             EETTE
T ss_pred             EeCcE
Confidence            76654

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=94.54  E-value=0.032  Score=41.77  Aligned_cols=77  Identities=12%  Similarity=0.120  Sum_probs=53.6

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEE-EEEee------------CC-CC-CcccEEEEEecCHHHHHHHHHHhCCC
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVS-TRILR------------DN-NN-TSKGVGFARLESKDKCDQMIQLFNGS  201 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~-v~i~~------------~~-~g-~~~g~afV~f~~~~~A~~Ai~~l~g~  201 (305)
                      ...|.|-+.|.+.+ ..+.+.|++||.|.+ +.+..            .+ -. ....+..|+|.+..+|.+||. .||.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            34566777776654 556679999999876 22111            00 00 135688999999999999997 6999


Q ss_pred             CCCCCCccEEEEeccC
Q psy4086         202 TLPGSKEPLLVKFADS  217 (305)
Q Consensus       202 ~~~g~~~~l~v~~a~~  217 (305)
                      .|.|  ..|-|...++
T Consensus        85 ii~G--~mIGV~Py~~   98 (132)
T 3p3d_A           85 VFNG--VLLGVIPYTK   98 (132)
T ss_dssp             EETT--EECEEEECCH
T ss_pred             EeCc--EEEEEEECCH
Confidence            9999  4677877654

>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=91.75  E-value=0.55  Score=43.78  Aligned_cols=55  Identities=22%  Similarity=0.282  Sum_probs=45.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ  121 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~  121 (305)
                      ...++|+ +|..+...+|.++|+.||.+ +|+.+.+.       .|||.|.+.+.|..+++.++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt-------~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSS-------EEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCC-------eEEEEECCHHHHHHHHHHHH
Confidence            3456666 88899999999999999964 46655443       79999999999999999885

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=86.88  E-value=1.5  Score=40.86  Aligned_cols=53  Identities=17%  Similarity=0.339  Sum_probs=43.0

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhC
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN  199 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~  199 (305)
                      .++|+ ++..+...+|.++|+.||. .+|+++.+      ..|||.|.+.+.|..++..++
T Consensus       442 vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widd------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          442 VLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDD------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             EEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSS------SEEEEECSCHHHHHHHHHHHT
T ss_pred             EEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcC------CeEEEEECCHHHHHHHHHHHH
Confidence            35555 8889999999999999994 45555543      369999999999999999885

---

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	305
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-18
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-09
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	0.002
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	5e-18
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	6e-05
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	5e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	9e-14
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-07
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-13
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	8e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	4e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	7e-12
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-07
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-05
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	6e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-05
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	7e-11
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-10
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-05
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-05
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-10
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-05
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-10
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	5e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	8e-08
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	6e-10
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-08
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:) 7e-10
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:) 7e-07
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	7e-10
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	7e-10
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-06
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-06
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-07
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-09
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-04
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-09
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-08
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	4e-04
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	5e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-07
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-08
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-08
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	4e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	5e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-05
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	6e-08
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-05
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	7e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	5e-06
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	8e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-05
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	2e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-06
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-07
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	8e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-07
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	6e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-06
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-04
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-07
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	5e-07
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	7e-04
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-06
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.001
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-06
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-06
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	5e-04
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-06
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	6e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-04
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	4e-06
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	4e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	5e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	3e-05
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	7e-06
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	4e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	8e-06
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-05
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-05
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	6e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	9e-04
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-05
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-04
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	3e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-04
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	6e-05
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	8e-05
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-04
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	7e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	5e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	6e-04
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	6e-04
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	7e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	0.002
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	0.003
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.004

>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 = 78.5 bits (192), Expect = 4e-18
 Identities = 39/178 (21%), Positives = 69/178 (38%), Gaps = 18/178 (10%)

Query: 53  PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
           PEQL K  L+I GL+ +TTD+ L +   Q+G +     + D  T + RG+GFV + +   
Sbjct: 3   PEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 113 ALAAVKALQD------------KGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAK 160
             AA+ A                                +++  +  + +E  L     +
Sbjct: 61  VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 120

Query: 161 YVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
           Y  +    I+ D  +   +G  F   +  D  D+++      T+ G      V+ A S
Sbjct: 121 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGH--NCEVRKALS 175

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (127), Expect = 3e-09
 Identities = 18/111 (16%), Positives = 40/111 (36%), Gaps = 4/111 (3%)

Query: 29  QNGGTHPITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIIST 88
           +            +      +      L+   +++ G+ +DT +  L +   QYG I   
Sbjct: 68  RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVI 127

Query: 89  KAILDKTTNKCRGYGFVDFESGGYALAAV----KALQDKGIHAQMARQQEQ 135
           + + D+ + K RG+ FV F+        V      +       + A  +++
Sbjct: 128 EIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE 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 = 36.5 bits (83), Expect = 0.002
 Identities = 14/70 (20%), Positives = 29/70 (41%), Gaps = 1/70 (1%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDK 190
           ++ +    L+I  L     +  L S   ++ T+    ++RD N   S+G GF    + ++
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 191 CDQMIQLFNG 200
            D  +     
Sbjct: 61  VDAAMNARPH 70

>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 = 76.0 bits (186), Expect = 5e-18
 Identities = 55/101 (54%), Positives = 73/101 (72%), Gaps = 6/101 (5%)

Query: 120 LQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKG 179
           L+  G+ AQMA+QQEQDPTNLYI+NLPL+  E +LE++L  +  V+STRILRD++ TS+G
Sbjct: 1   LKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG 60

Query: 180 VGFARLESKDKCDQMIQLFNGSTL------PGSKEPLLVKF 214
           VGFAR+ES +KC+ +I  FNG  +          EPLL KF
Sbjct: 61  VGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKF 101

>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 = 39.0 bits (90), Expect = 6e-05
 Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 1/97 (1%)

Query: 41  VQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCR 100
           ++ +G        ++   TNLYI  L     +++L NM   +G +IST+ +   ++   R
Sbjct: 1   LKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRIL-RDSSGTSR 59

Query: 101 GYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDP 137
           G GF   ES     A +     K I          +P
Sbjct: 60  GVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP 96

>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 = 64.2 bits (156), Expect = 5e-14
 Identities = 23/73 (31%), Positives = 34/73 (46%)

Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
           E +  TNLY+  L +  TD  L  +  +YG I+    + DK T + RG  FV +     A
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 114 LAAVKALQDKGIH 126
             A+ AL +    
Sbjct: 62  QEAISALNNVIPE 74

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 59.2 bits (143), Expect = 3e-12
 Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT-SKGVGFARLESKDKCDQM 194
             TNLY+ NLP    +  L+++  KY ++V   ILRD      +GV F R   +++  + 
Sbjct: 5   KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 195 IQLFNGSTLPGSKEPLLVKFA 215
           I   N     G  +PL V+ A
Sbjct: 65  ISALNNVIPEGGSQPLSVRLA 85

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.8 bits (155), Expect = 9e-14
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 4/82 (4%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           ++L + GL   TT++DL    S +G ++  +   D  T   +G+GFV F      +  + 
Sbjct: 9   SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 119 A---LQDKGIHAQMAR-QQEQD 136
               +  +    ++   +Q QD
Sbjct: 69  QRHMIDGRWCDCKLPNSKQSQD 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 = 45.7 bits (108), Expect = 3e-07
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 5/88 (5%)

Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKD 189
           ++  Q  ++L +  LP    E DL+   + +  V+  ++ +D     SKG GF R    +
Sbjct: 2   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 61

Query: 190 KCDQMIQLFNGSTLPGSKEPLLVKFADS 217
              +++       + G       K  +S
Sbjct: 62  TQVKVMS--QRHMIDGRW--CDCKLPNS 85

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.9 bits (150), Expect = 5e-13
 Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 53  PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT-TNKCRGYGFVDFESGG 111
           P++ + + + +R +      +++  + S +G + + +     T T   RG+GFVDF +  
Sbjct: 3   PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 112 YALAAVKALQDK 123
            A  A  AL   
Sbjct: 63  DAKKAFNALCHS 74

>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 = 55.7 bits (134), Expect = 8e-11
 Identities = 18/98 (18%), Positives = 44/98 (44%), Gaps = 7/98 (7%)

Query: 128 QMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLES 187
           Q+ +  +Q  + + + N+P    + ++  L + +  + + R+ +    T    GF  ++ 
Sbjct: 1   QVPK--KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDF 58

Query: 188 KDKCDQ---MIQLFNGSTLPGSKEPLLVKFADSGLKKR 222
             K D       L + + L G    L++++ADS +  +
Sbjct: 59  ITKQDAKKAFNALCHSTHLYGR--RLVLEWADSEVTVQ 94

>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 = 58.9 bits (142), Expect = 4e-12
 Identities = 25/68 (36%), Positives = 39/68 (57%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
            NLY+ GL +  T K+L  + SQYG II+++ ++D+ T   RG GF+ F+    A  A+K
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 119 ALQDKGIH 126
            L  +   
Sbjct: 67  GLNGQKPS 74

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.8 bits (139), Expect = 1e-11
 Identities = 29/79 (36%), Positives = 48/79 (60%), Gaps = 1/79 (1%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT-SKGVGFARLESKDKCDQMIQ 196
            NLY++ LP    + +LE L ++Y  ++++RIL D     S+GVGF R + + + ++ I+
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 197 LFNGSTLPGSKEPLLVKFA 215
             NG    G+ EP+ VKFA
Sbjct: 67  GLNGQKPSGATEPITVKFA 85

>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 = 59.3 bits (143), Expect = 7e-12
 Identities = 25/114 (21%), Positives = 44/114 (38%), Gaps = 15/114 (13%)

Query: 53  PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
           P ++++  LYIR L    T +++ ++  +YGPI   +      T + RG  +V +E    
Sbjct: 3   PPEVNRI-LYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFD 58

Query: 113 ALAAVKALQ-----DKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKY 161
           A  A   L      ++ +                   +    KE  L+ L  KY
Sbjct: 59  AKNACDHLSGFNVCNRYLVVLYYNANRAFQ------KMDTKKKEEQLKLLKEKY 106

>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 = 45.8 bits (108), Expect = 4e-07
 Identities = 15/80 (18%), Positives = 28/80 (35%), Gaps = 4/80 (5%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
             LYI NLP      ++  +  KY  +   R    N   ++G  +   E           
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIR--VGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 198 FNGSTLPGSKEPLLVKFADS 217
            +G  +      L+V + ++
Sbjct: 66  LSGFNVCNR--YLVVLYYNA 83

>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 = 57.4 bits (138), Expect = 3e-11
 Identities = 26/87 (29%), Positives = 44/87 (50%), Gaps = 6/87 (6%)

Query: 53  PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
            EQ  K  L+I GL+ +TT++ L N   Q+G +     + D  + + RG+GFV F S   
Sbjct: 17  KEQFRK--LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 74

Query: 113 ALAAVKA----LQDKGIHAQMARQQEQ 135
             AA+ A    +  + +  + A  +E+
Sbjct: 75  VDAAMAARPHSIDGRVVEPKRAVAREE 101

>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 = 40.0 bits (93), Expect = 3e-05
 Identities = 16/96 (16%), Positives = 39/96 (40%), Gaps = 4/96 (4%)

Query: 123 KGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVG 181
           + +  +  +++++    L+I  L     E  L +   ++  +    ++RD  +  S+G G
Sbjct: 6   ETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 65

Query: 182 FARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
           F    S  + D  +      ++ G    +  K A +
Sbjct: 66  FVTFSSMAEVDAAMAA-RPHSIDGRV--VEPKRAVA 98

>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 = 55.8 bits (134), Expect = 6e-11
 Identities = 25/67 (37%), Positives = 38/67 (56%), Gaps = 2/67 (2%)

Query: 53  PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
           PEQL K  L+I GL+ +TTD+ L +   Q+G +     + D  T + RG+GFV + +   
Sbjct: 3   PEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 113 ALAAVKA 119
             AA+ A
Sbjct: 61  VDAAMNA 67

>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 = 40.8 bits (95), Expect = 1e-05
 Identities = 18/87 (20%), Positives = 35/87 (40%), Gaps = 4/87 (4%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDK 190
           ++ +    L+I  L     +  L S   ++ T+    ++RD N   S+G GF    + ++
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADS 217
            D  +       + G    +  K A S
Sbjct: 61  VDAAMNA-RPHKVDGRV--VEPKRAVS 84

>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 = 55.3 bits (133), Expect = 7e-11
 Identities = 20/67 (29%), Positives = 31/67 (46%)

Query: 60  NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           +LY+  L  D T+  L    S  GPI+S +   D  T +  GY +V+F+    A  A+  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 120 LQDKGIH 126
           +    I 
Sbjct: 62  MNFDVIK 68

>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 = 48.4 bits (115), Expect = 2e-08
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 3/78 (3%)

Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT-SKGVGFARLESKDKCDQMIQL 197
           +LY+ +L  +  E  L    +    ++S R+ RD     S G  +   +     ++ +  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 198 FNGSTLPGSKEPLLVKFA 215
            N   + G   P+ + ++
Sbjct: 62  MNFDVIKGK--PVRIMWS 77

>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 = 54.6 bits (131), Expect = 1e-10
 Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 4/74 (5%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA- 119
           ++I GL+  TT + L     Q+G +     + D  T + RG+GFV F         +   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 120 ---LQDKGIHAQMA 130
              L  K I  ++A
Sbjct: 63  RHELDSKTIDPKVA 76

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.2 bits (91), Expect = 4e-05
 Identities = 14/77 (18%), Positives = 28/77 (36%), Gaps = 4/77 (5%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLF 198
           ++I  L     +  L     ++  V    ++RD     S+G GF     +   D+++   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61

Query: 199 NGSTLPGSKEPLLVKFA 215
           +   L      +  K A
Sbjct: 62  SRHELDSKT--IDPKVA 76

>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 = 55.0 bits (132), Expect = 1e-10
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 54  EQLSK--TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           E+L K    LY+  L+  TT++ +  + S+ G I      LDK      G+ FV++ S  
Sbjct: 1   EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRA 60

Query: 112 YALAAVKALQDKGIH 126
            A  A++ +    + 
Sbjct: 61  DAENAMRYINGTRLD 75

>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 = 40.7 bits (95), Expect = 1e-05
 Identities = 16/89 (17%), Positives = 31/89 (34%), Gaps = 3/89 (3%)

Query: 135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQ 193
           +    LY+ NL     E  +  L +K   +    +  D    T+ G  F    S+   + 
Sbjct: 5   KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 64

Query: 194 MIQLFNGSTLPGSKEPLLVKFADSGLKKR 222
            ++  NG+ L      +   +     + R
Sbjct: 65  AMRYINGTRLDDR--IIRTDWDAGFKEGR 91

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.7 bits (131), Expect = 1e-10
 Identities = 24/82 (29%), Positives = 39/82 (47%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           SKTNL +  L Q+ T ++  ++    G I S K + DK T +  GYGFV++     A  A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 117 VKALQDKGIHAQMARQQEQDPT 138
           +  L    +  +  +     P+
Sbjct: 61  INTLNGLRLQTKTIKVSYARPS 82

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 1e-05
 Identities = 18/79 (22%), Positives = 26/79 (32%), Gaps = 3/79 (3%)

Query: 138 TNLYIANLPLNFKECDLESLLAKY-VTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
           TNL +  LP N  + +  SL            +       S G GF         ++ I 
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 197 LFNGSTLPGSKEPLLVKFA 215
             NG  L      + V +A
Sbjct: 63  TLNGLRLQTK--TIKVSYA 79

>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 = 54.7 bits (131), Expect = 2e-10
 Identities = 23/70 (32%), Positives = 35/70 (50%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           +K  LY+ GL ++  DK L      +G I   +  LD  T K RG+ FV+FE    A AA
Sbjct: 4   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 117 VKALQDKGIH 126
           +  + +  + 
Sbjct: 64  IDNMNESELF 73

>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 = 40.8 bits (95), Expect = 1e-05
 Identities = 18/88 (20%), Positives = 28/88 (31%), Gaps = 7/88 (7%)

Query: 129 MARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN-TSKGVGFARLES 187
           MA  +      LY+  L     +  L +    +  +   +I  D      +G  F   E 
Sbjct: 1   MATTK----RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 56

Query: 188 KDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
            +     I   N S L G    + V  A
Sbjct: 57  AEDAAAAIDNMNESELFGR--TIRVNLA 82

>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 = 54.0 bits (129), Expect = 2e-10
 Identities = 47/72 (65%), Positives = 56/72 (77%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           LYIRGL   TTD+DL+ +C  YG I+STKAILDKTTNKC+GYGFVDF+S   A  AV AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 121 QDKGIHAQMARQ 132
           +  G+ AQMA+Q
Sbjct: 61  KASGVQAQMAKQ 72

>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 = 53.9 bits (129), Expect = 3e-10
 Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 7/92 (7%)

Query: 52  GP--EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           GP  E+     +Y+ GL +  ++  L  +  Q GP+++T    D+ T + +GYGFV+F S
Sbjct: 1   GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 60

Query: 110 GGYALAAVKALQ-----DKGIHAQMARQQEQD 136
              A  A+K +       K I    A    ++
Sbjct: 61  EEDADYAIKIMDMIKLYGKPIRVNKASAHNKN 92

>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 = 43.5 bits (102), Expect = 2e-06
 Identities = 21/88 (23%), Positives = 37/88 (42%), Gaps = 4/88 (4%)

Query: 132 QQEQDP-TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT-SKGVGFARLESKD 189
             E++    +Y+  L     E  L  L  +   VV+T + +D      +G GF    S++
Sbjct: 3   ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 62

Query: 190 KCDQMIQLFNGSTLPGSKEPLLVKFADS 217
             D  I++ +   L G   P+ V  A +
Sbjct: 63  DADYAIKIMDMIKLYGK--PIRVNKASA 88

>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 = 53.1 bits (127), Expect = 5e-10
 Identities = 25/70 (35%), Positives = 35/70 (50%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           S TNL +  L QD TD++L  +    GPI + + + D  T    GY FVDF S   +  A
Sbjct: 1   SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 60

Query: 117 VKALQDKGIH 126
           +K L    + 
Sbjct: 61  IKVLNGITVR 70

>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 = 46.9 bits (111), Expect = 8e-08
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 3/82 (3%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVS-TRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
           TNL +  LP +  + +L +L      + +   +       S G  F    S+    + I+
Sbjct: 3   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 62

Query: 197 LFNGSTLPGSKEPLLVKFADSG 218
           + NG T+      L V +A  G
Sbjct: 63  VLNGITVRNK--RLKVSYARPG 82

>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 = 53.5 bits (128), Expect = 6e-10
 Identities = 17/93 (18%), Positives = 35/93 (37%), Gaps = 4/93 (4%)

Query: 46  SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
            P     PE+     ++   L      +DL +  S  G +   + I D+ + + +G  +V
Sbjct: 6   EPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYV 65

Query: 106 DFESGGYALAAVKA----LQDKGIHAQMARQQE 134
           +F        A+      L    I  Q ++ ++
Sbjct: 66  EFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEK 98

>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 = 49.6 bits (118), Expect = 1e-08
 Identities = 21/87 (24%), Positives = 36/87 (41%), Gaps = 4/87 (4%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT-SKGVGFARLESKDK 190
            +E+D   ++   L    +  DLE   +    V   RI+ D N+  SKG+ +        
Sbjct: 13  PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 72

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADS 217
               I L  G  L G   P++V+ + +
Sbjct: 73  VPLAIGL-TGQRLLGV--PIIVQASQA 96

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 7e-10
 Identities = 11/94 (11%), Positives = 31/94 (32%), Gaps = 2/94 (2%)

Query: 121 QDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGV 180
           ++    +Q A       +++ +      F E     +  KY  V    +  +  +   G 
Sbjct: 11  RNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGN 70

Query: 181 GFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF 214
            + +   ++  ++ +   N     G   P+  + 
Sbjct: 71  VYVKFRREEDAEKAVIDLNNRWFNGQ--PIHAEL 102

>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 = 44.6 bits (105), Expect = 7e-07
 Identities = 11/68 (16%), Positives = 27/68 (39%), Gaps = 1/68 (1%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           +++ ++    +  ++    M  +YG +     + D   +   G  +V F     A  AV 
Sbjct: 28  SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVI 86

Query: 119 ALQDKGIH 126
            L ++  +
Sbjct: 87  DLNNRWFN 94

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.3 bits (125), Expect = 7e-10
 Identities = 14/59 (23%), Positives = 30/59 (50%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           +++ GL+ DT ++ +      +G + S +  +D  TNK RG+ F+ F+        ++ 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 7e-10
 Identities = 14/70 (20%), Positives = 28/70 (40%), Gaps = 2/70 (2%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIIST--KAILDKTTNKCRGYGFVDFESGGYALAA 116
             L+I G+ +    ++++   ++    +             K RG+ FV++ES   A  A
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 117 VKALQDKGIH 126
            + L    I 
Sbjct: 62  RRKLMPGRIQ 71

>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 = 42.8 bits (100), Expect = 3e-06
 Identities = 14/82 (17%), Positives = 27/82 (32%), Gaps = 3/82 (3%)

Query: 138 TNLYIANLPLNFKECDLESLLAKY---VTVVSTRILRDNNNTSKGVGFARLESKDKCDQM 194
             L+I  +P   K  ++   +AK    V  V       +   ++G  F   ES       
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 195 IQLFNGSTLPGSKEPLLVKFAD 216
            +      +      + V +A+
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWAE 83

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.0 bits (124), Expect = 1e-09
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT---TNKCRGYGFVDFESGGYALAAV 117
           L+I+ L   TT++ L  + S+ G I S      K         G+GFV+++    A  A+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 118 KALQ-----DKGIHAQMARQQEQ 135
           K LQ        +  +++ +  +
Sbjct: 61  KQLQGHTVDGHKLEVRISERATK 83

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.5 bits (102), Expect = 1e-06
 Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 6/85 (7%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGV----GFARLESKDKCDQMI 195
           L+I NL  +  E  L+ + +K   + S  I +  N     +    GF   +  ++  + +
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 196 QLFNGSTLPGSKEPLLVKFADSGLK 220
           +   G T+ G    L V+ ++   K
Sbjct: 61  KQLQGHTVDGH--KLEVRISERATK 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 = 51.9 bits (124), Expect = 1e-09
 Identities = 14/66 (21%), Positives = 27/66 (40%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L+I GL     D  +  + + +GP+ +   + D  T   +GY F ++        A+  L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 121 QDKGIH 126
               + 
Sbjct: 64  NGMQLG 69

>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 = 46.2 bits (109), Expect = 1e-07
 Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 3/82 (3%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT-SKGVGFARLESKDKCDQMIQLF 198
           L+I  LP    +  ++ LL  +  + +  +++D+    SKG  F      +  DQ I   
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 199 NGSTLPGSKEPLLVKFADSGLK 220
           NG  L      LLV+ A  G K
Sbjct: 64  NGMQLGDK--KLLVQRASVGAK 83

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.6 bits (123), Expect = 2e-09
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 2/79 (2%)

Query: 48  GTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
           G  +G      T + ++ +    +  ++++    Y  I  +  +         G   V F
Sbjct: 1   GASSGKP--GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 58

Query: 108 ESGGYALAAVKALQDKGIH 126
           ES   A AAV  L D+ I 
Sbjct: 59  ESRDEATAAVIDLNDRPIG 77

>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 = 50.8 bits (121), Expect = 3e-09
 Identities = 12/83 (14%), Positives = 27/83 (32%), Gaps = 3/83 (3%)

Query: 134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCD 192
           +  PT + + N+P      ++      Y  +  +  L+ N      G      ES+D+  
Sbjct: 6   KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 65

Query: 193 QMIQLFNGSTLPGSKEPLLVKFA 215
             +   N   +      + +   
Sbjct: 66  AAVIDLNDRPIGSR--KVKLVLG 86

>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 = 51.1 bits (122), Expect = 2e-09
 Identities = 20/59 (33%), Positives = 32/59 (54%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
           ++I GL+ DTT KDL +  S++G ++     LD  T + RG+GFV F+        +  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

>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 = 35.3 bits (81), Expect = 7e-04
 Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 2/69 (2%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLF 198
           ++I  L  +  + DL+   +K+  VV   +  D     S+G GF   +  +  D+++   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ- 60

Query: 199 NGSTLPGSK 207
               L G  
Sbjct: 61  KEHKLNGKV 69

>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 = 50.3 bits (120), Expect = 4e-09
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           L ++NL     + D++ L A++ T+    +  D +  S G      E K    + ++ +N
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 200 GSTLPGSKEPLLVKFADS 217
           G  L G   P+ ++   S
Sbjct: 63  GVPLDGR--PMNIQLVTS 78

>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 = 48.0 bits (114), Expect = 3e-08
 Identities = 13/66 (19%), Positives = 26/66 (39%), Gaps = 1/66 (1%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L +  L    +D D+  + +++G +     +    + +  G   V FE    AL A+K  
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAA-VHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 121 QDKGIH 126
               + 
Sbjct: 62  NGVPLD 67

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.5 bits (120), Expect = 4e-09
 Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 2/79 (2%)

Query: 48  GTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
           G    P+      L + GL+  TT++DL  + S+YGPI     + D+ + + RG+ FV F
Sbjct: 1   GNRANPDP--NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 58

Query: 108 ESGGYALAAVKALQDKGIH 126
           E+   A  A +      + 
Sbjct: 59  ENVDDAKEAKERANGMELD 77

>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 = 36.6 bits (84), Expect = 4e-04
 Identities = 20/78 (25%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 131 RQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN-TSKGVGFARLESKD 189
           R        L +  L L   E DL  + +KY  +    I+ D  +  S+G  F   E+ D
Sbjct: 3   RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 62

Query: 190 KCDQMIQLFNGSTLPGSK 207
              +  +  NG  L G +
Sbjct: 63  DAKEAKERANGMELDGRR 80

>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 = 50.8 bits (121), Expect = 5e-09
 Identities = 20/79 (25%), Positives = 30/79 (37%), Gaps = 3/79 (3%)

Query: 48  GTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
           G   GP   +   +Y+  L  D   KD+ ++  +YG I   + I  K       + FV+F
Sbjct: 4   GVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAI---RDIDLKNRRGGPPFAFVEF 60

Query: 108 ESGGYALAAVKALQDKGIH 126
           E    A  AV         
Sbjct: 61  EDPRDAEDAVYGRDGYDYD 79

>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 = 47.0 bits (111), Expect = 1e-07
 Identities = 20/90 (22%), Positives = 33/90 (36%), Gaps = 7/90 (7%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
           +   +Y+ NLP + +  D+E +  KY  +    +            F   E     +  +
Sbjct: 13  NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG--PPFAFVEFEDPRDAEDAV 70

Query: 196 QLFNGSTLPGSKEPLLVKFADSGLKKRGAG 225
              +G    G    L V+F  SG   RG G
Sbjct: 71  YGRDGYDYDGY--RLRVEFPRSG---RGTG 95

>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 = 49.5 bits (118), Expect = 1e-08
 Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 10/84 (11%)

Query: 45  GSPG-TPTGPEQLSKTNLYIRGLTQDTTDK-DLINMCSQYGPIISTKAILDKTTNKCRGY 102
           GS G +     +   + ++I  L      K D+  + S+YG I+             +G+
Sbjct: 1   GSSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCS--------VHKGF 52

Query: 103 GFVDFESGGYALAAVKALQDKGIH 126
            FV + +   A AAV     + I 
Sbjct: 53  AFVQYVNERNARAAVAGEDGRMIA 76

>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 = 49.0 bits (116), Expect = 1e-08
 Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAI-LDKTTNKCRGYGFVDFESGGYALAAVKA 119
           ++I  L  +  +K L +  S +G I+ T  I  D  T   +GY F++F S   + AA++A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 120 -----LQDKGIHAQMARQQEQ 135
                L ++ I    A +++ 
Sbjct: 61  MNGQYLCNRPITVSYAFKKDS 81

>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 = 43.6 bits (102), Expect = 1e-06
 Identities = 22/86 (25%), Positives = 35/86 (40%), Gaps = 5/86 (5%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT--SKGVGFARLESKDKCDQMIQL 197
           ++I NL     E  L    + +  ++ T  +  + +T  SKG  F    S D  D  I+ 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 198 FNGSTLPGSKEPLLVKFADSGLKKRG 223
            NG  L     P+ V +A      +G
Sbjct: 61  MNGQYLCNR--PITVSYAFKK-DSKG 83

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 2e-08
 Identities = 18/98 (18%), Positives = 34/98 (34%), Gaps = 17/98 (17%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           GS G+         + +++   T D T+ +L    SQYG ++             R + F
Sbjct: 1   GSSGS---------SGVFVGRCTGDMTEDELREFFSQYGDVMD-----VFIPKPFRAFAF 46

Query: 105 VDFESGGYALAAVKA---LQDKGIHAQMARQQEQDPTN 139
           V F     A +       ++   +H   A  +    + 
Sbjct: 47  VTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNSNSG 84

>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 = 37.3 bits (86), Expect = 2e-04
 Identities = 8/93 (8%), Positives = 24/93 (25%), Gaps = 8/93 (8%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
             + +++     +  E +L    ++Y  V+            +   F           + 
Sbjct: 4   GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVF----IPKPFRAFAFVTFADDQIAQSLC 59

Query: 196 QLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
                  + G    + +  A+         + G
Sbjct: 60  G--EDLIIKGI--SVHISNAEPKHNSNSGPSSG 88

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 4e-08
 Identities = 19/86 (22%), Positives = 42/86 (48%), Gaps = 3/86 (3%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKC 191
           + +  P  L+++N+P  F++ DL  +  ++  ++   I+ +    SKG GF   E+    
Sbjct: 6   ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADA 64

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADS 217
           D+  +  +G+ + G    + V  A +
Sbjct: 65  DRAREKLHGTVVEGR--KIEVNNATA 88

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 1e-06
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 7/83 (8%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           +G+  + + P       L++  +     D DL  M  Q+G I+  + I ++  +K   +G
Sbjct: 2   SGNSESKSTP-----KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG--FG 54

Query: 104 FVDFESGGYALAAVKALQDKGIH 126
           FV FE+   A  A + L    + 
Sbjct: 55  FVTFENSADADRAREKLHGTVVE 77

>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 = 47.4 bits (112), Expect = 5e-08
 Identities = 23/66 (34%), Positives = 38/66 (57%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++ GL+ DT ++ L  + S+YG I     + D+ T + RG+GFV FE+   A  A+ A+
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 121 QDKGIH 126
             K + 
Sbjct: 68  NGKSVD 73

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 2e-05
 Identities = 21/88 (23%), Positives = 36/88 (40%), Gaps = 3/88 (3%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT-SKGVGFARLESKDKCDQM 194
           D   L++  L  +  E  LE + +KY  +    +++D     S+G GF   E+ D     
Sbjct: 4   DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 195 IQLFNGSTLPGSKEPLLVKFADSGLKKR 222
           +   NG ++ G    + V  A      R
Sbjct: 64  MMAMNGKSVDGR--QIRVDQAGKSSDNR 89

>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 = 47.3 bits (112), Expect = 6e-08
 Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 12/90 (13%)

Query: 53  PEQLSKT-NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
            + +S    LY+R L   T+++ +    +   P    +        K R Y FV F +  
Sbjct: 2   EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVER------VKKIRDYAFVHFSNRE 55

Query: 112 YALAAVKALQ-----DKGIHAQMARQQEQD 136
            A+ A+KAL         I   +A+  ++D
Sbjct: 56  DAVEAMKALNGKVLDGSPIEVTLAKPVDKD 85

>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 = 40.0 bits (93), Expect = 2e-05
 Identities = 17/76 (22%), Positives = 30/76 (39%), Gaps = 7/76 (9%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           LY+ NL L+  E  +E            R+ +      +   F    +++   + ++  N
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKALN 65

Query: 200 GSTLPGSKEPLLVKFA 215
           G  L GS  P+ V  A
Sbjct: 66  GKVLDGS--PIEVTLA 79

>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 = 48.7 bits (115), Expect = 7e-08
 Identities = 33/109 (30%), Positives = 47/109 (43%), Gaps = 13/109 (11%)

Query: 47  PGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVD 106
           P T   PE     NL +  +     +  L  +  +YGPI S K + D+ T + RGYGFV 
Sbjct: 31  PPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVK 90

Query: 107 FESGGYALAAVKALQ-----DKGIHAQMARQQEQDP--------TNLYI 142
           F+SG  A  A+  L      +K +   +A    Q P         N Y+
Sbjct: 91  FQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 43.4 bits (101), Expect = 5e-06
 Identities = 26/115 (22%), Positives = 38/115 (33%), Gaps = 5/115 (4%)

Query: 121 QDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGV 180
           Q + I       +     NL +  +P    E  L  L  +Y  + S +I+ D        
Sbjct: 26  QQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRG 85

Query: 181 GFAR-LESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAG--AGGPNIY 232
                 +S     Q I   NG  +      L V  A SG ++ G     G  N Y
Sbjct: 86  YGFVKFQSGSSAQQAIAGLNGFNILNK--RLKVALAASGHQRPGIAGAVGDGNGY 138

>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 = 47.0 bits (111), Expect = 8e-08
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 2/68 (2%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
             LY+  L++D T+  ++ + SQ GP  S K I +        Y FV+F     A AA+ 
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAALA 66

Query: 119 ALQDKGIH 126
           A+  + I 
Sbjct: 67  AMNGRKIL 74

>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 = 46.2 bits (109), Expect = 2e-07
 Identities = 14/91 (15%), Positives = 34/91 (37%), Gaps = 3/91 (3%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKC 191
           + +  P  LY+ NL  +  E  +  L ++     S +++ ++ +      F         
Sbjct: 3   EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYC-FVEFYEHRDA 61

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKR 222
              +   NG  + G    + V +A +   ++
Sbjct: 62  AAALAAMNGRKILGK--EVKVNWATTPSSQK 90

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (111), Expect = 1e-07
 Identities = 18/97 (18%), Positives = 41/97 (42%), Gaps = 12/97 (12%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           + +PG P          LY++ L+   T++DL+++ +++             T + RG  
Sbjct: 11  SYNPGEPN-------KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQA 63

Query: 104 FVDFESGGYALAAVKALQ-----DKGIHAQMARQQEQ 135
           F+ F +   A  A+  +       K +  +  + ++Q
Sbjct: 64  FITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ 100

>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 = 41.3 bits (96), Expect = 1e-05
 Identities = 23/84 (27%), Positives = 35/84 (41%), Gaps = 4/84 (4%)

Query: 136 DPTN-LYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQ 193
           +P   LY+ NL     E DL SL A++       I         +G  F    +K+   Q
Sbjct: 16  EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 75

Query: 194 MIQLFNGSTLPGSKEPLLVKFADS 217
            + L NG  L G    L+++F  +
Sbjct: 76  ALHLVNGYKLYGK--ILVIEFGKN 97

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 1e-07
 Identities = 23/82 (28%), Positives = 32/82 (39%), Gaps = 8/82 (9%)

Query: 53  PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI--------LDKTTNKCRGYGF 104
            E    + +Y++GL    T  DL +   Q G +   K          LDK T K +G   
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 105 VDFESGGYALAAVKALQDKGIH 126
           V +E    A AAV+    K   
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQ 84

>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 = 39.0 bits (90), Expect = 6e-05
 Identities = 16/93 (17%), Positives = 27/93 (29%), Gaps = 11/93 (11%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD---------NNNTSKGVGF 182
            ++ D + +Y+  L  +    DL     +   V   +                  KG   
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 183 ARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
              E        ++ F+G    GS   L V  A
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQGS--KLKVSLA 93

>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 = 46.7 bits (110), Expect = 1e-07
 Identities = 22/65 (33%), Positives = 27/65 (41%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           T +++ GL   TTD  L      +G I     I D+ T K RGYGFV       A  A K
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 119 ALQDK 123
                
Sbjct: 71  DPNPI 75

>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 = 43.6 bits (102), Expect = 2e-06
 Identities = 18/106 (16%), Positives = 37/106 (34%), Gaps = 7/106 (6%)

Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN-TSKGVGFARLESK 188
             Q++   T +++  LP +  +  L      +  +    ++ D     S+G GF  +  +
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 189 DKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPNIYRG 234
              ++  +  N   + G      V  A  G K R   +       G
Sbjct: 63  AAAERACKDPNP-IIDGR--KANVNLAYLGAKPR---SLQTGFAIG 102

>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 = 46.5 bits (110), Expect = 2e-07
 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
               +Y  G+    TD+ +    S +G I+  +          +GY FV F +   A  A
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHA 70

Query: 117 VKALQDKGIHAQMAR 131
           + ++    I   + +
Sbjct: 71  IVSVNGTTIEGHVVK 85

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (101), Expect = 3e-06
 Identities = 10/88 (11%), Positives = 27/88 (30%), Gaps = 7/88 (7%)

Query: 128 QMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLES 187
            +  Q       +Y   +     +  +    + +  ++  R+  +         F R  +
Sbjct: 9   DVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-----YSFVRFST 63

Query: 188 KDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
            +     I   NG+T+ G    +   + 
Sbjct: 64  HESAAHAIVSVNGTTIEGH--VVKCYWG 89

>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 = 46.2 bits (109), Expect = 2e-07
 Identities = 31/101 (30%), Positives = 53/101 (52%), Gaps = 4/101 (3%)

Query: 40  NVQHNGSPGT-PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNK 98
             Q  G+ G+   GPE     NL+I  L Q+  D+DL+ M   +G ++S K  +DK TN 
Sbjct: 2   TQQSIGAAGSQKEGPE---GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNL 58

Query: 99  CRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTN 139
            + +GFV +++   A AA++++    I  +  + Q +   N
Sbjct: 59  SKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKN 99

>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 = 41.6 bits (97), Expect = 8e-06
 Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 3/92 (3%)

Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVS-TRILRDNNNTSKGVGFARL 185
           A  ++++  +  NL+I +LP  F + DL  +   +  VVS    +    N SK  GF   
Sbjct: 8   AAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 67

Query: 186 ESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
           ++       IQ  NG  +      L V+   S
Sbjct: 68  DNPVSAQAAIQSMNGFQIGMK--RLKVQLKRS 97

>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 = 45.8 bits (108), Expect = 2e-07
 Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 3/81 (3%)

Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
             N++I NL  +     L    + +  ++S +++  + N SKG GF   E+++  ++ I+
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC-DENGSKGYGFVHFETQEAAERAIE 66

Query: 197 LFNGSTLPGSKEPLLVKFADS 217
             NG  L      + V    S
Sbjct: 67  KMNGMLLNDR--KVFVGRFKS 85

>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 = 44.6 bits (105), Expect = 6e-07
 Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 7/82 (8%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
            N++I+ L +   +K L +  S +G I+S K + D+  +K   YGFV FE+   A  A++
Sbjct: 9   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQEAAERAIE 66

Query: 119 ALQ-----DKGIHAQMARQQEQ 135
            +      D+ +     + +++
Sbjct: 67  KMNGMLLNDRKVFVGRFKSRKE 88

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 2e-07
 Identities = 17/68 (25%), Positives = 30/68 (44%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
             + +  L++DT + DL  +   +G I       DKTT + +G+ F+ F     A  A+ 
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 119 ALQDKGIH 126
            +   G  
Sbjct: 69  GVSGFGYD 76

>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 = 42.7 bits (100), Expect = 3e-06
 Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 3/85 (3%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDK 190
           ++  D   + + NL  + +E DL+ L   + ++    + +D     SKG  F     ++ 
Sbjct: 3   RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 62

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFA 215
             + I   +G         L V++A
Sbjct: 63  AARAIAGVSGFGYDHL--ILNVEWA 85

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.1 bits (106), Expect = 3e-07
 Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA- 119
           +++ GL+ +TT +D+ +   Q+G +     + DKTTN+ RG+GFV FES        +  
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 120 ---LQDKGIHAQMA 130
              + +K +  + A
Sbjct: 62  FHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.2 bits (83), Expect = 4e-04
 Identities = 13/77 (16%), Positives = 33/77 (42%), Gaps = 4/77 (5%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT-SKGVGFARLESKDKCDQMIQLF 198
           +++  L +N    D++    ++  V    ++ D      +G GF   ES+D  +++ ++ 
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI- 60

Query: 199 NGSTLPGSKEPLLVKFA 215
           +   +      +  K A
Sbjct: 61  HFHEINNK--MVECKKA 75

>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 = 45.1 bits (106), Expect = 3e-07
 Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 6/63 (9%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           LYI  L+   T  DL  +       +              GY FVD+    +A+ A++ L
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIETL 57

Query: 121 QDK 123
             K
Sbjct: 58  SGK 60

>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 = 42.8 bits (100), Expect = 2e-06
 Identities = 16/78 (20%), Positives = 28/78 (35%), Gaps = 6/78 (7%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
           LYI NL       DL  L       ++ ++L        G  F     ++   + I+  +
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLS 58

Query: 200 GSTLPGSKEPLLVKFADS 217
           G      K  + V ++ S
Sbjct: 59  GKVELHGK-IMEVDYSVS 75

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 5e-07
 Identities = 16/58 (27%), Positives = 29/58 (50%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           +++ G+ +DT +  L +   QYG I   + + D+ + K RG+ FV F+        V 
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (82), Expect = 7e-04
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 4/77 (5%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLF 198
           +++  +  + +E  L     +Y  +    I+ D  +   +G  F   +  D  D+++   
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ- 63

Query: 199 NGSTLPGSKEPLLVKFA 215
              T+ G      V+ A
Sbjct: 64  KYHTVNGH--NCEVRKA 78

>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 = 44.0 bits (103), Expect = 1e-06
 Identities = 9/62 (14%), Positives = 25/62 (40%), Gaps = 5/62 (8%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIIS-----TKAILDKTTNKCRGYGFVDFESGGYALA 115
           LY+  +    T++ +++  +    +          +L    N+ + + F++F S      
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 116 AV 117
           A+
Sbjct: 64  AM 65

>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 = 35.5 bits (81), Expect = 0.001
 Identities = 12/73 (16%), Positives = 22/73 (30%), Gaps = 5/73 (6%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRD----NNNTSKGVGFARLESKDKCD-QM 194
           LY+ N+P    E  +       + +                ++   FA LE +   +   
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 195 IQLFNGSTLPGSK 207
              F+G    G  
Sbjct: 64  AMAFDGIIFQGQS 76

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 2e-06
 Identities = 11/79 (13%), Positives = 24/79 (30%), Gaps = 4/79 (5%)

Query: 53  PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
             Q     + +  L    T   L  + S++G ++         T   +    + +     
Sbjct: 2   AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKII----TFTKNNQFQALLQYADPVS 57

Query: 113 ALAAVKALQDKGIHAQMAR 131
           A  A  +L  + I+     
Sbjct: 58  AQHAKLSLDGQNIYNACCT 76

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 2e-06
 Identities = 10/78 (12%), Positives = 24/78 (30%), Gaps = 3/78 (3%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
             + + NL        L  + +K+ TV+       N   ++     +             
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLS 64

Query: 198 FNGSTLPGSKEPLLVKFA 215
            +G  +  +   L + F+
Sbjct: 65  LDGQNIYNACCTLRIDFS 82

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.7 bits (102), Expect = 2e-06
 Identities = 10/86 (11%), Positives = 26/86 (30%), Gaps = 4/86 (4%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           +K   +I  +    T  D++          +   +L     +  G   V F++   A  +
Sbjct: 7   AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKS 66

Query: 117 VKA----LQDKGIHAQMARQQEQDPT 138
            +     L  +     +   ++    
Sbjct: 67  ERLHRKKLNGREAFVHVVTLEDMREI 92

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.6 bits (102), Expect = 2e-06
 Identities = 14/101 (13%), Positives = 28/101 (27%), Gaps = 15/101 (14%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           GS G+      L          ++  T     ++   Y    + +        K      
Sbjct: 1   GSSGSSG----LIACVANDDVFSESETRAKFESLFRTYDKDTTFQY------FKSFKRVR 50

Query: 105 VDFESGGYALAAVKALQ-----DKGIHAQMARQQEQDPTNL 140
           ++F +   A  A   L       K +    A+      ++L
Sbjct: 51  INFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHIGSSHL 91

>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 = 43.3 bits (101), Expect = 2e-06
 Identities = 15/74 (20%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 50  PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           P+   +     ++IR L+ D+ ++ L  +  Q+G +   + +L   T   +G  F  F +
Sbjct: 2   PSDVTE--GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMT 59

Query: 110 GGYALAAVKALQDK 123
              A   + A   +
Sbjct: 60  QEAAQKCLAAASLE 73

>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 = 36.7 bits (84), Expect = 5e-04
 Identities = 17/95 (17%), Positives = 39/95 (41%), Gaps = 7/95 (7%)

Query: 135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT-SKGVGFARLESKDKCDQ 193
            +   ++I NL  + +E  L  +L ++  +   R++   +   SKG  FA+  +++   +
Sbjct: 6   TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 65

Query: 194 MIQLFNGSTLPGSKE----PLLVKFADSGLKKRGA 224
            +   +     G  +     L V  A +  +   A
Sbjct: 66  CLAAASLEAEGGGLKLDGRQLKVDLAVT--RDEAA 98

>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 = 42.7 bits (100), Expect = 3e-06
 Identities = 12/86 (13%), Positives = 35/86 (40%), Gaps = 9/86 (10%)

Query: 137 PTN-LYIANLPLNFKECDLE----SLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKC 191
           P + +YI NL    K+ +L+    ++ +++  ++   +    +   +G  F   +     
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV--SRSLKMRGQAFVIFKEVSSA 59

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADS 217
              ++   G        P+ +++A +
Sbjct: 60  TNALRSMQGFPFYDK--PMRIQYAKT 83

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 6e-05
 Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 2/71 (2%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQY-GPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
           + T +YI  L +     +L                IL   + K RG  FV F+    A  
Sbjct: 3   NHT-IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 116 AVKALQDKGIH 126
           A++++Q    +
Sbjct: 62  ALRSMQGFPFY 72

>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 = 42.4 bits (99), Expect = 3e-06
 Identities = 18/68 (26%), Positives = 33/68 (48%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
             L++  + ++  + ++      YG I +    LD+ T   +GY  V++E+   ALAA +
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 119 ALQDKGIH 126
           AL    I 
Sbjct: 68  ALNGAEIM 75

>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 = 36.6 bits (84), Expect = 4e-04
 Identities = 14/93 (15%), Positives = 35/93 (37%), Gaps = 7/93 (7%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN-TSKGVGFARLESKDK 190
           Q+  +   L++ ++    +E +++     Y  + +  +  D     SKG      E+  +
Sbjct: 2   QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 61

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRG 223
                +  NG+ + G    + V +       +G
Sbjct: 62  ALAAKEALNGAEIMGQ--TIQVDWC----FVKG 88

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.3 bits (99), Expect = 4e-06
 Identities = 14/69 (20%), Positives = 31/69 (44%), Gaps = 6/69 (8%)

Query: 58  KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
           ++ L++  L  D T++++  +  +YG             +K +G+GF+  E+   A  A 
Sbjct: 8   RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVF------IHKDKGFGFIRLETRTLAEIAK 61

Query: 118 KALQDKGIH 126
             L +  + 
Sbjct: 62  VELDNMPLR 70

>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 = 37.6 bits (87), Expect = 2e-04
 Identities = 21/81 (25%), Positives = 33/81 (40%), Gaps = 7/81 (8%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
           + L++ NLP +  E ++  L  KY       I +D        GF RLE++   +     
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-----FGFIRLETRTLAEIAKVE 63

Query: 198 FNGSTLPGSKEPLLVKFADSG 218
            +   L G    L V+FA   
Sbjct: 64  LDNMPLRGK--QLRVRFACHS 82

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.9 bits (100), Expect = 4e-06
 Identities = 15/89 (16%), Positives = 24/89 (26%), Gaps = 10/89 (11%)

Query: 43  HNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
           H+GS     G         +   L   T  +DL  + S +G I     +           
Sbjct: 1   HHGSLEEKIGC-----LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIIL-- 53

Query: 103 GFVDFESGGYALAAVKALQDKGIHAQMAR 131
                E    AL   K   +  +  +   
Sbjct: 54  ---FKEKAKEALGKAKDANNGNLQLRNKE 79

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 5e-06
 Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 3/85 (3%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKC 191
           + +    ++YI   P +    D++  L     V++ ++ R  +   KG  F   +S +  
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 60

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFAD 216
            + ++   G     +   LL+ F D
Sbjct: 61  KKFVET-PGQKYKETD--LLILFKD 82

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 3e-05
 Identities = 14/83 (16%), Positives = 29/83 (34%), Gaps = 5/83 (6%)

Query: 54  EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
             +   ++YI+G   D T  D+       G +++ +          +G  FV F+S   A
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR-RTLHKAFKGSIFVVFDSIESA 60

Query: 114 LAAVKA----LQDKGIHAQMARQ 132
              V+      ++  +       
Sbjct: 61  KKFVETPGQKYKETDLLILFKDD 83

>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 = 41.6 bits (97), Expect = 7e-06
 Identities = 14/92 (15%), Positives = 36/92 (39%), Gaps = 6/92 (6%)

Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKC 191
           ++ +    L   NL  N  E +L+ +    + +         +  SKG+ +   +S+   
Sbjct: 11  KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADA 66

Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKRG 223
           ++ ++   G+ + G    + + +       RG
Sbjct: 67  EKNLEEKQGAEIDGR--SVSLYYTGEKGGTRG 96

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 39.6 bits (92), Expect = 4e-05
 Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 5/68 (7%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
             L  + L+ + T+ +L  +      I            K +G  +++F+S   A   ++
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 119 ALQDKGIH 126
             Q   I 
Sbjct: 72  EKQGAEID 79

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.3 bits (96), Expect = 8e-06
 Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 3/78 (3%)

Query: 140 LYIANLPLNFKECDLESLLAKYVTVV-STRILRDNNNTSKGVGFARLESKDKCDQMIQLF 198
           L++ N P ++ + ++  LL     V  S R+     NTS+   +  + SK+     ++  
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 199 NGSTLPGSKEPLLVKFAD 216
           NG  + G    L+ K ++
Sbjct: 64  NGLKIEGY--TLVTKVSN 79

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 40.5 bits (94), Expect = 2e-05
 Identities = 11/77 (14%), Positives = 27/77 (35%)

Query: 61  LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
           L++       T +++ ++      +  +  +     N  R + ++D  S   A   V+ L
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 121 QDKGIHAQMARQQEQDP 137
               I       +  +P
Sbjct: 64  NGLKIEGYTLVTKVSNP 80

>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 = 41.3 bits (96), Expect = 1e-05
 Identities = 18/70 (25%), Positives = 42/70 (60%)

Query: 57  SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
           S  ++++  +  + T++ L ++ S+ GP++S + + D+ T K +GYGF +++    AL+A
Sbjct: 7   SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66

Query: 117 VKALQDKGIH 126
           ++ L  +   
Sbjct: 67  MRNLNGREFS 76

>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 = 39.4 bits (91), Expect = 6e-05
 Identities = 25/102 (24%), Positives = 44/102 (43%), Gaps = 6/102 (5%)

Query: 134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN-TSKGVGFARLESKDKCD 192
           ++   ++++ N+P    E  L+ + ++   VVS R++ D      KG GF   + ++   
Sbjct: 5   DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64

Query: 193 QMIQLFNGSTLPGSKEPLLVKFADSGLKK---RGAGAGGPNI 231
             ++  NG    G    L V  A S   K   +  G G P I
Sbjct: 65  SAMRNLNGREFSGR--ALRVDNAASEKNKEELKSLGTGAPVI 104

>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 = 41.2 bits (96), Expect = 1e-05
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 6/82 (7%)

Query: 45  GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
           GS G+           L++R L+  ++++DL  + S YGP+      +D  T K +G+ F
Sbjct: 1   GSSGSS------GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAF 54

Query: 105 VDFESGGYALAAVKALQDKGIH 126
           V F    +A+ A   +  +   
Sbjct: 55  VTFMFPEHAVKAYAEVDGQVFQ 76

>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 = 35.8 bits (82), Expect = 9e-04
 Identities = 21/96 (21%), Positives = 30/96 (31%), Gaps = 6/96 (6%)

Query: 135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQ 193
                L++ NL     E DLE L + Y  +       D      KG  F      +   +
Sbjct: 6   SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 194 MIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGP 229
                +G    G    L V  +     K+ A   GP
Sbjct: 66  AYAEVDGQVFQGR--MLHVLPSTI---KKEASQSGP 96

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 40.3 bits (93), Expect = 2e-05
 Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 5/84 (5%)

Query: 52  GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
           G E  +  NL+I  L  + +  +L    S+         +  + T   R +G+VDFES  
Sbjct: 7   GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAE 65

Query: 112 YALAAV----KALQDKGIHAQMAR 131
               A+      +    I  +  +
Sbjct: 66  DLEKALELTGLKVFGNEIKLEKPK 89

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 37.6 bits (86), Expect = 2e-04
 Identities = 15/90 (16%), Positives = 38/90 (42%), Gaps = 3/90 (3%)

Query: 128 QMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLES 187
            +   +   P NL+I NL  N    +L+  +++        ++     T++  G+   ES
Sbjct: 4   MVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFES 63

Query: 188 KDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
            +  ++ ++L  G  + G+   + ++    
Sbjct: 64  AEDLEKALEL-TGLKVFGN--EIKLEKPKG 90

>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 = 40.6 bits (94), Expect = 2e-05
 Identities = 17/96 (17%), Positives = 37/96 (38%), Gaps = 5/96 (5%)

Query: 45  GSPGT-PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           GS G+    P+  +   + +RGL    + ++++   S    + +   +      +  G  
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 104 FVDFESGGYALAAV----KALQDKGIHAQMARQQEQ 135
           FV F S   A  A+    + +  + I    + + E 
Sbjct: 61  FVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEV 96

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.9 bits (93), Expect = 3e-05
 Identities = 15/81 (18%), Positives = 26/81 (32%), Gaps = 5/81 (6%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
            P +     L LN    DL    +K+  +    +   +     GV        ++ D  I
Sbjct: 18  HPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHP---DGVASVSFRDPEEADYCI 74

Query: 196 QLFNGSTLPGSKEPLLVKFAD 216
           Q  +G    G    +  +  D
Sbjct: 75  QTLDGRWFGGR--QITAQAWD 93

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.0 bits (88), Expect = 2e-04
 Identities = 15/68 (22%), Positives = 21/68 (30%), Gaps = 4/68 (5%)

Query: 74  DLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ 133
           DL   CS++G I               G   V F     A   ++ L  +    +    Q
Sbjct: 35  DLRVECSKFGQIRKLLLF----DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ 90

Query: 134 EQDPTNLY 141
             D T  Y
Sbjct: 91  AWDGTTDY 98

>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 = 39.8 bits (92), Expect = 4e-05
 Identities = 12/100 (12%), Positives = 32/100 (32%), Gaps = 6/100 (6%)

Query: 132 QQEQDPTN-LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
             +   +  +++  L  +  E DL   L K+ T+    ++               E+ D 
Sbjct: 9   HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQ-----ALVEFENIDS 63

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPN 230
             + +       +  + +     ++ S    R   +G  +
Sbjct: 64  AKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSS 103

>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 = 39.4 bits (91), Expect = 6e-05
 Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 7/88 (7%)

Query: 45  GSPGTPTGPEQLSKTN-LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           GS G+     ++S +  +++RGL +   + DL+    ++G I              +   
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTIC------YVMMMPFKRQA 54

Query: 104 FVDFESGGYALAAVKALQDKGIHAQMAR 131
            V+FE+   A   V    D  ++    +
Sbjct: 55  LVEFENIDSAKECVTFAADVPVYIAGQQ 82

>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 = 39.3 bits (91), Expect = 6e-05
 Identities = 18/81 (22%), Positives = 26/81 (32%), Gaps = 5/81 (6%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
           T L++  L  N     L     ++       I   ++       + + ES D        
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRF-----GSIRTIDHVKGDSFAYIQYESLDAAQAACAK 72

Query: 198 FNGSTLPGSKEPLLVKFADSG 218
             G  L G    L V FA SG
Sbjct: 73  MRGFPLGGPDRRLRVDFAKSG 93

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 38.3 bits (88), Expect = 8e-05
 Identities = 15/85 (17%), Positives = 35/85 (41%), Gaps = 7/85 (8%)

Query: 133 QEQDPTN--LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDK 190
           Q + P N  L++ NLP    E  L  L  ++      R++ + ++ +    F    ++ +
Sbjct: 2   QTEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIA----FVEFTTELQ 57

Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFA 215
            +   +   G  +  +   + + FA
Sbjct: 58  SNAAKEALQGFKITPTH-AMKITFA 81

>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 = 38.6 bits (89), Expect = 1e-04
 Identities = 21/100 (21%), Positives = 33/100 (33%), Gaps = 4/100 (4%)

Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRI-LRDNNNTSKGVGFARLESK 188
           +R  +  P   ++ NLP +  E  ++                  N    KG G+A  E  
Sbjct: 8   SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDL 67

Query: 189 DKCDQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
           D     + L N  +L      + V  AD    K    + G
Sbjct: 68  DSLLSALSL-NEESLGNK--RIRVDVADQAQDKDSGPSSG 104

>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 = 36.2 bits (83), Expect = 7e-04
 Identities = 19/100 (19%), Positives = 38/100 (38%), Gaps = 6/100 (6%)

Query: 44  NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           +GS G+   P+    T  ++  L  D T++ +                      + +G+G
Sbjct: 3   SGSSGSRL-PKSPPYT-AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFG 60

Query: 104 FVDFESGGYALAAVKA----LQDKGIHAQMARQQEQDPTN 139
           + +FE     L+A+      L +K I   +A Q +   + 
Sbjct: 61  YAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDSG 100

>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 = 37.8 bits (87), Expect = 2e-04
 Identities = 10/76 (13%), Positives = 22/76 (28%), Gaps = 8/76 (10%)

Query: 52  GPEQLSKTNLYIRGLTQD-TTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESG 110
           G  +  +  ++I    +       L+ +   +G I +                F++  + 
Sbjct: 3   GRVETRRV-VHIMDFQRGKNLRYQLLQLVEPFGVISNHL------ILNKINEAFIEMATT 55

Query: 111 GYALAAVKALQDKGIH 126
             A AAV         
Sbjct: 56  EDAQAAVDYYTTTPAL 71

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (85), Expect = 3e-04
 Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 5/82 (6%)

Query: 137 PTN-LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
           P+  L+++N+P +  E DL+ L +    VV        +         ++ S ++  Q +
Sbjct: 9   PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMA---LIQMGSVEEAVQAL 65

Query: 196 QLFNGSTLPGSKEPLLVKFADS 217
              +   L  +   L V F+ S
Sbjct: 66  IDLHNHDLGENH-HLRVSFSKS 86

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 36.0 bits (82), Expect = 5e-04
 Identities = 7/51 (13%), Positives = 17/51 (33%), Gaps = 2/51 (3%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
           T + ++ L +      +       GPI      +  +  K   +  ++F  
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPI--IHVDVADSLKKNFRFARIEFAR 49

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 35.6 bits (81), Expect = 6e-04
 Identities = 8/60 (13%), Positives = 21/60 (35%), Gaps = 3/60 (5%)

Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
           T + + NLP ++ +  +         ++   +        +   FAR+E       +  +
Sbjct: 1   TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR---FARIEFARYDGALAAI 57

>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 = 36.3 bits (83), Expect = 6e-04
 Identities = 9/68 (13%), Positives = 25/68 (36%), Gaps = 7/68 (10%)

Query: 59  TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
           + + ++ L QD+  +++ ++   Y              ++ +   FV   +G  A  A++
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 119 ALQDKGIH 126
                   
Sbjct: 59  MFHQYSFR 66

>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 = 35.9 bits (82), Expect = 7e-04
 Identities = 16/93 (17%), Positives = 34/93 (36%), Gaps = 8/93 (8%)

Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMI 195
             + + + NLP +    ++  LL  Y             + +K   F  L + ++    I
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYDLK------YCYVDRNKRTAFVTLLNGEQAQNAI 57

Query: 196 QLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGG 228
           Q+F+  +  G    L+V+   +        + G
Sbjct: 58  QMFHQYSFRGK--DLIVQLQPTDALLCSGPSSG 88

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 34.3 bits (78), Expect = 0.002
 Identities = 15/84 (17%), Positives = 31/84 (36%), Gaps = 6/84 (7%)

Query: 56  LSKTNLYIRGLTQDTTDKDLINM--CSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
           L    + IR L+ +  D++L+                   K  +      F+ FE+   A
Sbjct: 2   LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSA 61

Query: 114 LAAVKA----LQDKGIHAQMARQQ 133
             A++     L ++ I   +A ++
Sbjct: 62  ERALQMNRSLLGNREISVSLADKK 85

>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 = 34.4 bits (78), Expect = 0.003
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 8/83 (9%)

Query: 45  GSPGTPTGP-EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
           GS G+  GP  + S   + + GL    + +DL +   + G +            +  G G
Sbjct: 1   GSSGSSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDV-------CYADVQKDGMG 53

Query: 104 FVDFESGGYALAAVKALQDKGIH 126
            V++        A++ L D    
Sbjct: 54  MVEYLRKEDMEYALRKLDDTKFR 76

>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 = 34.5 bits (78), Expect = 0.004
 Identities = 9/90 (10%), Positives = 26/90 (28%), Gaps = 7/90 (7%)

Query: 133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCD 192
             +  T +   NLP      +++   +++ ++                         +  
Sbjct: 6   SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVL-----LPEGGITAIVEFLEPLEAR 60

Query: 193 QMIQLFNGSTLPGSKEPLLVKFADSGLKKR 222
           +  +    S       PL +++A  G+   
Sbjct: 61  KAFRHLAYSKFHHV--PLYLEWAPIGVFGA 88

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	305
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	100.0
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.87
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.85
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.85
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.85
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.85
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.85
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.84
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.84
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.84
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.84
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.84
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.84
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.84
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.84
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.83
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.83
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.83
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.83
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.83
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.83
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.82
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.82
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.82
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.82
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.82
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.82
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.82
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.81
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.81
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.81
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.81
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.81
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.81
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.81
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.81
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.81
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.81
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.81
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.81
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.8
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.8
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.8
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.8
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.8
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.79
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.79
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.79
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.79
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.79
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.79
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.79
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.79
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.79
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.79
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.78
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.78
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.78
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.78
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.78
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.77
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.77
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.77
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.77
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.77
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.77
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.77
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.77
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.77
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.77
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.77
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.76
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.76
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.76
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.76
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.76
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.76
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.75
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.75
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.75
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.75
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.75
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.75
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.74
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.74
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.74
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.74
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.74
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.74
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.74
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.74
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.74
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.74
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.73
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.73
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.73
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.73
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.72
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.72
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.72
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.72
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.72
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.72
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.71
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.71
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.71
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.7
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.7
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.7
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.7
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.69
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.69
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.69
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.69
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.69
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.68
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.68
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.68
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.67
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.67
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.66
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.66
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.66
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.66
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.65
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.65
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.64
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.64
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.64
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.63
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.63
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.62
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.62
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.62
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	99.62
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.61
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.6
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.6
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.59
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.56
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.56
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.56
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.55
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.53
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	99.53
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.51
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.51
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.5
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.47
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.47
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.46
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.44
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.41
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.38
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.31
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.21
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.88
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.68
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.58
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.15
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.71
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.55
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.34
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.51

>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=100.00  E-value=7.3e-34  Score=232.25  Aligned_cols=160  Identities=21%  Similarity=0.376  Sum_probs=139.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc-----
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR-----  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~-----  131 (305)
                      ..++|||+|||+++|+++|+++|++||.|.++.++++..++.++|||||+|.+.++|++|+..++ ..+..+.+.     
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~-~~~~~~~~~~~~~~   83 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP-HKVDGRVVEPKRAV   83 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCS-CEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcC-Ccccccchhhhhhh
Confidence            34789999999999999999999999999999999999999999999999999999999998644 323222211     


Q ss_pred             --------cccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCC
Q psy4086         132 --------QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGST  202 (305)
Q Consensus       132 --------~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~  202 (305)
                              ......++|||+|||+.+|+++|+++|+.||.|..+.|+.++ ++.++|||||+|.+.++|.+||+ +++..
T Consensus        84 ~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~  162 (183)
T d1u1qa_          84 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHT  162 (183)
T ss_dssp             CTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEE
T ss_pred             hcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCe
Confidence                    222345789999999999999999999999999999999988 78999999999999999999997 78889


Q ss_pred             CCCCCccEEEEeccCCCc
Q psy4086         203 LPGSKEPLLVKFADSGLK  220 (305)
Q Consensus       203 ~~g~~~~l~v~~a~~~~~  220 (305)
                      |.|  +.|+|++|.++..
T Consensus       163 ~~G--~~i~V~~A~~k~e  178 (183)
T d1u1qa_         163 VNG--HNCEVRKALSKQE  178 (183)
T ss_dssp             ETT--EEEEEEECCCHHH
T ss_pred             ECC--EEEEEEecCCccc
Confidence            999  7799999977543

>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=99.87  E-value=6.6e-22  Score=139.99  Aligned_cols=81  Identities=36%  Similarity=0.692  Sum_probs=76.7

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||.++|+++|+++|++||.|.+++|+.++ +|.++|||||+|.+.++|++|++.|||..+.|+.++|+|+
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            345789999999999999999999999999999999998 7899999999999999999999999999999987889999


Q ss_pred             ec
Q psy4086         214 FA  215 (305)
Q Consensus       214 ~a  215 (305)
                      ||
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            96

>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=99.85  E-value=2.1e-21  Score=137.38  Aligned_cols=81  Identities=32%  Similarity=0.628  Sum_probs=76.3

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++++++|+++|++||.|.+++|++++ ++.++|||||+|.+.++|.+|++.|||..+.+..++|+|+
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            345779999999999999999999999999999999987 8999999999999999999999999999998877889999


Q ss_pred             ec
Q psy4086         214 FA  215 (305)
Q Consensus       214 ~a  215 (305)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            97

>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=99.85  E-value=2.1e-21  Score=139.69  Aligned_cols=83  Identities=25%  Similarity=0.364  Sum_probs=77.9

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ..++|||+|||.++|+++|+++|++||.|.+|+|++++ +|.++|||||+|.+.++|++|++.|||..|.|  +.|+|++
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g--~~l~V~~   85 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYG--KPIRVNK   85 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSS--CBCEEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECC--EEEEEEE
Confidence            45789999999999999999999999999999999998 89999999999999999999999999999999  7799999


Q ss_pred             ccCCCc
Q psy4086         215 ADSGLK  220 (305)
Q Consensus       215 a~~~~~  220 (305)
                      |..+.+
T Consensus        86 A~~~~~   91 (93)
T d1x5ua1          86 ASAHNK   91 (93)
T ss_dssp             TTTTSC
T ss_pred             cCCCCC
Confidence            987653

>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=99.85  E-value=2.9e-21  Score=140.73  Aligned_cols=85  Identities=20%  Similarity=0.268  Sum_probs=78.9

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++++++|+++|++||.|.+|+|+.++ ++.++|||||+|.+.++|++||+.||+..|.|  ++|+|.
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~g--r~i~V~   83 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG--RMLHVL   83 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSS--CEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECC--EEEEEE
Confidence            346789999999999999999999999999999999988 89999999999999999999999999999999  779999


Q ss_pred             eccCCCcC
Q psy4086         214 FADSGLKK  221 (305)
Q Consensus       214 ~a~~~~~~  221 (305)
                      ++..+...
T Consensus        84 ~a~~~~~~   91 (99)
T d1whwa_          84 PSTIKKEA   91 (99)
T ss_dssp             ECCCCSTT
T ss_pred             ECCCCCcc
Confidence            99986543

>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=99.85  E-value=9.6e-22  Score=140.44  Aligned_cols=84  Identities=20%  Similarity=0.289  Sum_probs=78.4

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ..++|||+|||+++++++|+++|++||.|.+|+|+.|+ +|.++|||||+|.+.++|++|++.|||..|.|  ++|+|++
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g--~~l~v~~   81 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG--RTIRVNL   81 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETT--EEEEEEE
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECC--EEEEEEE
Confidence            45789999999999999999999999999999999998 79999999999999999999999999999999  7899999


Q ss_pred             ccCCCcC
Q psy4086         215 ADSGLKK  221 (305)
Q Consensus       215 a~~~~~~  221 (305)
                      |++++.+
T Consensus        82 a~p~~~k   88 (89)
T d2cqba1          82 AKPMRIK   88 (89)
T ss_dssp             CCCCCCC
T ss_pred             eCCCCCC
Confidence            9875443

>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=2.5e-21  Score=139.33  Aligned_cols=82  Identities=18%  Similarity=0.281  Sum_probs=77.5

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ..+++|||+|||+++|+++|+++|++||.|.+|.|+.++ ++.++|||||+|.+.++|++|++.|||..|.|  ++|+|.
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g--r~i~V~   82 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD--RIIRTD   82 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETT--EECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECC--EEEEEE
Confidence            457899999999999999999999999999999999998 88999999999999999999999999999999  789999


Q ss_pred             eccCC
Q psy4086         214 FADSG  218 (305)
Q Consensus       214 ~a~~~  218 (305)
                      |+...
T Consensus        83 ~a~~~   87 (93)
T d1h2vz_          83 WDAGF   87 (93)
T ss_dssp             EESCC
T ss_pred             EcCCC
Confidence            98754

>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=99.85  E-value=1.3e-21  Score=137.57  Aligned_cols=79  Identities=28%  Similarity=0.438  Sum_probs=75.2

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||.++++++|+++|++||.|.+++|++++ +|.++|||||+|.+.++|++||+.|||..+.+  ++|+|+||
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g--~~l~v~~a   79 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN--KRLKVSYA   79 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETT--EECEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECC--EEEEEEEc
Confidence            4679999999999999999999999999999999987 88999999999999999999999999999999  78999998


Q ss_pred             cC
Q psy4086         216 DS  217 (305)
Q Consensus       216 ~~  217 (305)
                      ++
T Consensus        80 ~p   81 (82)
T d1b7fa1          80 RP   81 (82)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.84  E-value=3.4e-21  Score=141.08  Aligned_cols=85  Identities=28%  Similarity=0.418  Sum_probs=79.4

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      .+.++|||+|||+++++++|+++|+.||.|.+++++.++ +|.++|||||+|.+.++|++||+.|||..|.|  +.|+|+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g--~~i~V~   93 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM--KRLKVQ   93 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECC--EEEEEE
Confidence            445789999999999999999999999999999999987 88999999999999999999999999999999  789999


Q ss_pred             eccCCCcC
Q psy4086         214 FADSGLKK  221 (305)
Q Consensus       214 ~a~~~~~~  221 (305)
                      |+.++..+
T Consensus        94 ~a~~k~~~  101 (102)
T d2cpza1          94 LKRSKNDS  101 (102)
T ss_dssp             CCCCSCCC
T ss_pred             EeCCCCCC
Confidence            99887654

>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=99.84  E-value=6.7e-21  Score=137.34  Aligned_cols=86  Identities=17%  Similarity=0.455  Sum_probs=78.5

Q ss_pred             ccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC--CCCcccEEEEEecCHHHHHHHHHHh-CCCCCCCCCcc
Q psy4086         133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN--NNTSKGVGFARLESKDKCDQMIQLF-NGSTLPGSKEP  209 (305)
Q Consensus       133 ~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~--~g~~~g~afV~f~~~~~A~~Ai~~l-~g~~~~g~~~~  209 (305)
                      +....++|||+|||+++++++|+++|+.||.|.+|+|+.+.  +|.++|||||+|.+.++|.+||+.| |+..|.|  ++
T Consensus         4 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~G--r~   81 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG--RR   81 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSS--CB
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECC--EE
Confidence            34567889999999999999999999999999999998875  6899999999999999999999998 8999999  77


Q ss_pred             EEEEeccCCCc
Q psy4086         210 LLVKFADSGLK  220 (305)
Q Consensus       210 l~v~~a~~~~~  220 (305)
                      |+|+||+....
T Consensus        82 l~V~~A~~~~~   92 (94)
T d2cpha1          82 LVLEWADSEVT   92 (94)
T ss_dssp             CEEEECCCCCC
T ss_pred             EEEEEcCCCCC
Confidence            99999987644

>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=2.7e-21  Score=135.19  Aligned_cols=77  Identities=18%  Similarity=0.374  Sum_probs=73.9

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      +|||+|||+++|+++|+++|++||.|.+|+|++++ +|.++|||||+|.+.++|.+|++.|||..+.|  ++|+|.||+.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~g--r~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKG--KPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETT--EECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECC--EEEEEEEeCC
Confidence            69999999999999999999999999999999998 79999999999999999999999999999999  7899999864

>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=99.84  E-value=3.5e-21  Score=136.17  Aligned_cols=80  Identities=28%  Similarity=0.432  Sum_probs=75.8

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      .+|||+|||+++|+++|+++|++||.|++|+|++|+ +|.++|||||+|.+.++|++|++.|||..|.|  ++|+|++|.
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~   79 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD--KKLLVQRAS   79 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSS--SCCEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECC--EEEEEEECC
Confidence            479999999999999999999999999999999998 79999999999999999999999999999999  779999998


Q ss_pred             CCC
Q psy4086         217 SGL  219 (305)
Q Consensus       217 ~~~  219 (305)
                      ...
T Consensus        80 ~~~   82 (85)
T d2u2fa_          80 VGA   82 (85)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.84  E-value=3.3e-21  Score=137.26  Aligned_cols=82  Identities=15%  Similarity=0.258  Sum_probs=76.6

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      .+..+|||+|||.++++++|+++|++||.|.+|+|++|+ +|.++|||||+|.+.++|++|++.|||..|.|  +.|+|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g--~~l~V~   82 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG--QTIQVD   82 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECC--EEEEEE
Confidence            346789999999999999999999999999999999987 89999999999999999999999999999999  779999


Q ss_pred             eccCC
Q psy4086         214 FADSG  218 (305)
Q Consensus       214 ~a~~~  218 (305)
                      ||..+
T Consensus        83 ~a~~k   87 (88)
T d1rk8a_          83 WCFVK   87 (88)
T ss_dssp             ESEEC
T ss_pred             EecCC
Confidence            98764

>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=5e-21  Score=148.33  Aligned_cols=85  Identities=28%  Similarity=0.468  Sum_probs=78.6

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++|+++|+++|++||.|++|+|++++ +++++|||||+|.+.++|++||+.|||..|.|  +.|+|+
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~g--r~l~V~  117 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN--KRLKVA  117 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSS--CEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECC--EEEEEE
Confidence            344689999999999999999999999999999999998 78999999999999999999999999999999  779999


Q ss_pred             eccCCCcC
Q psy4086         214 FADSGLKK  221 (305)
Q Consensus       214 ~a~~~~~~  221 (305)
                      ||..+..+
T Consensus       118 ~a~~~~~~  125 (139)
T d1u6fa1         118 LAASGHQR  125 (139)
T ss_dssp             ESSCCCCC
T ss_pred             EcCCCCCC
Confidence            99876554

>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=99.84  E-value=4.9e-21  Score=134.63  Aligned_cols=79  Identities=27%  Similarity=0.452  Sum_probs=74.8

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||.++++++|+++|++||.|.+|+++.+. ++.++|||||+|.+.++|++|++.|||..|.|  ++|+|.||
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g--~~l~v~~A   79 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQT--KTIKVSYA   79 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT--EECEEEEC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECC--EEEEEEEe
Confidence            3579999999999999999999999999999999987 78999999999999999999999999999999  77999998


Q ss_pred             cC
Q psy4086         216 DS  217 (305)
Q Consensus       216 ~~  217 (305)
                      ++
T Consensus        80 kP   81 (82)
T d1fxla1          80 RP   81 (82)
T ss_dssp             CC
T ss_pred             eC
Confidence            75

>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=99.84  E-value=3.7e-21  Score=133.77  Aligned_cols=77  Identities=23%  Similarity=0.451  Sum_probs=73.9

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      +|||+|||+++++++|+++|++||.|.+++|..+++++++|||||+|.+.++|++|++.|||..+.|  ++|+|+++..
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDG--RPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETT--EECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECC--EEEEEEEeeC
Confidence            6999999999999999999999999999999999999999999999999999999999999999999  7899999863

>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=99.84  E-value=8.1e-21  Score=135.89  Aligned_cols=86  Identities=24%  Similarity=0.493  Sum_probs=79.0

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      .+..+|||+|||+++++++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|++||+.|||..|.|  +.|+|+
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g--~~l~V~   80 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDG--RQIRVD   80 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTS--CCCEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECC--EEEEEE
Confidence            356789999999999999999999999999999999887 78999999999999999999999999999999  779999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      +|.++...+
T Consensus        81 ~a~~~~~~r   89 (90)
T d1x5sa1          81 QAGKSSDNR   89 (90)
T ss_dssp             EEECCCCCC
T ss_pred             EcCCCCCCC
Confidence            998765543

>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=99.84  E-value=3.8e-21  Score=137.60  Aligned_cols=83  Identities=20%  Similarity=0.350  Sum_probs=77.7

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ..+.++|||+|||.++++++|+++|++||.|.+|+|+.++ +|.++|||||+|.+.++|++|++.|||..|.|  +.|+|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g--~~i~v   82 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDH--LILNV   82 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETT--EECEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECC--EEEEE
Confidence            3456789999999999999999999999999999999998 78999999999999999999999999999999  77999


Q ss_pred             EeccCC
Q psy4086         213 KFADSG  218 (305)
Q Consensus       213 ~~a~~~  218 (305)
                      +||+++
T Consensus        83 ~~akp~   88 (90)
T d2cq0a1          83 EWAKPS   88 (90)
T ss_dssp             EESSCC
T ss_pred             EeeeCC
Confidence            999864

>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=99.83  E-value=5.3e-21  Score=134.44  Aligned_cols=75  Identities=32%  Similarity=0.455  Sum_probs=70.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      .++|||+|||+++|+++|+++|++||+|.+++|++++.+|+++|||||+|.+.++|++|++.|||..+.++.++.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v   76 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKV   76 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            477999999999999999999999999999999999999999999999999999999999999999988876653

>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=99.83  E-value=1.2e-20  Score=138.44  Aligned_cols=83  Identities=18%  Similarity=0.358  Sum_probs=75.6

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++++++|+++|++||.|.+|+|+.++ +|.++|||||+|.+.++|++||+.+|+ .|.|  +.|+|+
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~G--r~l~V~   84 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDG--RKANVN   84 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETT--EECEEE
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCC--EEEEEE
Confidence            345679999999999999999999999999999999998 799999999999999999999998875 7899  779999


Q ss_pred             eccCCCc
Q psy4086         214 FADSGLK  220 (305)
Q Consensus       214 ~a~~~~~  220 (305)
                      +|.....
T Consensus        85 ~a~~~~~   91 (103)
T d2cqda1          85 LAYLGAK   91 (103)
T ss_dssp             ESTTTCC
T ss_pred             EcCCCCC
Confidence            9987544

>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=99.83  E-value=1.2e-20  Score=132.65  Aligned_cols=75  Identities=29%  Similarity=0.430  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      +++|||+|||+++++++|+++|++||+|.+|+++++..+++++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v   76 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKV   76 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            577999999999999999999999999999999999999999999999999999999999999999988876653

>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=99.83  E-value=8.9e-21  Score=133.54  Aligned_cols=75  Identities=29%  Similarity=0.463  Sum_probs=70.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~   82 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   82 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeE
Confidence            346799999999999999999999999999999999999999999999999999999999999999999887654

>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=99.83  E-value=1.4e-20  Score=135.29  Aligned_cols=76  Identities=28%  Similarity=0.443  Sum_probs=70.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ..++|||+|||.++|+++|+++|++||+|.+|+|++++.+|.++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   83 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   83 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            4578999999999999999999999999999999999999999999999999999999999999998888776653

>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=2e-20  Score=133.77  Aligned_cols=85  Identities=16%  Similarity=0.339  Sum_probs=77.0

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ..+.++|||+|||.++++++|+++|+.||.|.+|+|+.++.. .++||||+|.+.++|++|++.|||..|.|  +.|+|.
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~~~g--~~i~v~   81 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILG--KEVKVN   81 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETT--EEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCEECC--EEEEEE
Confidence            445789999999999999999999999999999999998743 37899999999999999999999999999  779999


Q ss_pred             eccCCCcC
Q psy4086         214 FADSGLKK  221 (305)
Q Consensus       214 ~a~~~~~~  221 (305)
                      ||.++..+
T Consensus        82 ~a~~~~~~   89 (90)
T d2cqia1          82 WATTPSSQ   89 (90)
T ss_dssp             ECCCTTCC
T ss_pred             EcCCCCCC
Confidence            99876554

>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=99.83  E-value=1.5e-20  Score=132.90  Aligned_cols=72  Identities=35%  Similarity=0.590  Sum_probs=68.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccce
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ  128 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~  128 (305)
                      +.++|||+|||+++|+++|+++|++||+|.+++|++|+.+|+++|||||+|.+.++|++|++.|||..+.++
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~   76 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA   76 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCC
Confidence            457799999999999999999999999999999999999999999999999999999999999999988764

>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=1.7e-20  Score=132.61  Aligned_cols=74  Identities=31%  Similarity=0.490  Sum_probs=69.4

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      ++.+.++|||+|||+++++++|+++|++||+|.+++|++++.+|+++|||||+|.+.++|++|++.|||..+.+
T Consensus         2 ~~~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   75 (85)
T d1b7fa2           2 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG   75 (85)
T ss_dssp             STTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCC
Confidence            34567889999999999999999999999999999999999999999999999999999999999999987765

>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=99.82  E-value=6e-21  Score=132.18  Aligned_cols=75  Identities=19%  Similarity=0.357  Sum_probs=71.1

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      |+|||+|||+++|+++|+++|++||.|.+++|++|+ +|+++|||||+|.+.++|++|++ ++++.|+|  +.|+|+.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~G--r~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDS--KTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSS--CCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECC--eEEEEEEC
Confidence            689999999999999999999999999999999998 79999999999999999999997 79999999  66999876

>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=99.82  E-value=9e-21  Score=132.91  Aligned_cols=79  Identities=22%  Similarity=0.378  Sum_probs=69.2

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||+++|+++|+++|++||.|..+.++.+. .|.++|||||+|.+.++|++|++.|||..+.|  ++|+|+++
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g--~~i~V~~a   78 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG--YTLVTKVS   78 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETT--EECEEEEC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECC--EEEEEEEc
Confidence            3789999999999999999999999999988887776 78999999999999999999999999999999  78999998


Q ss_pred             cC
Q psy4086         216 DS  217 (305)
Q Consensus       216 ~~  217 (305)
                      ++
T Consensus        79 ~P   80 (81)
T d2ghpa1          79 NP   80 (81)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>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=99.82  E-value=2.6e-20  Score=132.54  Aligned_cols=76  Identities=25%  Similarity=0.435  Sum_probs=70.5

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .+.++|||+|||+++|+++|+++|++||+|.+|+|++|+.+|+++|||||+|.+.++|++|++.|||..|.++.++
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~   80 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ   80 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3457899999999999999999999999999999999999999999999999999999999999999988877654

>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=99.82  E-value=2.7e-20  Score=132.77  Aligned_cols=82  Identities=22%  Similarity=0.342  Sum_probs=74.8

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+|||+++|+++|+++|+.||.|.+|+|+.|+ +|.++|||||+|.+.++|++||+.+  ..|+|  +.|.|+
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~G--r~i~v~   81 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDG--RWCDCK   81 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETT--EEEEEE
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCC--EEeEEE
Confidence            456889999999999999999999999999999999998 7999999999999999999999854  47888  789999


Q ss_pred             eccCCCc
Q psy4086         214 FADSGLK  220 (305)
Q Consensus       214 ~a~~~~~  220 (305)
                      ++..+..
T Consensus        82 ~a~~k~~   88 (90)
T d2cqga1          82 LPNSKQS   88 (90)
T ss_dssp             CCCTTCC
T ss_pred             eCCCCCC
Confidence            9987654

>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=99.82  E-value=1.4e-20  Score=131.53  Aligned_cols=72  Identities=29%  Similarity=0.441  Sum_probs=69.0

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .|||+|||+++|+++|+++|++||+|.+|+|++|+.+|+++|||||+|.+.++|.+|++.|||..+.++.++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~   73 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVR   73 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECE
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            599999999999999999999999999999999999999999999999999999999999999998887765

>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=99.82  E-value=2.8e-20  Score=133.78  Aligned_cols=75  Identities=24%  Similarity=0.371  Sum_probs=71.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .+++|||+|||+++|+++|+++|++||+|.+|.|++++.+++++|||||+|.+.++|+.|++.|||..|.++.++
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~   80 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIR   80 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            457899999999999999999999999999999999999999999999999999999999999999988887655

>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=99.82  E-value=2.5e-20  Score=132.92  Aligned_cols=75  Identities=21%  Similarity=0.425  Sum_probs=67.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHH---hccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA---LQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~---l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|+.||.|.+|+|++|+.+|+++|||||+|.+.++|++|++.   |+|+.|.++++.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCCccCCEEeEEEeCC
Confidence            446799999999999999999999999999999999999999999999999999999999986   456666555544

>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=1.6e-20  Score=137.98  Aligned_cols=83  Identities=25%  Similarity=0.439  Sum_probs=77.1

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||+++++++|+++|++||.|.+|+|++++ +|.++|||||+|.+.++|++|++.|||..|.|  +.|+|+++
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g--~~i~V~~a   85 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSG--RALRVDNA   85 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSS--SCBEEEET
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECC--EEEEEEEC
Confidence            3689999999999999999999999999999999988 78999999999999999999999999999999  77999999


Q ss_pred             cCCCcC
Q psy4086         216 DSGLKK  221 (305)
Q Consensus       216 ~~~~~~  221 (305)
                      .....+
T Consensus        86 ~~~~~~   91 (104)
T d1p1ta_          86 ASEKNK   91 (104)
T ss_dssp             TCTTHH
T ss_pred             CCCCCc
Confidence            875443

>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=99.82  E-value=1.3e-20  Score=134.47  Aligned_cols=75  Identities=32%  Similarity=0.508  Sum_probs=70.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      +++|||+|||+++|+++|+++|++||+|.+|+|++|+.+|+++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v   79 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV   79 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            467999999999999999999999999999999999999999999999999999999999999998888776653

>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=99.81  E-value=9.4e-20  Score=141.05  Aligned_cols=77  Identities=31%  Similarity=0.500  Sum_probs=71.0

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ....++|||+|||+++|+++|+++|++||+|.+|+|++++.+|+++|||||+|.+.++|++||+.|||..|.++.++
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~  115 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLK  115 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            33456899999999999999999999999999999999999999999999999999999999999998888776655

>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=99.81  E-value=1.7e-20  Score=132.12  Aligned_cols=79  Identities=29%  Similarity=0.434  Sum_probs=72.8

Q ss_pred             eEEecCCCCCCHHHHHHHHhhCCCeEEE-EEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         140 LYIANLPLNFKECDLESLLAKYVTVVST-RILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       140 l~V~nlp~~~te~~l~~~F~~~g~v~~v-~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      |||+|||+++|+++|+++|++||.|.++ +|++++ +|+++|||||+|.+.++|++|++.|||..+.|  ++|+|++|.+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~g--r~l~v~~a~~   78 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCN--RPITVSYAFK   78 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETT--EECEEEESCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECC--EEEEEEEecC
Confidence            7999999999999999999999999765 788887 78999999999999999999999999999999  7899999987


Q ss_pred             CCc
Q psy4086         218 GLK  220 (305)
Q Consensus       218 ~~~  220 (305)
                      +..
T Consensus        79 k~~   81 (83)
T d1x5ta1          79 KDS   81 (83)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            543

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=3e-20  Score=132.83  Aligned_cols=77  Identities=22%  Similarity=0.408  Sum_probs=71.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ  133 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~  133 (305)
                      ..++|||+|||.++|+++|+++|++||+|.+|+|++|+.+|.++|||||+|.+.++|++|++.|||..|.++.++..
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~   83 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   83 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45679999999999999999999999999999999999999999999999999999999999999988887766543

>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=99.81  E-value=8.1e-20  Score=133.60  Aligned_cols=75  Identities=31%  Similarity=0.518  Sum_probs=70.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      .++|||+|||+++++++|+++|+.||.|.+++++.++.+|+++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus        18 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V   92 (102)
T d2cpza1          18 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   92 (102)
T ss_dssp             TCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEE
Confidence            356999999999999999999999999999999999999999999999999999999999999999888876653

>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=7.2e-20  Score=131.61  Aligned_cols=83  Identities=23%  Similarity=0.532  Sum_probs=76.2

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||+++++++|+++|++||.|.+|+++.++.+ ++|||||+|.+.++|++||+.||+..|.|  +.|+|+
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g--~~l~V~   84 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEG--RKIEVN   84 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECC--EEEEEE
Confidence            345678999999999999999999999999999999998754 68999999999999999999999999999  779999


Q ss_pred             eccCCC
Q psy4086         214 FADSGL  219 (305)
Q Consensus       214 ~a~~~~  219 (305)
                      +|.++.
T Consensus        85 ~A~~r~   90 (93)
T d2cq3a1          85 NATARV   90 (93)
T ss_dssp             ECCSSC
T ss_pred             ecCcCC
Confidence            998753

>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=2.4e-20  Score=136.03  Aligned_cols=75  Identities=16%  Similarity=0.255  Sum_probs=69.6

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++|+++|+++|+.||+|.+|+|++++.+|+++|||||+|.+.++|.+|++ |||..|.++.++
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~   90 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPII   90 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEE
Confidence            345789999999999999999999999999999999999999999999999999999999995 999988887655

>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=99.81  E-value=1.8e-20  Score=133.72  Aligned_cols=82  Identities=24%  Similarity=0.411  Sum_probs=75.1

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ...+|||+|||+++++++|+++|++||.|.+++|+.++. .++|||||+|.+.++|++||+.|||..|.|  +.|+|.++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g--~~i~V~~a   83 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLND--RKVFVGRF   83 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT-BCCSCEEEEESCHHHHHHHTTSSSEEEETT--EEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC-CCcceeEEEECCHHHHHHHHHHcCCCEECC--EEEEEEEC
Confidence            346799999999999999999999999999999999874 468999999999999999999999999999  77999999


Q ss_pred             cCCCc
Q psy4086         216 DSGLK  220 (305)
Q Consensus       216 ~~~~~  220 (305)
                      .++..
T Consensus        84 ~~~~~   88 (89)
T d1cvja2          84 KSRKE   88 (89)
T ss_dssp             CCTTT
T ss_pred             CCCCC
Confidence            87654

>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=99.81  E-value=1.4e-20  Score=130.32  Aligned_cols=72  Identities=22%  Similarity=0.400  Sum_probs=66.8

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      |+|||+|||+++|+++|+++|++||+|.+++|++|+.+|++||||||+|.+.++|++|++ +|+..|.++.++
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~   72 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTID   72 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEE
Confidence            679999999999999999999999999999999999999999999999999999999997 688777776543

>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=99.81  E-value=2.4e-20  Score=131.81  Aligned_cols=72  Identities=19%  Similarity=0.391  Sum_probs=68.5

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +|||+|||+++|+++|+++|++||+|.+|+|++|+.+|+++|||||+|.+.++|++|++.|||..|.++.++
T Consensus         3 rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~   74 (85)
T d2u2fa_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL   74 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCE
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            599999999999999999999999999999999999999999999999999999999999999888877654

>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=99.81  E-value=3.5e-20  Score=131.10  Aligned_cols=77  Identities=23%  Similarity=0.442  Sum_probs=71.0

Q ss_pred             eEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CC---CcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NN---TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       140 l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g---~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      |||+|||+++|+++|+++|++||.|.+++|+.++ ++   .++|||||+|.+.++|++|++.|||..+.|  +.|+|+++
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g--~~i~V~~a   78 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDG--HKLEVRIS   78 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETT--EECEEECS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECC--EEEEEEEC
Confidence            7999999999999999999999999999999886 32   468999999999999999999999999999  77999998


Q ss_pred             cCC
Q psy4086         216 DSG  218 (305)
Q Consensus       216 ~~~  218 (305)
                      +..
T Consensus        79 ~~~   81 (85)
T d2cpfa1          79 ERA   81 (85)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            653

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=4.3e-20  Score=127.27  Aligned_cols=74  Identities=23%  Similarity=0.407  Sum_probs=69.4

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      +|||+|||++++|++|+++|++||.|.+++|+.++ +++++|||||+|.+.++|++||+ +++..|.|  +.|+|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~G--r~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNG--KVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTT--BCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECC--CEEEeeEC
Confidence            59999999999999999999999999999999998 79999999999999999999997 79999999  77998754

>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=99.81  E-value=4.2e-20  Score=130.03  Aligned_cols=75  Identities=27%  Similarity=0.385  Sum_probs=70.9

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      ..++|||+|||+++|+++|+++|++||.|.+|+|+.++ ++.++|||||+|.+.++|++|++.|||..|.|  +.|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g--r~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG--RRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETT--EEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECC--EEeEC
Confidence            35789999999999999999999999999999999998 78999999999999999999999999999999  66876

>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=5.9e-20  Score=129.39  Aligned_cols=74  Identities=26%  Similarity=0.466  Sum_probs=68.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++||+|.+++|++|+.+|+++|||||+|.+.++|++|++ +++..|.++.++
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~   78 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVE   78 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEE
Confidence            34679999999999999999999999999999999999999999999999999999999997 577777777654

>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=99.80  E-value=3.3e-20  Score=135.47  Aligned_cols=91  Identities=53%  Similarity=0.852  Sum_probs=80.2

Q ss_pred             ccceecccccCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCC
Q psy4086         125 IHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLP  204 (305)
Q Consensus       125 i~~~~~~~~~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~  204 (305)
                      +..+..+....++++|||+|||.++++++|+++|+.||.|..+.+..+.++.++|||||+|.+.++|.+||+.|||..|.
T Consensus         6 ~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~   85 (101)
T d1x5oa1           6 VQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIK   85 (101)
T ss_dssp             CCCCCCSCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCC
T ss_pred             cccchhccccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEEC
Confidence            34455556667788999999999999999999999999999999999988899999999999999999999999999999


Q ss_pred             CCCccEEEEeccC
Q psy4086         205 GSKEPLLVKFADS  217 (305)
Q Consensus       205 g~~~~l~v~~a~~  217 (305)
                      |  +++.|.++++
T Consensus        86 g--r~~~v~~~~P   96 (101)
T d1x5oa1          86 T--PPGVSAPTEP   96 (101)
T ss_dssp             C--CTTSCCCSSC
T ss_pred             C--cCCccCCCCC
Confidence            9  6677666543

>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=99.80  E-value=5e-20  Score=134.07  Aligned_cols=74  Identities=26%  Similarity=0.460  Sum_probs=69.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .++|||+|||+++|+++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|++|++.|||..|.++.++
T Consensus         8 ~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~   81 (99)
T d1whwa_           8 SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLH   81 (99)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEE
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            46799999999999999999999999999999999999999999999999999999999999998888777665

>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=99.80  E-value=8.3e-20  Score=128.62  Aligned_cols=77  Identities=21%  Similarity=0.346  Sum_probs=72.4

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||+++++++|+++|++||.|.+++|+.|+ +|.++|||||+|.+.++|++||+ +++..|.|  +.|+|+.|
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~G--r~i~V~~A   82 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDG--RVVEPKRA   82 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETT--EECEEEEC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECC--EEEEEEee
Confidence            4689999999999999999999999999999999998 79999999999999999999997 68899999  77999987


Q ss_pred             c
Q psy4086         216 D  216 (305)
Q Consensus       216 ~  216 (305)
                      .
T Consensus        83 ~   83 (84)
T d1l3ka1          83 V   83 (84)
T ss_dssp             C
T ss_pred             e
Confidence            5

>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=99.80  E-value=7.6e-20  Score=133.72  Aligned_cols=80  Identities=20%  Similarity=0.333  Sum_probs=74.6

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      ++|||+|||+++++++|+++|++||.|..+.|.+|+ ++.++|||||+|.+.++|++||+ +++..|.|  +.|.|++|.
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G--~~i~V~~a~   97 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDG--RVVEPKRAV   97 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETT--EEEEEECCS
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECC--EEEEEEECc
Confidence            689999999999999999999999999999999998 78899999999999999999996 79999999  789999998


Q ss_pred             CCCc
Q psy4086         217 SGLK  220 (305)
Q Consensus       217 ~~~~  220 (305)
                      ++..
T Consensus        98 ~ke~  101 (103)
T d1x4ba1          98 AREE  101 (103)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            7654

>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=99.80  E-value=1.9e-20  Score=136.60  Aligned_cols=79  Identities=22%  Similarity=0.407  Sum_probs=74.1

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||+++++++|+++|+.||.|.+|+|+.++ +|.++|||||+|.+.++|.+|++ |||..|.|  +.|+|+++
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G--~~l~V~~a   94 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLG--VPIIVQAS   94 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETT--EEEEEEEH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECC--EEEEEEEC
Confidence            4689999999999999999999999999999999998 79999999999999999999995 99999999  78999998


Q ss_pred             cCC
Q psy4086         216 DSG  218 (305)
Q Consensus       216 ~~~  218 (305)
                      ...
T Consensus        95 ~~~   97 (101)
T d2cq4a1          95 QAE   97 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            653

>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=99.80  E-value=4.7e-20  Score=126.16  Aligned_cols=71  Identities=65%  Similarity=1.062  Sum_probs=68.8

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        61 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      |||+|||+++|+++|+++|++||.|..+++.+++.++.++|||||+|.+.++|++|++.|||+.|.++.++
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            89999999999999999999999999999999999999999999999999999999999999999998765

>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=99.79  E-value=8.9e-20  Score=125.66  Aligned_cols=71  Identities=28%  Similarity=0.542  Sum_probs=65.9

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +|||+|||+++|+++|+++|++||+|.++.|++++.+++++|||||+|.+.++|++|++ +++..|.++.++
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~   71 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVID   71 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCE
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEE
Confidence            49999999999999999999999999999999999999999999999999999999997 687777776554

>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=3e-19  Score=130.35  Aligned_cols=77  Identities=30%  Similarity=0.445  Sum_probs=70.8

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      +.+.++|||+|||+++|+++|+++|++||+|..+.++.+. ++.++|||||+|.+.++|++|++.|||+.|.++.+..
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v   91 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   91 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCcc
Confidence            3345789999999999999999999999999999999886 7899999999999999999999999999999887654

>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=99.79  E-value=4.9e-20  Score=126.72  Aligned_cols=74  Identities=15%  Similarity=0.269  Sum_probs=68.8

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      +|||+|||+++|+++|+++|++||.|.+|+|+.++ +++++|||||+|.+.++|++||+ +++..|.|  +.|.|+.|
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-KKYHNVGL--SKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTT--BCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECC--EEeEEEEC
Confidence            59999999999999999999999999999999998 89999999999999999999997 47788999  66988875

>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=99.79  E-value=1.2e-19  Score=132.98  Aligned_cols=75  Identities=32%  Similarity=0.439  Sum_probs=66.8

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...++|||+|||+++|+++|+++|++||+|.+|+|++++.+|+++|||||+|.+.++|++|++.+|+ .|.++.++
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~   82 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKAN   82 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECE
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEE
Confidence            3457799999999999999999999999999999999999999999999999999999999998764 45555443

>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=99.79  E-value=1.3e-19  Score=125.76  Aligned_cols=71  Identities=20%  Similarity=0.338  Sum_probs=67.3

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +|||+|||+++++++|+++|++||.|.+++|+.++ +++++|||||+|.+.++|++|++.|||+.+.++.++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~   72 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMN   72 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            49999999999999999999999999999999987 799999999999999999999999999998887765

>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=99.79  E-value=4.2e-20  Score=127.06  Aligned_cols=69  Identities=20%  Similarity=0.420  Sum_probs=62.3

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccccee
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQM  129 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~  129 (305)
                      +|||+|||+++|+++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++|++. ++..|.++.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~   69 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSK   69 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEE
Confidence            499999999999999999999999999999999999999999999999999999999974 444555443

>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=99.79  E-value=1e-19  Score=127.38  Aligned_cols=74  Identities=14%  Similarity=0.206  Sum_probs=63.3

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      |+|||+|||+++|+++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++|++.|||..+.++.++.
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V   75 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVT   75 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            78999999999999999999999999999999988889999999999999999999999999999998877653

>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=99.79  E-value=1.5e-19  Score=124.57  Aligned_cols=74  Identities=19%  Similarity=0.363  Sum_probs=70.2

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      +|||+|||+++||++|+++|++||.|..+.++.++ ++.+++||||+|.+.++|++|++ |||+.|.|  ++|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~g--r~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINN--KMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTT--BCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECC--eEEEEEEC
Confidence            59999999999999999999999999999999988 78999999999999999999996 99999999  77999886

>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=99.79  E-value=1.7e-19  Score=128.90  Aligned_cols=75  Identities=32%  Similarity=0.572  Sum_probs=69.7

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +.++|||+|||+++|+++|+++|++||.|..+.++.+..++.++|||||+|.+.++|++|++.|||..|.++.++
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~   78 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIR   78 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            346699999999999999999999999999999999999999999999999999999999999999888777655

>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=99.79  E-value=8.7e-20  Score=129.19  Aligned_cols=80  Identities=21%  Similarity=0.300  Sum_probs=70.5

Q ss_pred             CCCceEEecCCCCCC-HHHHHHHHhhCCCeEEEEEeeCC--CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         136 DPTNLYIANLPLNFK-ECDLESLLAKYVTVVSTRILRDN--NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       136 ~~~~l~V~nlp~~~t-e~~l~~~F~~~g~v~~v~i~~~~--~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      +.++|||+|||++++ +++|+++|++||.|++|+|..+.  ++.++|||||+|.+.++|++|++ ||+..|.|  +.|+|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~g--r~l~V   79 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGN--REISV   79 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETT--EEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECC--EEEEE
Confidence            467999999999986 55699999999999999987753  78999999999999999999995 99999999  78999


Q ss_pred             EeccCC
Q psy4086         213 KFADSG  218 (305)
Q Consensus       213 ~~a~~~  218 (305)
                      ++++++
T Consensus        80 ~~a~~k   85 (86)
T d2ghpa3          80 SLADKK   85 (86)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            999864

>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=99.79  E-value=2.5e-19  Score=124.78  Aligned_cols=76  Identities=17%  Similarity=0.361  Sum_probs=71.2

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+|||+++|+++|+++|++||.|..+.+..++ ++.++|||||+|.+.++|++|++ +||..|+|  +.|+|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~G--r~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNG--HNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETT--EECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECC--EEEEEEEC
Confidence            3689999999999999999999999999999999998 88999999999999999999985 89999999  77999876

>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=99.79  E-value=1e-19  Score=133.66  Aligned_cols=74  Identities=24%  Similarity=0.572  Sum_probs=69.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .++|||+|||+++|+++|+++|++||+|.+|+|++++.+|+++|||||+|.+.++|++|++.|||..|.++.++
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~   81 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALR   81 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBE
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            46799999999999999999999999999999999999999999999999999999999999999988776544

>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=99.79  E-value=2.3e-19  Score=129.13  Aligned_cols=75  Identities=20%  Similarity=0.379  Sum_probs=67.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCC-CCCCccceEEEEecchhhHHHHHHHh-ccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDK-TTNKCRGYGFVDFESGGYALAAVKAL-QDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~-~~g~~~G~afV~f~~~~~A~~a~~~l-~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||.|.+|+|+++. .+|+++|||||+|.+.++|++|++.| ||..|.++.++
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~   83 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   83 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEE
Confidence            45679999999999999999999999999999999885 47999999999999999999999998 78777766554

>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=99.78  E-value=4e-19  Score=129.04  Aligned_cols=83  Identities=22%  Similarity=0.366  Sum_probs=74.9

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhC------CCCCCCCC
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFN------GSTLPGSK  207 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~------g~~~~g~~  207 (305)
                      .+.++|||+|||+++|+++|+++|++||.|.++.++.++ .+.++|||||+|.+.++|.+||+.||      |..+.|  
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g--   83 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG--   83 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS--
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC--
Confidence            346789999999999999999999999999999999988 78899999999999999999999987      456777  


Q ss_pred             ccEEEEeccCCC
Q psy4086         208 EPLLVKFADSGL  219 (305)
Q Consensus       208 ~~l~v~~a~~~~  219 (305)
                      +.|+|.++.++.
T Consensus        84 r~l~v~~a~~k~   95 (98)
T d1x4ha1          84 RQLKVDLAVTRD   95 (98)
T ss_dssp             CEEEEECCCCCC
T ss_pred             EEEEEEECCCCC
Confidence            779999998753

>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=99.78  E-value=3.5e-19  Score=128.48  Aligned_cols=80  Identities=20%  Similarity=0.366  Sum_probs=72.7

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....++|||+|||.++++++|+++|+.||.|..+.+..+.  ..++||||+|.+.++|++||+.|||+.|.+  ++|+|+
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~--~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g--~~l~V~   86 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--GGPPFAFVEFEDPRDAEDAVYGRDGYDYDG--YRLRVE   86 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSS--SSSCCEEEEESCHHHHHHHHHHHTTCEETT--EECEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccc--cccceEEEEECCHHHHHHHHHHhCCCEECC--EEEEEE
Confidence            3456789999999999999999999999999999876654  568999999999999999999999999999  779999


Q ss_pred             eccC
Q psy4086         214 FADS  217 (305)
Q Consensus       214 ~a~~  217 (305)
                      ||+.
T Consensus        87 ~a~~   90 (95)
T d1x4aa1          87 FPRS   90 (95)
T ss_dssp             CCCC
T ss_pred             eccC
Confidence            9875

>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=99.78  E-value=9e-19  Score=126.76  Aligned_cols=79  Identities=22%  Similarity=0.335  Sum_probs=72.9

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      .+.++|||+|||.++++++|+++|++||.|+.+++.++     ++||||+|.+.++|++|++.||+..|.+..++|+|+|
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            45689999999999999999999999999999999854     7799999999999999999999999998778899999


Q ss_pred             ccCC
Q psy4086         215 ADSG  218 (305)
Q Consensus       215 a~~~  218 (305)
                      ++..
T Consensus        90 ak~~   93 (97)
T d1whya_          90 AKSG   93 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9863

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=4.9e-19  Score=126.38  Aligned_cols=75  Identities=31%  Similarity=0.444  Sum_probs=67.7

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +...++|||+|||.++|+++|+++|+.||+|.+|+|++++.++  +|||||+|.+.++|++|++.|||..|.++.++
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~   79 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVK   79 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3455789999999999999999999999999999999987654  89999999999999999999999888877665

>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=99.78  E-value=4.4e-19  Score=130.25  Aligned_cols=84  Identities=23%  Similarity=0.400  Sum_probs=73.8

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC--CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN--NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLV  212 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~--~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v  212 (305)
                      .++++|||+|||+++|+++|+++|+.|| |.+++++.++  ++.++|||||+|.+.++|++|+ .||+..|.+  +.|+|
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~g--r~l~V   88 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN--KRIRV   88 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETT--EECEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECC--EEEEE
Confidence            3568999999999999999999999998 7888887765  6789999999999999998666 599999999  77999


Q ss_pred             EeccCCCcCC
Q psy4086         213 KFADSGLKKR  222 (305)
Q Consensus       213 ~~a~~~~~~~  222 (305)
                      ++|..+..+.
T Consensus        89 ~~a~~~~~~~   98 (104)
T d1wi8a_          89 DVADQAQDKD   98 (104)
T ss_dssp             EECCCCCCCC
T ss_pred             EECCCCCCCC
Confidence            9998765554

>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=99.77  E-value=1.6e-19  Score=131.94  Aligned_cols=74  Identities=28%  Similarity=0.487  Sum_probs=66.2

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|++||+|.++.|.+|+.++.++|||||+|.+.++|++|++ +++..|.++.+.
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~   92 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVE   92 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEE
Confidence            34679999999999999999999999999999999999999999999999999999999997 566666555543

>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=99.77  E-value=5.6e-19  Score=122.98  Aligned_cols=72  Identities=22%  Similarity=0.437  Sum_probs=67.6

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ++|||+|||+++|+++|+++|++||.|..++++.++.++.++|||||+|.+.++|++|++ +||+.|.++.++
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~   74 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCE   74 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEE
Confidence            579999999999999999999999999999999999999999999999999999999996 899888887665

>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=2.6e-20  Score=133.26  Aligned_cols=80  Identities=18%  Similarity=0.343  Sum_probs=74.0

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ...+|||+|||+++++++|+++|++||.|..++|+.+++|+++|||||+|.+.++|++||+ |||..|.|  +.|+|.+|
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g--~~i~V~~a   88 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFG--NEIKLEKP   88 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETT--EEEEEECC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECC--EEEEEEec
Confidence            4568999999999999999999999999999998877789999999999999999999996 99999999  77999998


Q ss_pred             cCC
Q psy4086         216 DSG  218 (305)
Q Consensus       216 ~~~  218 (305)
                      +.+
T Consensus        89 k~k   91 (91)
T d1fjeb1          89 KGR   91 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            763

>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=99.77  E-value=4.5e-19  Score=129.48  Aligned_cols=85  Identities=20%  Similarity=0.288  Sum_probs=75.6

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeE--------EEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCC
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVV--------STRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPG  205 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~--------~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  205 (305)
                      ...++|||+|||.++|+++|+++|+.||.|.        .+.+..++ ++++++||||+|.+.++|.+||+.|||..|.|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            4567999999999999999999999999874        46667776 78999999999999999999999999999999


Q ss_pred             CCccEEEEeccCCCcC
Q psy4086         206 SKEPLLVKFADSGLKK  221 (305)
Q Consensus       206 ~~~~l~v~~a~~~~~~  221 (305)
                        +.|+|++|+.+..+
T Consensus        86 --r~i~V~~a~~~~p~   99 (101)
T d2cpea1          86 --SKLKVSLARKKPPM   99 (101)
T ss_dssp             --EECEEECSSCCCCS
T ss_pred             --EEEEEEEcCCCCCC
Confidence              78999999875443

>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=1e-19  Score=133.27  Aligned_cols=85  Identities=26%  Similarity=0.379  Sum_probs=78.3

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      .+.++|||+|||.++++++|+++|+.||.|..+.+..+. +|.+++||||+|.+.++|.+|++.|||..|.|  ++|+|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g--~~l~V~   93 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYG--KILVIE   93 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSS--CBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECC--EEEEEE
Confidence            346789999999999999999999999999999888877 78999999999999999999999999999999  779999


Q ss_pred             eccCCCcC
Q psy4086         214 FADSGLKK  221 (305)
Q Consensus       214 ~a~~~~~~  221 (305)
                      ||+.+..+
T Consensus        94 ~ak~k~~r  101 (102)
T d2cpxa1          94 FGKNKKQR  101 (102)
T ss_dssp             ECCCCSCC
T ss_pred             eCCCcccC
Confidence            99886554

>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=99.77  E-value=6.3e-19  Score=127.23  Aligned_cols=76  Identities=14%  Similarity=0.374  Sum_probs=70.9

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ..++|||+|||.++++++|+++|++||.|.+|+|+.+     +|||||+|.+.++|++|++.|||..|.|  ++|+|.|+
T Consensus        17 ~~~~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          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEG--HVVKCYWG   89 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETT--EECEEECC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECC--EEEEEEEc
Confidence            4578999999999999999999999999999999965     7899999999999999999999999999  77999998


Q ss_pred             cCC
Q psy4086         216 DSG  218 (305)
Q Consensus       216 ~~~  218 (305)
                      +..
T Consensus        90 k~~   92 (96)
T d1x4ga1          90 KES   92 (96)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.77  E-value=6.2e-19  Score=124.34  Aligned_cols=79  Identities=20%  Similarity=0.341  Sum_probs=73.5

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ..++|||+|||.++|+++|+++|+.||.|..|+|..++++.++|||||+|.+.++|++||+ +++..+.|  +.|+|.++
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g--~~l~v~~~   81 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKE--TDLLILFK   81 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETT--EECEEEEG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECC--EEEEEEEc
Confidence            4578999999999999999999999999999999998899999999999999999999996 79999999  77999986


Q ss_pred             cC
Q psy4086         216 DS  217 (305)
Q Consensus       216 ~~  217 (305)
                      +.
T Consensus        82 ~d   83 (85)
T d1zh5a2          82 DD   83 (85)
T ss_dssp             GG
T ss_pred             CC
Confidence            53

>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=99.77  E-value=2.2e-19  Score=125.20  Aligned_cols=77  Identities=22%  Similarity=0.337  Sum_probs=69.5

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCC-CCCCCCccEEEEecc
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGS-TLPGSKEPLLVKFAD  216 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~-~~~g~~~~l~v~~a~  216 (305)
                      ++|||+|||.++|+++|+++|++||.|.++++..     .+|||||+|.+.++|++|++.|||. .+.|  ++|+|+|+.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~-----~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G--~~i~V~~a~   74 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLSGKVELHG--KIMEVDYSV   74 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-----ETTEEEECCSCHHHHHHHHHHHTTTCEETT--EECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec-----ccceEEEEECCHHHHHHHHHHhCCCeEECC--EEEEEEEcC
Confidence            5799999999999999999999999998877774     4789999999999999999999996 5999  789999999


Q ss_pred             CCCcC
Q psy4086         217 SGLKK  221 (305)
Q Consensus       217 ~~~~~  221 (305)
                      ++..+
T Consensus        75 ~k~~r   79 (80)
T d2cqha1          75 SKKLR   79 (80)
T ss_dssp             CCCCC
T ss_pred             CcCcC
Confidence            86544

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.9e-18  Score=123.98  Aligned_cols=76  Identities=24%  Similarity=0.403  Sum_probs=67.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ  133 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~  133 (305)
                      ...++|||+|||+++++++|+++|++||+|.+|+++.++.  .++|||||+|.+.++|++|++.|||..|.++.++..
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456799999999999999999999999999999999874  479999999999999999999999998888766533

>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=99.77  E-value=4.7e-19  Score=125.15  Aligned_cols=72  Identities=28%  Similarity=0.411  Sum_probs=66.4

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCC---CccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTN---KCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        61 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g---~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      |||+|||+++|+++|+++|++||+|.+++|++++.++   +++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V   75 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   75 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            8999999999999999999999999999999988665   57999999999999999999999999888877653

>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=99.77  E-value=9.1e-19  Score=123.76  Aligned_cols=77  Identities=30%  Similarity=0.490  Sum_probs=71.0

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ..++|||+|||.++++++|+++|++||.|.+|++..+     ++||||+|.+.++|++|++.|||..|.|  +.|+|+||
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i~g--~~l~V~~A   79 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRG--KQLRVRFA   79 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTT--BCCEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEECC--EEEEEEEC
Confidence            3467999999999999999999999999999999854     7899999999999999999999999999  77999999


Q ss_pred             cCCC
Q psy4086         216 DSGL  219 (305)
Q Consensus       216 ~~~~  219 (305)
                      ....
T Consensus        80 ~~~~   83 (86)
T d2cpja1          80 CHSA   83 (86)
T ss_dssp             SCCS
T ss_pred             CCcC
Confidence            8753

>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=1.2e-18  Score=130.00  Aligned_cols=79  Identities=18%  Similarity=0.302  Sum_probs=72.6

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ..++|||+|||.++++++|+++|++||.|.+|++..+  +.++|||||+|.+.++|..||+.|||..|.|  +.|+|.++
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~--~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~g--r~l~V~~a   81 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLSGFNVCN--RYLVVLYY   81 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTEEEEEESSHHHHHHHHHHHTTCEETT--EECEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc--CCcCCeEEEEECCHHHHHHHHHHhCCCEECC--EEEEEEEc
Confidence            4578999999999999999999999999999998765  4678999999999999999999999999999  78999998


Q ss_pred             cCC
Q psy4086         216 DSG  218 (305)
Q Consensus       216 ~~~  218 (305)
                      ...
T Consensus        82 ~~~   84 (114)
T d2f9da1          82 NAN   84 (114)
T ss_dssp             CHH
T ss_pred             CCC
Confidence            653

>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=99.76  E-value=9.4e-19  Score=126.46  Aligned_cols=82  Identities=17%  Similarity=0.274  Sum_probs=72.7

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCC-eEEEEEeeCC--CCCcccEEEEEecCHHHHHHHHHHhCCCCC--CCCCccEEE
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVT-VVSTRILRDN--NNTSKGVGFARLESKDKCDQMIQLFNGSTL--PGSKEPLLV  212 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~-v~~v~i~~~~--~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~--~g~~~~l~v  212 (305)
                      |+|||+|||.++++++|+++|+.||. |..++++.+.  .++++|||||+|.+.++|.+|++.|++..+  .+  ++|+|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g--~~i~V   79 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWG--HQIAV   79 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTT--BCCEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECC--EEEEE
Confidence            67999999999999999999999996 8999999885  578999999999999999999999976554  56  78999


Q ss_pred             EeccCCCcC
Q psy4086         213 KFADSGLKK  221 (305)
Q Consensus       213 ~~a~~~~~~  221 (305)
                      +||+++...
T Consensus        80 ~~A~p~~~~   88 (96)
T d2disa1          80 DWAEPEIDV   88 (96)
T ss_dssp             EESCSSCST
T ss_pred             EEcCCCCCC
Confidence            999875544

>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=99.76  E-value=1.8e-18  Score=121.44  Aligned_cols=78  Identities=15%  Similarity=0.344  Sum_probs=70.2

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ..+.++|||+|||.++++++|+++|++||.|.+|+++.+    .+|||||+|.+.++|.+|++.|||..|.+. ++|+|.
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 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFTTELQSNAAKEALQGFKITPT-HAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT----TCSCEEEEESSHHHHHHHHHHHTTCBSSTT-CBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc----cceeEEEecCCHHHHHHHHHHhCCcEeCCC-cEEEEE
Confidence            445678999999999999999999999999999999865    368999999999999999999999998543 679999


Q ss_pred             ecc
Q psy4086         214 FAD  216 (305)
Q Consensus       214 ~a~  216 (305)
                      ||+
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            986

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=3.4e-19  Score=125.30  Aligned_cols=72  Identities=26%  Similarity=0.438  Sum_probs=66.6

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEE-EEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          61 LYIRGLTQDTTDKDLINMCSQYGPIIST-KAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        61 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~-~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      |||+|||+++|+++|+++|++||.|.++ +|++++.+|+++|||||+|.+.++|++|++.|||..+.++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v   73 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITV   73 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEE
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEE
Confidence            8999999999999999999999998664 78999999999999999999999999999999999888877653

>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=99.76  E-value=2e-18  Score=122.63  Aligned_cols=77  Identities=21%  Similarity=0.275  Sum_probs=69.8

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCC-CCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTL-PGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~-~g~~~~l~v~~  214 (305)
                      +.++|||+|||.++++++|+++|++||.|.++.+..+   +.++||||+|.+.++|.+|+..|||..| +|  ++|+|+|
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~---~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g--~~l~v~~   83 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDLGEN--HHLRVSF   83 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS---SSTTCEEEEESSHHHHHHHHHHHTTCBSSSS--CBCEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee---cccceeEEEECCHHHHHHHHHhccCCEecCC--CEEEEEe
Confidence            4678999999999999999999999999998887765   4578999999999999999999999988 46  7799999


Q ss_pred             ccC
Q psy4086         215 ADS  217 (305)
Q Consensus       215 a~~  217 (305)
                      ++.
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            875

>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=5.7e-19  Score=131.83  Aligned_cols=102  Identities=23%  Similarity=0.263  Sum_probs=80.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccccCCC
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQDP  137 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~~~~  137 (305)
                      +++|||+|||.++|+++|+++|++||.|.+|++..+   +.++|||||+|.+.++|..|++.|||+.|.++.++......
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            478999999999999999999999999999998764   56799999999999999999999999999888776432221


Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCC
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVT  163 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~  163 (305)
                      ... .........+++++.+.+++|.
T Consensus        84 ~~~-~~~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          84 NRA-FQKMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             HHH-TTTSCHHHHHHHHHHHHHHHCC
T ss_pred             Cch-hhhhHHHHHHHHHHHHHHHhCC
Confidence            110 1122223456778888888874

>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=99.76  E-value=1.1e-18  Score=126.45  Aligned_cols=79  Identities=23%  Similarity=0.400  Sum_probs=69.7

Q ss_pred             CCCCceEEecCC-CCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLP-LNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp-~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ...++|||+||+ ..+++++|+++|++||.|++|+|.       +|||||+|.+.++|++||+.|||+.|.|  +.|+|+
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~-------rg~aFV~f~~~~~A~~Ai~~lng~~~~g--~~l~V~   83 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-------KGFAFVQYVNERNARAAVAGEDGRMIAG--QVLDIN   83 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE-------TEEEEEEESSHHHHHHHHHTTTTCEETT--EECEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe-------CCeEEEEECCHHHHHHHHHHcCCCEECC--EEEEEE
Confidence            345789999996 578889999999999999999984       7899999999999999999999999999  779999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      ++..+...+
T Consensus        84 ~a~~~~~~~   92 (98)
T d1wf2a_          84 LAAEPKVNR   92 (98)
T ss_dssp             ETTSCCCCS
T ss_pred             ECCCCCCCC
Confidence            998654433

>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=99.75  E-value=1.5e-18  Score=128.88  Aligned_cols=76  Identities=12%  Similarity=0.187  Sum_probs=70.0

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      .++|||+|||+++++++|+++|++||.|..|.|.     ..++||||+|.+.++|++||+.|||..|.+  ++|.|+|+.
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~-----~~kg~afV~f~~~~~A~~A~~~lng~~~~g--r~l~v~~a~   82 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPLEARKAFRHLAYSKFHH--VPLYLEWAP   82 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-----SSSSCEEEEESCHHHHHHHHHHHTTCBSSS--SBCEEEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEee-----ccCceEEEEEcCHHHHHHHHHHHcCCccCC--CeEEEEECC
Confidence            4689999999999999999999999999999885     457899999999999999999999999999  779999987


Q ss_pred             CCC
Q psy4086         217 SGL  219 (305)
Q Consensus       217 ~~~  219 (305)
                      ...
T Consensus        83 ~~~   85 (111)
T d1whxa_          83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            644

>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=99.75  E-value=2.2e-18  Score=125.07  Aligned_cols=66  Identities=21%  Similarity=0.379  Sum_probs=62.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhcc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQD  122 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g  122 (305)
                      +.++|||+|||+++|+++|+++|++||+|.++.++.++.++.++|||||+|.+.++|.+|++.||+
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~   72 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASL   72 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCT
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHccc
Confidence            457799999999999999999999999999999999999999999999999999999999998863

>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=99.75  E-value=7.7e-19  Score=121.01  Aligned_cols=71  Identities=31%  Similarity=0.561  Sum_probs=67.0

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++ +||+.|.++.++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~   71 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVE   71 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEE
Confidence            49999999999999999999999999999999999999999999999999999999997 999988887665

>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=99.75  E-value=6.9e-19  Score=124.75  Aligned_cols=74  Identities=12%  Similarity=0.200  Sum_probs=66.9

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      ++|||+|||+++++++|+++|++||.|.+++|..      +|||||+|.+.++|++||+.|||..|.|  +.|+|.++..
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~l~g~~~~g--~~i~v~~~~~   72 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKLDNTKFRS--HEGETAYIRV   72 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT------TSEEEEEESSHHHHHHHHHHHTTCBCCC--TTSCCCBCEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc------cceeeEEeCCHHHHHHHHHHhCCCEECC--cEeEEeEEec
Confidence            4799999999999999999999999999999864      3799999999999999999999999999  6688888765


Q ss_pred             CC
Q psy4086         218 GL  219 (305)
Q Consensus       218 ~~  219 (305)
                      ..
T Consensus        73 ~~   74 (87)
T d3begb1          73 KV   74 (87)
T ss_dssp             EE
T ss_pred             Cc
Confidence            43

>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=99.75  E-value=7e-19  Score=127.14  Aligned_cols=82  Identities=16%  Similarity=0.331  Sum_probs=72.7

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      .+.++|||+|||+++|+++|+++|+.||.|..++.    ++.+++||||+|.+.++|++|++.|||..|.|  ++|+|.|
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g--r~i~V~~   87 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG--RSVSLYY   87 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETT--EEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcCCCEECC--EEEEEEE
Confidence            34578999999999999999999999998766542    46789999999999999999999999999999  7899999


Q ss_pred             ccCCCcCC
Q psy4086         215 ADSGLKKR  222 (305)
Q Consensus       215 a~~~~~~~  222 (305)
                      +.++..++
T Consensus        88 a~~k~~~r   95 (96)
T d1fjca_          88 TGEKGGTR   95 (96)
T ss_dssp             CSSSCCCC
T ss_pred             eCCCCCCC
Confidence            99876654

>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=99.75  E-value=1.8e-18  Score=126.30  Aligned_cols=84  Identities=7%  Similarity=0.079  Sum_probs=74.8

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ....+|||+|||+++|+++|+++|+.|+ +..+.++.+.++..+|||||+|.+.++|++|++ ||+..|.+  |.|+|.+
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~g--R~I~V~~   88 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQH--RYVELFL   88 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSS--SCCEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECC--EEEEEEE
Confidence            4457899999999999999999999997 568888888888999999999999999999986 89999999  7799999


Q ss_pred             ccCCCcCC
Q psy4086         215 ADSGLKKR  222 (305)
Q Consensus       215 a~~~~~~~  222 (305)
                      +......+
T Consensus        89 s~~~~~~~   96 (102)
T d1weza_          89 NSTAGTSG   96 (102)
T ss_dssp             ECCCCCCC
T ss_pred             cCCCCCCC
Confidence            88765443

>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=99.75  E-value=3.2e-18  Score=118.95  Aligned_cols=75  Identities=16%  Similarity=0.286  Sum_probs=68.2

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...++|||+|++  +|+++|+++|++||.|.++++..     .++||||+|.+.++|.+|++.|||..+.|  +.|+|+|
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~-----~~~~afV~f~~~~~A~~Ai~~lng~~~~g--~~l~V~~   73 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP-----PRNCAFVTYEKMESADQAVAELNGTQVES--VQLKVNI   73 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCBCSS--CBCEEEE
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeecc-----CCCEEEEEEcccHHHHHHHHHhCCCEECC--EEEEEEE
Confidence            346799999986  89999999999999999999984     47899999999999999999999999999  6799999


Q ss_pred             ccCC
Q psy4086         215 ADSG  218 (305)
Q Consensus       215 a~~~  218 (305)
                      ++.+
T Consensus        74 a~~~   77 (79)
T d2bz2a1          74 ARKQ   77 (79)
T ss_dssp             CCSS
T ss_pred             ecCC
Confidence            9754

>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=99.74  E-value=8.7e-19  Score=124.70  Aligned_cols=76  Identities=14%  Similarity=0.272  Sum_probs=68.3

Q ss_pred             CCCCeEEEcCCCCCCcHHHH---HHHHhccCCeeEEEEeeCCCCCCc---cceEEEEecchhhHHHHHHHhccCccccee
Q psy4086          56 LSKTNLYIRGLTQDTTDKDL---INMCSQYGPIISTKAILDKTTNKC---RGYGFVDFESGGYALAAVKALQDKGIHAQM  129 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L---~~~f~~~G~i~~~~i~~~~~~g~~---~G~afV~f~~~~~A~~a~~~l~g~~i~~~~  129 (305)
                      ..+++|||+|||+++++++|   +++|++||+|.+|.|++++.++.+   +|||||+|.+.++|.+|++.|||..+.++.
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            34567999999999999999   778999999999999999877654   499999999999999999999999999987


Q ss_pred             cc
Q psy4086         130 AR  131 (305)
Q Consensus       130 ~~  131 (305)
                      ++
T Consensus        86 lk   87 (89)
T d2cpia1          86 LK   87 (89)
T ss_dssp             EE
T ss_pred             EE
Confidence            65

>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=99.74  E-value=2.3e-18  Score=124.71  Aligned_cols=80  Identities=10%  Similarity=0.167  Sum_probs=71.5

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ....+|||+|||+++++++|+++|++||.|++++|..      +|||||+|.+.++|++||+.|||..|.|  +.|+|.+
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~~~g--~~i~v~~   84 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKFRS--HEGETSY   84 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEEEC--TTSCEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEeCC--eEEEEEE
Confidence            3457899999999999999999999999999999863      5799999999999999999999999999  6699999


Q ss_pred             ccCCCcCC
Q psy4086         215 ADSGLKKR  222 (305)
Q Consensus       215 a~~~~~~~  222 (305)
                      ++....+.
T Consensus        85 ~~~~~~~~   92 (98)
T d1wg4a_          85 IRVYPERS   92 (98)
T ss_dssp             EEEECCCS
T ss_pred             EecCCCCC
Confidence            87655443

>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=99.74  E-value=5.5e-18  Score=125.35  Aligned_cols=76  Identities=20%  Similarity=0.335  Sum_probs=69.7

Q ss_pred             CCceEEecCCC-CCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         137 PTNLYIANLPL-NFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       137 ~~~l~V~nlp~-~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|||+||++ .+|+++|+++|++||.|++|+|++++    +|||||+|.+.++|.+|++.|||..|.|  +.|+|.|+
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   75 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHG--KPIRITLS   75 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSS--SBCEEECC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCEECC--EEEEEEEC
Confidence            46899999955 69999999999999999999999874    7899999999999999999999999999  77999998


Q ss_pred             cCC
Q psy4086         216 DSG  218 (305)
Q Consensus       216 ~~~  218 (305)
                      +..
T Consensus        76 ~~~   78 (109)
T d2adca1          76 KHQ   78 (109)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            754

>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=99.74  E-value=2.6e-18  Score=126.86  Aligned_cols=80  Identities=11%  Similarity=0.113  Sum_probs=72.3

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      ..+|||+|||+++|+++|+++|++||.|.+|.|+.+   +.+|||||+|.+.++|++|++.|||..|.+..+.|+|.|++
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~---~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~   83 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK   83 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE---TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee---CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecC
Confidence            457999999999999999999999999999999987   46899999999999999999999999996555789999987


Q ss_pred             CCC
Q psy4086         217 SGL  219 (305)
Q Consensus       217 ~~~  219 (305)
                      ...
T Consensus        84 ~~~   86 (108)
T d2adba1          84 LTS   86 (108)
T ss_dssp             SCS
T ss_pred             Ccc
Confidence            643

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=3.1e-18  Score=124.94  Aligned_cols=79  Identities=28%  Similarity=0.378  Sum_probs=70.4

Q ss_pred             CCCCCCeEEEcCCCCCCcHHHHHHHHhccCCee--------EEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcc
Q psy4086          54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPII--------STKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGI  125 (305)
Q Consensus        54 ~~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~--------~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i  125 (305)
                      ++...++|||+|||+++|+++|+++|+.||+|.        .+.+.+++.+++++|||||+|.+.++|++|++.|||..|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            344567899999999999999999999999874        577888888999999999999999999999999999988


Q ss_pred             cceeccc
Q psy4086         126 HAQMARQ  132 (305)
Q Consensus       126 ~~~~~~~  132 (305)
                      .++.++.
T Consensus        84 ~gr~i~V   90 (101)
T d2cpea1          84 QGSKLKV   90 (101)
T ss_dssp             TTEECEE
T ss_pred             CCEEEEE
Confidence            8877663

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=3.7e-18  Score=120.70  Aligned_cols=77  Identities=22%  Similarity=0.323  Sum_probs=70.0

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      .++|||+|||+++++++|+++|++||.|..+.+.     .++|||||+|.+.++|.+|+..|||..|.|  +.|+|+||+
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~-----~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g--~~i~V~~ak   80 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAFVHFSNREDAVEAMKALNGKVLDG--SPIEVTLAK   80 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE-----ECSSEEEEEESSHHHHHHHHHHHSSEEETT--EEEEEECCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc-----cccEEEEEEeCCHHHHHHHHHHcCCCEECC--EEEEEEecc
Confidence            4689999999999999999999999999888875     458899999999999999999999999999  779999998


Q ss_pred             CCCc
Q psy4086         217 SGLK  220 (305)
Q Consensus       217 ~~~~  220 (305)
                      ++.+
T Consensus        81 P~~~   84 (86)
T d2cpda1          81 PVDK   84 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.74  E-value=1.2e-18  Score=123.92  Aligned_cols=77  Identities=10%  Similarity=0.191  Sum_probs=68.8

Q ss_pred             CCCCceEEecCCCCCCHHHH---HHHHhhCCCeEEEEEeeCC-CCC---cccEEEEEecCHHHHHHHHHHhCCCCCCCCC
Q psy4086         135 QDPTNLYIANLPLNFKECDL---ESLLAKYVTVVSTRILRDN-NNT---SKGVGFARLESKDKCDQMIQLFNGSTLPGSK  207 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l---~~~F~~~g~v~~v~i~~~~-~g~---~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~  207 (305)
                      ...++|||+|||+++++++|   +++|++||.|.+|.|++++ ++.   .+|||||+|.+.++|.+|++.|||..+.|  
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~g--   83 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG--   83 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT--
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECC--
Confidence            34578999999999999999   7789999999999999987 433   45899999999999999999999999999  


Q ss_pred             ccEEEE
Q psy4086         208 EPLLVK  213 (305)
Q Consensus       208 ~~l~v~  213 (305)
                      ++|+|+
T Consensus        84 r~lkvS   89 (89)
T d2cpia1          84 RTLKAS   89 (89)
T ss_dssp             EEEEEE
T ss_pred             EEEEEC
Confidence            779885

>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=99.74  E-value=2.7e-18  Score=121.84  Aligned_cols=77  Identities=19%  Similarity=0.358  Sum_probs=67.1

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ..++|||+|||+++++++|+++|++|| +..+.+.     ..++||||+|.+.++|++||+.||++.|.|  +.|+|+|+
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~-----~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G--~~l~V~~a   75 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRG--KDLIVQLQ   75 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETT--EEEEEEEC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee-----ccCCceEEEECCHHHHHHHHHHhCCCEECC--EEEEEEEc
Confidence            357899999999999999999999999 3344443     568999999999999999999999999999  77999999


Q ss_pred             cCCCc
Q psy4086         216 DSGLK  220 (305)
Q Consensus       216 ~~~~~  220 (305)
                      ..+..
T Consensus        76 ~~~~~   80 (88)
T d1wg1a_          76 PTDAL   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

>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=99.74  E-value=9.4e-19  Score=124.32  Aligned_cols=78  Identities=10%  Similarity=0.246  Sum_probs=69.2

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ..++|||+|||+++||++|+++|++||.|.+|++..    .+++||||+|.+.++|++|+.  ++..|.|  ++|+|+++
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~----~~~gfafV~f~~~~~a~~a~~--~~~~i~g--~~l~v~~a   75 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSLCG--EDLIIKG--ISVHISNA   75 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS----SCCSCCEEECSCHHHHHHTTT--CEEEETT--EEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee----ccCceEEEEECCHHHHHHHHh--CCCEECC--EEeEEEeC
Confidence            468999999999999999999999999999998764    368899999999999999985  7888999  78999999


Q ss_pred             cCCCcC
Q psy4086         216 DSGLKK  221 (305)
Q Consensus       216 ~~~~~~  221 (305)
                      .++...
T Consensus        76 ~~k~~~   81 (88)
T d1wf0a_          76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            875544

>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=99.74  E-value=8.4e-19  Score=119.79  Aligned_cols=69  Identities=28%  Similarity=0.435  Sum_probs=65.7

Q ss_pred             eEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       140 l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      |||+|||.++|+++|+++|++||.|..+++..++ ++.++|||||+|.+.++|++|++.|||..|.|  +.|
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~G--r~~   70 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQA--QMA   70 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCE--ESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECC--EEC
Confidence            7999999999999999999999999999999988 78999999999999999999999999999999  445

>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=99.73  E-value=1.8e-18  Score=123.18  Aligned_cols=71  Identities=28%  Similarity=0.519  Sum_probs=65.4

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .+|||+|||+++|+++|+++|++||.|.+++|+.++.  .++|||||+|.+.++|++|++.|||..|.++.++
T Consensus         9 ~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~   79 (89)
T d1cvja2           9 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF   79 (89)
T ss_dssp             TEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            4699999999999999999999999999999999873  4789999999999999999999999888877655

>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=99.73  E-value=4.1e-18  Score=120.05  Aligned_cols=73  Identities=19%  Similarity=0.228  Sum_probs=66.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||.++|+++|+++|+.||+|..|+|..+. +|+++|||||+|.+.++|++|++ +++..+.++.++
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~   77 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLL   77 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECE
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEE
Confidence            45789999999999999999999999999999998886 79999999999999999999997 788888777665

>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=99.73  E-value=1.2e-18  Score=123.22  Aligned_cols=75  Identities=16%  Similarity=0.172  Sum_probs=63.7

Q ss_pred             CCCeEEEcCCCCCCc-HHHHHHHHhccCCeeEEEEeeC-CCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          57 SKTNLYIRGLTQDTT-DKDLINMCSQYGPIISTKAILD-KTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t-~~~L~~~f~~~G~i~~~~i~~~-~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      +.++|||+|||+++| +++|+++|++||+|++|+|..+ ..+++++|||||+|.+.++|++|++ |||..+.++.++.
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V   79 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISV   79 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            467899999999976 5679999999999999998765 5689999999999999999999996 9999888877653

>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=99.73  E-value=1.1e-17  Score=122.57  Aligned_cols=85  Identities=9%  Similarity=0.158  Sum_probs=73.7

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....+|||+|||+++||++|+++|..+|.|..+.++.+. ++.++|||||+|.+.++|++|++ +|+..|.+  |.|+|.
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~g--R~i~V~   89 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGH--RYIEIF   89 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSS--SCCEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcc--eEEEEE
Confidence            345679999999999999999999999998876555554 88999999999999999999996 89999999  779999


Q ss_pred             eccCCCcCC
Q psy4086         214 FADSGLKKR  222 (305)
Q Consensus       214 ~a~~~~~~~  222 (305)
                      ++...+.+.
T Consensus        90 ~~~~~~~~~   98 (104)
T d1wg5a_          90 KSSRAEVRT   98 (104)
T ss_dssp             EECTTTSCC
T ss_pred             ECCHHHhcc
Confidence            998765544

>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=2.4e-18  Score=121.69  Aligned_cols=78  Identities=13%  Similarity=0.274  Sum_probs=70.7

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEE-EEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVS-TRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~-v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...+|||+|||+++++++|+++|+.||.+.. +.+..+.++.++|+|||+|.+.++|++|++.||+..|.+  ++|+|++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~g--r~i~v~l   85 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS--RKVKLVL   85 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETT--EECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECC--EEEEEEE
Confidence            3467999999999999999999999999876 466666689999999999999999999999999999999  7799987


Q ss_pred             c
Q psy4086         215 A  215 (305)
Q Consensus       215 a  215 (305)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.72  E-value=2.1e-17  Score=118.95  Aligned_cols=75  Identities=21%  Similarity=0.267  Sum_probs=66.2

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ  133 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~  133 (305)
                      ...++|||+|||+++|+++|+++|++||.|..+.+..+   +.++|||||+|.+.++|++||+.|||..|.++.++..
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~   86 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   86 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34578999999999999999999999999999887654   4578999999999999999999999999888776643

>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=99.72  E-value=4.6e-17  Score=119.13  Aligned_cols=82  Identities=16%  Similarity=0.203  Sum_probs=71.2

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhC--CCCCCCCCccEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN--GSTLPGSKEPLL  211 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~--g~~~~g~~~~l~  211 (305)
                      ....++|||+|||..++|++|+++|++||.|+++++.+     .+++|||+|.+.++|++|++.|+  +..+.+  ++|+
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~-----~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g--~~l~   84 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP-----FKRQALVEFENIDSAKECVTFAADVPVYIAG--QQAF   84 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHHHSCCBSSS--SBCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe-----cceeEEEEeCCHHHHHHHHHHHcCCCcEEee--EEEE
Confidence            34567899999999999999999999999999999984     47899999999999999999885  456677  7799


Q ss_pred             EEeccCCCcCC
Q psy4086         212 VKFADSGLKKR  222 (305)
Q Consensus       212 v~~a~~~~~~~  222 (305)
                      |.|++.++..+
T Consensus        85 v~~s~~~~~~~   95 (104)
T d1wexa_          85 FNYSTSKRITR   95 (104)
T ss_dssp             EEECSSSSCCC
T ss_pred             EEEcCCCccCC
Confidence            99998765544

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.72  E-value=7.8e-19  Score=125.44  Aligned_cols=75  Identities=21%  Similarity=0.246  Sum_probs=67.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ  133 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~  133 (305)
                      ..++|||+|||+++|+++|+++|++||.|..++|+.+ .+|+++|||||+|.+.++|++|++ |||..|.++.++..
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~   86 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE   86 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEE
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEE
Confidence            4567999999999999999999999999999988765 489999999999999999999996 99999888876543

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.72  E-value=1.2e-17  Score=114.75  Aligned_cols=74  Identities=9%  Similarity=0.144  Sum_probs=67.5

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      ++|||+|||+++++++|+++|+.||.|..+++..++.+. ++||||+|.+.++|++|+. +|++.|+|  ++|.|+.+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~-~~~afV~F~~~~~a~~Al~-~~~~~i~g--~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAIT-KTHKVVGQ--NEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHHT-TTTCEETT--EECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHHH-hcCcEECC--EEEEEEEC
Confidence            479999999999999999999999999999999988544 5699999999999999985 89999999  77999865

>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=99.72  E-value=1.6e-17  Score=114.00  Aligned_cols=71  Identities=23%  Similarity=0.360  Sum_probs=64.3

Q ss_pred             eEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccCC
Q psy4086         140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADSG  218 (305)
Q Consensus       140 l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~~  218 (305)
                      |||+|||.++++++|+++|++|| +..+.+.     +.+|||||+|.+.++|++|++.|||..+.|  ++|+|+|+...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~-----~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g--~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD-----KYKGTAFVTLLNGEQAEAAINTFHQSRLRE--RELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE-----TTTTEEEEEESSHHHHHHHHHHHTTEESSS--CEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec-----ccceeEEEEECCHHHHHHHHHHhCCccCCC--CEEEEEEeCCC
Confidence            79999999999999999999999 5555554     568999999999999999999999999999  77999998764

>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=4.8e-18  Score=121.38  Aligned_cols=80  Identities=15%  Similarity=0.368  Sum_probs=70.9

Q ss_pred             CCCceEEecCCCCCCHHHHHH----HHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         136 DPTNLYIANLPLNFKECDLES----LLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~----~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      +.++|||+|||.++++++|++    +|++||.|.+|++..  ++.++|||||+|.+.++|.+|++.|||..+.|  +.|+
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g--~~l~   77 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYD--KPMR   77 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETT--EECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCEECC--EEEE
Confidence            457899999999999998864    689999999988754  34678999999999999999999999999999  7899


Q ss_pred             EEeccCCC
Q psy4086         212 VKFADSGL  219 (305)
Q Consensus       212 v~~a~~~~  219 (305)
                      |.||+.+.
T Consensus        78 v~~ak~~~   85 (91)
T d1nu4a_          78 IQYAKTDS   85 (91)
T ss_dssp             EEECSSCC
T ss_pred             EEEeCCCc
Confidence            99998754

>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=99.71  E-value=5.3e-18  Score=119.88  Aligned_cols=74  Identities=20%  Similarity=0.252  Sum_probs=65.8

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .++|||+|||++++++||+++|+.||.|....++.+..+++++|||||+|.+.++|++|++.||++.|.++.++
T Consensus         9 ~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~   82 (86)
T d2cqpa1           9 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   82 (86)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEE
Confidence            46799999999999999999999999987754444455899999999999999999999999999999888764

>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=99.71  E-value=1.6e-17  Score=119.66  Aligned_cols=69  Identities=22%  Similarity=0.449  Sum_probs=63.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      .++|||+|||.++++++|+++|++||+|.+|+|+++      +|||||+|.+.++|++|+..|||+.|.++.++.
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v   86 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKC   86 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            477999999999999999999999999999999865      679999999999999999999999988877653

>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=99.71  E-value=2e-17  Score=121.15  Aligned_cols=74  Identities=18%  Similarity=0.242  Sum_probs=65.9

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +..+|||+|||+++|++||+++|+.||.|..+.++.+..+++++|||||+|.++++|++|++ +|+..|.++.++
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~   87 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIE   87 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEE
Confidence            34569999999999999999999999999887777777789999999999999999999996 888888777665

>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=99.71  E-value=7.8e-18  Score=124.93  Aligned_cols=70  Identities=19%  Similarity=0.111  Sum_probs=62.9

Q ss_pred             CCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..+++|||+|||+++++++|+++|++||+|.+|.|.      +.+|||||+|.+.++|++|++.|||..|.++.+.
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~   77 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLY   77 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEE
Confidence            356789999999999999999999999999999874      3578999999999999999999999988877654

>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=1.4e-17  Score=114.32  Aligned_cols=70  Identities=17%  Similarity=0.224  Sum_probs=63.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ++|||+|||+++++++|+++|+.||+|..+++..++..  .++||||+|.++++|++|++ +|++.|.++.+.
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~--~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~   70 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEII   70 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcEECCEEEE
Confidence            57999999999999999999999999999999998753  45799999999999999996 899988887654

>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=99.70  E-value=4.9e-18  Score=124.07  Aligned_cols=74  Identities=18%  Similarity=0.357  Sum_probs=68.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +++|||+|||.++++++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++|++.|||..|.++.++
T Consensus        18 s~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~   91 (102)
T d2cpxa1          18 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILV   91 (102)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEE
Confidence            46799999999999999999999999999999999888899999999999999999999999998888776655

>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=99.70  E-value=2.7e-17  Score=120.51  Aligned_cols=72  Identities=17%  Similarity=0.373  Sum_probs=63.3

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCC-CCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDK-TTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~-~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .++|||+|||+++|+++|+++|+.|| |.+++++.+. .+++++|||||+|.+.++|++|++ ||+..|.++.++
T Consensus        15 ~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~   87 (104)
T d1wi8a_          15 PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIR   87 (104)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECE
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEE
Confidence            37899999999999999999999999 7788887765 478999999999999999987775 998888877665

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1.6e-17  Score=119.82  Aligned_cols=66  Identities=20%  Similarity=0.357  Sum_probs=60.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCC-eeEEEEeeCC-CCCCccceEEEEecchhhHHHHHHHhccC
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGP-IISTKAILDK-TTNKCRGYGFVDFESGGYALAAVKALQDK  123 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~-i~~~~i~~~~-~~g~~~G~afV~f~~~~~A~~a~~~l~g~  123 (305)
                      +|+|||+|||.++|+++|+++|++||+ |.++.|+++. .+++++|||||+|.+.++|.+|++.|++.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~   68 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPG   68 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTC
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCC
Confidence            478999999999999999999999996 9999999886 46899999999999999999999987543

>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=99.69  E-value=2.4e-17  Score=121.84  Aligned_cols=71  Identities=21%  Similarity=0.367  Sum_probs=63.3

Q ss_pred             CCeEEEcCCCC-CCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc
Q psy4086          58 KTNLYIRGLTQ-DTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ  133 (305)
Q Consensus        58 ~~~l~V~~Lp~-~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~  133 (305)
                      +++|||+||++ .+|+++|+++|+.||+|.+|+|++++     +|||||+|.+.++|++|++.|||..|.++.++..
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~   73 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT   73 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            46799999965 59999999999999999999999874     6899999999999999999999998887766533

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.69  E-value=5.4e-17  Score=113.75  Aligned_cols=64  Identities=22%  Similarity=0.312  Sum_probs=59.1

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH  126 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~  126 (305)
                      +++|||+|||.++|+++|+++|++||.|.+|++++++     +|||||+|.+.++|.+|++.|||..|.
T Consensus         8 ~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~   71 (83)
T d2b0ga1           8 NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKIT   71 (83)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSS
T ss_pred             CCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeC
Confidence            4789999999999999999999999999999997653     689999999999999999999998874

>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=99.69  E-value=2.2e-17  Score=119.44  Aligned_cols=67  Identities=24%  Similarity=0.398  Sum_probs=59.8

Q ss_pred             CCeEEEcCCC-CCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          58 KTNLYIRGLT-QDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        58 ~~~l~V~~Lp-~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      .++|||+||+ ..+++++|+++|++||+|.+|+|        ++|||||+|.+.++|++||+.|||+.|.++.++.
T Consensus        15 ~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V   82 (98)
T d1wf2a_          15 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDI   82 (98)
T ss_dssp             CCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEE
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            3569999997 56889999999999999999998        3689999999999999999999999888877653

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=6.7e-17  Score=114.59  Aligned_cols=79  Identities=18%  Similarity=0.323  Sum_probs=70.0

Q ss_pred             cCCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHh--CCCCCCCCCccEE
Q psy4086         134 EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF--NGSTLPGSKEPLL  211 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l--~g~~~~g~~~~l~  211 (305)
                      ..+.++|||+|||.++++++|+++|++||.|.++++..+     ++||||+|.+.++|++|++.+  ++..+.|  ++|+
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g--~~l~   77 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRN--QPIY   77 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETT--EECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCC--CEEE
Confidence            456788999999999999999999999999999998844     689999999999999999876  4567888  8899


Q ss_pred             EEeccCCC
Q psy4086         212 VKFADSGL  219 (305)
Q Consensus       212 v~~a~~~~  219 (305)
                      |.|++.+.
T Consensus        78 v~~sk~~~   85 (88)
T d2cq1a1          78 IQYSNHKE   85 (88)
T ss_dssp             EEECSCSS
T ss_pred             EEECCCCC
Confidence            99997654

>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=99.69  E-value=1.7e-17  Score=117.37  Aligned_cols=65  Identities=20%  Similarity=0.294  Sum_probs=59.8

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +|||+|||+++++++|+++|++||+|.+++|+++       |||||+|.+.++|++||+.|||..|.++.++
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~   66 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGE   66 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSC
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeE
Confidence            4999999999999999999999999999998653       7999999999999999999999998877654

>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=99.68  E-value=4.9e-17  Score=114.67  Aligned_cols=70  Identities=21%  Similarity=0.417  Sum_probs=63.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ..++|||+|||.++++++|+++|++||+|.+|++.++      +|||||+|.+.++|++|++.|||..|.++.++.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V   76 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRV   76 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3467999999999999999999999999999999865      569999999999999999999999988876653

>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=99.68  E-value=7.4e-17  Score=116.57  Aligned_cols=68  Identities=18%  Similarity=0.258  Sum_probs=60.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++++++|+++|++||+|++++|.+       +|||||+|.+.++|++||+.|||..+.++.++
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~   81 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGE   81 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEE
Confidence            346799999999999999999999999999999863       47999999999999999999998877766543

>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=99.68  E-value=4.8e-17  Score=118.59  Aligned_cols=72  Identities=18%  Similarity=0.279  Sum_probs=63.8

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ...+|||+|||+++|++||+++|+.|| +..+.++.+. ++.++|||||+|.+.++|++|++ +|++.|.++.++
T Consensus        14 ~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~   85 (102)
T d1weza_          14 TGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVE   85 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEE
Confidence            345799999999999999999999998 5578888887 58999999999999999999987 898888887665

>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=5.9e-18  Score=123.85  Aligned_cols=80  Identities=18%  Similarity=0.289  Sum_probs=70.9

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEE-EEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEe
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVS-TRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKF  214 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~-v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~  214 (305)
                      ...+|||+|||+++|+++|+++|..||.|.. +.+..+.+|.++|||||+|.+.++|++||+ ||+..|.|  +.|.|.+
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~g--r~i~V~~   83 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNG--REAFVHV   83 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETT--EEEEEEE
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECC--cEEEEEE
Confidence            3467999999999999999999999999876 455555689999999999999999999996 89999999  7799999


Q ss_pred             ccCC
Q psy4086         215 ADSG  218 (305)
Q Consensus       215 a~~~  218 (305)
                      +...
T Consensus        84 ~~~~   87 (103)
T d2cpya1          84 VTLE   87 (103)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            7653

>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=3e-17  Score=119.98  Aligned_cols=74  Identities=16%  Similarity=0.161  Sum_probs=65.5

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .+++|||+|||+++|+++|+++|+.||.|..+.++.+..+|+++|||||+|.+.++|++|++ ||++.|.++.+.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~   80 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAF   80 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEE
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEE
Confidence            34669999999999999999999999999876666666689999999999999999999997 899988887654

>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=99.66  E-value=1.1e-16  Score=115.91  Aligned_cols=79  Identities=16%  Similarity=0.286  Sum_probs=69.4

Q ss_pred             cCCCCceEEecCCCC-CCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHH--HhCCCCCCCCCccE
Q psy4086         134 EQDPTNLYIANLPLN-FKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ--LFNGSTLPGSKEPL  210 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~-~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~--~l~g~~~~g~~~~l  210 (305)
                      ....++|||+|||.+ +|+++|+++|+.||.|.++.+..+     ++||||+|.+.++|.+|++  .+++..|.|  ++|
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~g--r~l   87 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQG--RCV   87 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSS--SCC
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceECC--EEE
Confidence            344578999999985 899999999999999999999854     7899999999999999997  577888999  779


Q ss_pred             EEEeccCCC
Q psy4086         211 LVKFADSGL  219 (305)
Q Consensus       211 ~v~~a~~~~  219 (305)
                      +|.|++.+.
T Consensus        88 ~V~~s~~~~   96 (99)
T d1x4fa1          88 KVDLSEKYK   96 (99)
T ss_dssp             EEEEECSCS
T ss_pred             EEEEcCCcc
Confidence            999997643

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=7.5e-17  Score=118.87  Aligned_cols=65  Identities=14%  Similarity=0.149  Sum_probs=60.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH  126 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~  126 (305)
                      ..+|||+|||+++|+++|+++|++||.|.+|+|+.++    ++|||||+|.+.++|++|++.|||+.|.
T Consensus         7 ~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~   71 (108)
T d2adba1           7 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIY   71 (108)
T ss_dssp             EEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSS
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEec
Confidence            3569999999999999999999999999999999875    4799999999999999999999999874

>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=99.66  E-value=7.3e-17  Score=116.30  Aligned_cols=71  Identities=17%  Similarity=0.250  Sum_probs=63.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      ..++|||+|||+++|+++|+++|++||.|..+..     +++++|||||+|.+.++|++|++.|||..|.++.++.
T Consensus        15 ~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V   85 (96)
T d1fjca_          15 AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL   85 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEE
Confidence            4578999999999999999999999998866542     6789999999999999999999999998888877653

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.8e-16  Score=112.32  Aligned_cols=70  Identities=17%  Similarity=0.273  Sum_probs=60.9

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccc-ceecc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIH-AQMAR  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~-~~~~~  131 (305)
                      .++|||+|||+++|+++|+++|++||.|.++.++..    +++|||||+|.+.++|.+|+..|||..|. ++.++
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~   80 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLR   80 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCE
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEE
Confidence            467999999999999999999999999988887654    45789999999999999999999998873 45443

>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=99.65  E-value=1.7e-16  Score=115.77  Aligned_cols=79  Identities=13%  Similarity=0.072  Sum_probs=69.8

Q ss_pred             CCCceEEecCCCCC-CH----HHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccE
Q psy4086         136 DPTNLYIANLPLNF-KE----CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPL  210 (305)
Q Consensus       136 ~~~~l~V~nlp~~~-te----~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l  210 (305)
                      ..++|||+||+.++ ++    ++|+++|+.||.|++++++     ++++||||+|.+.++|.+|++.|||..|.|  ++|
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~-----k~~~~afV~f~~~~~A~~Ai~~lng~~~~g--~~l   76 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF-----KSFKRVRINFSNPLSAADARLRLHKTEFLG--KEM   76 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEE-----TTTTEEEEECSSTTHHHHHHHTSTTSEETT--EEC
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEe-----cCCCEEEEEECCHHHHHHHHHHhcccccCC--CEe
Confidence            46789999999986 33    5699999999999999998     457899999999999999999999999999  789


Q ss_pred             EEEeccCCCcC
Q psy4086         211 LVKFADSGLKK  221 (305)
Q Consensus       211 ~v~~a~~~~~~  221 (305)
                      +|.|++.....
T Consensus        77 ~v~~a~~~~~~   87 (104)
T d1weya_          77 KLYFAQTLHIG   87 (104)
T ss_dssp             EEECCCCSSCC
T ss_pred             EEeecccCCCC
Confidence            99999765443

>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=99.65  E-value=7.2e-17  Score=119.70  Aligned_cols=74  Identities=19%  Similarity=0.306  Sum_probs=66.0

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ..++|||+|||+++|+++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|++|++ |||..|.++.+.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~   90 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQ   90 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBE
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEE
Confidence            44679999999999999999999999998877677777789999999999999999999997 899988887653

>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=99.64  E-value=2e-16  Score=112.14  Aligned_cols=79  Identities=11%  Similarity=0.210  Sum_probs=69.2

Q ss_pred             cCCCCceEEecCCCC-CCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHh--CCCCCCCCCccE
Q psy4086         134 EQDPTNLYIANLPLN-FKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF--NGSTLPGSKEPL  210 (305)
Q Consensus       134 ~~~~~~l~V~nlp~~-~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l--~g~~~~g~~~~l  210 (305)
                      ...+++|||+|||.. +|++||+++|+.||.|.++.++.+     +++|||+|++.++|.+|++.|  ++..+.|  ++|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~g--r~l   77 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFG--KPV   77 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETT--EEC
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCC--ceE
Confidence            345788999999986 789999999999999999999855     679999999999999999976  5667888  889


Q ss_pred             EEEeccCCC
Q psy4086         211 LVKFADSGL  219 (305)
Q Consensus       211 ~v~~a~~~~  219 (305)
                      +|.|++...
T Consensus        78 ~V~~s~~~~   86 (89)
T d1x4da1          78 RVHLSQKYK   86 (89)
T ss_dssp             EEEEECCCT
T ss_pred             EEEECCCcc
Confidence            999998643

>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=99.64  E-value=7.1e-16  Score=111.22  Aligned_cols=65  Identities=20%  Similarity=0.346  Sum_probs=59.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccce
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQ  128 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~  128 (305)
                      .++|||+|||+++++++|+++|++||+|..+++.++      ++||||+|.+.++|++|++.||+..|.+.
T Consensus        17 s~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~   81 (97)
T d1whya_          17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGP   81 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSS
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCC
Confidence            467999999999999999999999999999998764      56999999999999999999999887654

>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=99.64  E-value=3.1e-16  Score=110.60  Aligned_cols=67  Identities=27%  Similarity=0.366  Sum_probs=60.2

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      ++|||+|||+++|+++|+++|++||.|..+.+.      +++|||||+|.+.++|.+|+..|||..|.++.++
T Consensus         9 k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~   75 (86)
T d2cpda1           9 KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIE   75 (86)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEE
Confidence            679999999999999999999999998877764      3578999999999999999999999888877665

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=7.2e-17  Score=114.38  Aligned_cols=66  Identities=23%  Similarity=0.363  Sum_probs=55.2

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      .++|||+|||+++|+++|+++|++||+|.+|++.     ..++|||||+|.+.++|++|+.  ++..|.++.+
T Consensus         5 s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l   70 (88)
T d1wf0a_           5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISV   70 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEe
Confidence            4679999999999999999999999999999864     3468899999999999999986  4444444433

>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=99.63  E-value=1.4e-16  Score=113.67  Aligned_cols=71  Identities=24%  Similarity=0.371  Sum_probs=62.6

Q ss_pred             CCeEEEcCCCCCCcHHHHHH----HHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          58 KTNLYIRGLTQDTTDKDLIN----MCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~----~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +++|||+|||++++++||++    +|++||+|.+|++.+   +++++|||||+|.+.++|.+|++.|||..+.++.++
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~   77 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   77 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            46799999999999999864    689999999988754   567899999999999999999999999888877655

>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=99.62  E-value=5.4e-16  Score=106.25  Aligned_cols=68  Identities=26%  Similarity=0.419  Sum_probs=58.7

Q ss_pred             EEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccccC
Q psy4086          61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQ  135 (305)
Q Consensus        61 l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~~  135 (305)
                      |||+|||+++++++|+++|++|| +..+++      ++++|||||+|.+.++|++|++.|||+.+.++.++....
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a   68 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQ   68 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEe
Confidence            79999999999999999999999 554443      456889999999999999999999999998887764433

>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=99.62  E-value=1.4e-16  Score=112.83  Aligned_cols=71  Identities=15%  Similarity=0.275  Sum_probs=60.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccccCC
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQEQD  136 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~~~~  136 (305)
                      ++|||+|||++++++||+++|++|| +..+.+      ++++|||||+|.+.++|++|++.||+..|.++.++.....
T Consensus         6 ~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           6 SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            5699999999999999999999999 333333      4568899999999999999999999999988887754443

>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=99.62  E-value=6.5e-16  Score=107.02  Aligned_cols=68  Identities=25%  Similarity=0.271  Sum_probs=60.3

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      +.++|||+||+  +|+++|+++|++||+|.+|++.++      +|||||+|.+.++|.+|++.|||..|.++.++.
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V   71 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKV   71 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEE
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEE
Confidence            45679999996  999999999999999999998754      569999999999999999999999888776653

>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=99.62  E-value=4.9e-17  Score=118.71  Aligned_cols=75  Identities=12%  Similarity=0.222  Sum_probs=70.7

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .++|.++..+++|++|+++|++||.|++|+|.++.++.++|||||+|.+.++|.+|++.|||++++|  ++|+|+|.
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~g--r~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNG--QPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETT--EECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECC--EEEEEEEC
Confidence            5778888889999999999999999999999988889999999999999999999999999999999  78999985

>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=99.61  E-value=1.4e-16  Score=118.12  Aligned_cols=80  Identities=13%  Similarity=0.178  Sum_probs=70.0

Q ss_pred             CCCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEE-eeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEE
Q psy4086         135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRI-LRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVK  213 (305)
Q Consensus       135 ~~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i-~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~  213 (305)
                      ....+|||+|||+++|+++|+++|+.||.+..+.+ ..+.+|.++|||||+|.+.++|++|++ ||+..|.+  +.|.|.
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~g--R~i~V~   92 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGN--RFIQVH   92 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTT--SCBEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCC--EEEEEE
Confidence            34568999999999999999999999999876544 445589999999999999999999996 89999999  779998


Q ss_pred             eccC
Q psy4086         214 FADS  217 (305)
Q Consensus       214 ~a~~  217 (305)
                      .+..
T Consensus        93 ~~~~   96 (112)
T d1wela1          93 PITK   96 (112)
T ss_dssp             EECH
T ss_pred             EcCh
Confidence            8764

>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=99.60  E-value=1.3e-17  Score=118.94  Aligned_cols=76  Identities=20%  Similarity=0.375  Sum_probs=65.1

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEee-----C-CCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEE
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILR-----D-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLL  211 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~-----~-~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~  211 (305)
                      ++|||+|||+++||++|+++|+.||.|..+.+..     + ..+.++|||||+|.+.++|++|++ |||..+.|  +.|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~G--r~l~   78 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQG--QSLK   78 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSS--SCCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECC--EEEE
Confidence            5799999999999999999999999887665432     2 256789999999999999999985 99999999  6799


Q ss_pred             EEecc
Q psy4086         212 VKFAD  216 (305)
Q Consensus       212 v~~a~  216 (305)
                      |+.++
T Consensus        79 V~r~k   83 (90)
T d1u2fa_          79 IRRPH   83 (90)
T ss_dssp             CBCTT
T ss_pred             ECCCC
Confidence            97544

>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=99.60  E-value=2.4e-17  Score=117.45  Aligned_cols=74  Identities=14%  Similarity=0.233  Sum_probs=64.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEe-----eCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecccc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAI-----LDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQQ  133 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~-----~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~~  133 (305)
                      ++|||+|||+++||++|+++|++||.|..+.+.     .+..+++++|||||+|.+.++|++|++ |||..+.++.++..
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            579999999999999999999999987766553     344578899999999999999999996 99999988877643

>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=99.59  E-value=6.2e-16  Score=107.38  Aligned_cols=67  Identities=27%  Similarity=0.514  Sum_probs=59.2

Q ss_pred             eEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccC-cccceeccc
Q psy4086          60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDK-GIHAQMARQ  132 (305)
Q Consensus        60 ~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~-~i~~~~~~~  132 (305)
                      +|||+|||+++|+++|+++|++||.|..+++.+      .+|||||+|.+.++|++|++.|||. .+.++.++.
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V   70 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   70 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEE
Confidence            499999999999999999999999988777665      4689999999999999999999986 577776653

>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=99.56  E-value=4.6e-15  Score=107.19  Aligned_cols=71  Identities=15%  Similarity=0.242  Sum_probs=58.7

Q ss_pred             CCCCCeEEEcCCCCC-CcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHH--hccCcccceecc
Q psy4086          55 QLSKTNLYIRGLTQD-TTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA--LQDKGIHAQMAR  131 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~-~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~--l~g~~i~~~~~~  131 (305)
                      ....++|||+|||.+ +|+++|+++|+.||.|.++.++++      +|||||+|.+.++|.+|++.  +++..+.++.++
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~   88 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   88 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEE
Confidence            345678999999985 899999999999999999999864      46999999999999999984  555555554443

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=3.6e-15  Score=108.08  Aligned_cols=79  Identities=22%  Similarity=0.279  Sum_probs=65.0

Q ss_pred             cCCCCceEEec--CCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCC-CC--CCc
Q psy4086         134 EQDPTNLYIAN--LPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTL-PG--SKE  208 (305)
Q Consensus       134 ~~~~~~l~V~n--lp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~-~g--~~~  208 (305)
                      ..+.++|||.|  |+.++|+++|+++|++||.|+++++..+     ++||||+|.+.++|.+|++.|||+.| ++  .+.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i~~~~~~~i   89 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCCCCCCCcEE
Confidence            34567889955  9999999999999999999999998854     67999999999999999999999987 33  223


Q ss_pred             cEEEEeccC
Q psy4086         209 PLLVKFADS  217 (305)
Q Consensus       209 ~l~v~~a~~  217 (305)
                      ++.+.|.+.
T Consensus        90 ~~~~~~~~~   98 (101)
T d2cq2a1          90 TLYLNFVEK   98 (101)
T ss_dssp             ECEEEEESC
T ss_pred             EEEEEeeee
Confidence            455566543

>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=99.56  E-value=8.7e-15  Score=103.44  Aligned_cols=69  Identities=16%  Similarity=0.274  Sum_probs=58.4

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhc--cCcccceecc
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ--DKGIHAQMAR  131 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~--g~~i~~~~~~  131 (305)
                      .+++|||+|||+++++++|+++|++||.|.++++.++      ++||||+|.+.++|++|++.++  +..+.++.++
T Consensus         7 Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           7 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            4578999999999999999999999999999998754      4699999999999999998754  4455555443

>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=99.55  E-value=1.8e-14  Score=105.10  Aligned_cols=59  Identities=22%  Similarity=0.327  Sum_probs=53.7

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhcc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQD  122 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g  122 (305)
                      .++|||+|||.++||++|+++|++||.|+++.+.++      ||+|||+|.+.++|++|++.|++
T Consensus        15 s~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~   73 (104)
T d1wexa_          15 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAAD   73 (104)
T ss_dssp             CSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcC
Confidence            467999999999999999999999999999998754      57999999999999999998753

>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=99.53  E-value=1.2e-14  Score=116.88  Aligned_cols=75  Identities=23%  Similarity=0.440  Sum_probs=66.6

Q ss_pred             CCCCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        55 ~~~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      ....++|||+|||+.+|+++|+++|+.||.|..+.|+.+..+++++|||||+|.+.++|++|++ +++..|.++.+
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i  168 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNC  168 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEE
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEE
Confidence            3345679999999999999999999999999999999999999999999999999999999997 56666655443

>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=99.53  E-value=4.8e-16  Score=113.31  Aligned_cols=72  Identities=15%  Similarity=0.189  Sum_probs=67.0

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      +.++|.++..+++|++|+++|++||+|.+|+|+++. +++++|||||+|.+.++|.+|++.|||+.+.++.++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~   99 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEE
Confidence            458899999999999999999999999999998775 799999999999999999999999999999998765

>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=99.51  E-value=1.9e-14  Score=101.77  Aligned_cols=70  Identities=14%  Similarity=0.189  Sum_probs=58.7

Q ss_pred             CCCCeEEEcCCCCC-CcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHh--ccCcccceecc
Q psy4086          56 LSKTNLYIRGLTQD-TTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL--QDKGIHAQMAR  131 (305)
Q Consensus        56 ~~~~~l~V~~Lp~~-~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l--~g~~i~~~~~~  131 (305)
                      ..+++|||+|||.. +|++||.++|+.||.|.+|.++.++      ++|||+|.+.++|..|++.|  ++..+.++.++
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            34577999999986 8999999999999999999998764      48999999999999999976  44455555544

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=2.3e-14  Score=106.06  Aligned_cols=73  Identities=12%  Similarity=0.059  Sum_probs=62.9

Q ss_pred             ceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCH-HHHHHHHHHhCCCCCCCCCccEEEEecc
Q psy4086         139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESK-DKCDQMIQLFNGSTLPGSKEPLLVKFAD  216 (305)
Q Consensus       139 ~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~-~~A~~Ai~~l~g~~~~g~~~~l~v~~a~  216 (305)
                      .+||||||..+|+++|+++|++||.|.+|.|+.     .++||||+|.+. ++|.+|+..||+..+.++...+.+.+..
T Consensus        13 ~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~-----~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~~   86 (113)
T d1owxa_          13 LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR-----GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLE   86 (113)
T ss_dssp             EEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT-----TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEECC
T ss_pred             EEEECCCCCCCCHHHHHHHHHhcCChheEEEec-----CCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeecc
Confidence            469999999999999999999999999999984     478999999985 7899999999999998865455555433

>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=99.50  E-value=1.5e-14  Score=104.66  Aligned_cols=64  Identities=16%  Similarity=0.259  Sum_probs=56.7

Q ss_pred             CCeEEE--cCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          58 KTNLYI--RGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        58 ~~~l~V--~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      .++|||  ||||+++|+++|+++|++||.|++|.++.+      ++||||+|.+.++|++|++.|||+.|..
T Consensus        18 t~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~~   83 (101)
T d2cq2a1          18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVD   83 (101)
T ss_dssp             CSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             CceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCCC
Confidence            356888  559999999999999999999999988754      4699999999999999999999998743

>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=99.47  E-value=1.9e-14  Score=104.71  Aligned_cols=69  Identities=10%  Similarity=0.035  Sum_probs=60.0

Q ss_pred             CCeEEEcCCCCCC-cH----HHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceeccc
Q psy4086          58 KTNLYIRGLTQDT-TD----KDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMARQ  132 (305)
Q Consensus        58 ~~~l~V~~Lp~~~-t~----~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~~  132 (305)
                      .++|||+||+.++ ++    ++|+++|+.||+|.++++++      +++||||+|.+.++|.+|++.|||+.|.++.++.
T Consensus         5 ~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v   78 (104)
T d1weya_           5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEE
Confidence            3669999999986 33    56899999999999999974      4669999999999999999999999988877763

>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=99.47  E-value=3.9e-14  Score=104.77  Aligned_cols=65  Identities=18%  Similarity=0.170  Sum_probs=57.7

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecch-hhHHHHHHHhccCccccee
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESG-GYALAAVKALQDKGIHAQM  129 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~-~~A~~a~~~l~g~~i~~~~  129 (305)
                      ..+||||||+++|+++|+++|++||+|.+|.|+++      +|||||+|.+. ++|..|+..+|+..+.++.
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~   77 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRN   77 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTS
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCc
Confidence            34699999999999999999999999999999854      67999999996 7899999999998877654

>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=99.46  E-value=6.6e-14  Score=100.92  Aligned_cols=80  Identities=19%  Similarity=0.322  Sum_probs=68.7

Q ss_pred             CCCCceEEecC--CCCCC---------HHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCC
Q psy4086         135 QDPTNLYIANL--PLNFK---------ECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTL  203 (305)
Q Consensus       135 ~~~~~l~V~nl--p~~~t---------e~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~  203 (305)
                      ...++|+|.||  |.++.         +++|++.|++||.|..|.+..+   ..+|+|||+|.+.++|.+|+..|||..+
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            44678999999  54432         3689999999999999998876   5689999999999999999999999999


Q ss_pred             CCCCccEEEEeccCCC
Q psy4086         204 PGSKEPLLVKFADSGL  219 (305)
Q Consensus       204 ~g~~~~l~v~~a~~~~  219 (305)
                      +|  ++|+|.|++++.
T Consensus        83 ~g--r~i~v~~~~g~~   96 (99)
T d2dita1          83 GG--RQITAQAWDGTT   96 (99)
T ss_dssp             TT--EECEEEECCSCC
T ss_pred             CC--EEEEEEEeCCcC
Confidence            99  889999987643

>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=99.44  E-value=1e-13  Score=95.86  Aligned_cols=75  Identities=17%  Similarity=0.113  Sum_probs=62.6

Q ss_pred             CCCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       136 ~~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      +.+.|+|+++|++.+++.| ++|++||+|.++++.     +.++||||+|.+.++|++||+ +||..|+|+ ..|.|+.+
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-KDGRIFGES-IMIGVKPC   74 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC-----SSSSEEEEEESSHHHHHHHHT-TTTCEETTT-EECEEEEC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec-----CCCCEEEEEEcccHHHHHHHh-cCCCeECCc-EEEEEEeC
Confidence            3467999999999987655 579999999999876     457899999999999999995 999999994 24568877


Q ss_pred             cCC
Q psy4086         216 DSG  218 (305)
Q Consensus       216 ~~~  218 (305)
                      .++
T Consensus        75 ~~k   77 (81)
T d1wwha1          75 IDK   77 (81)
T ss_dssp             CCH
T ss_pred             CCh
Confidence            654

>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=99.41  E-value=1.6e-13  Score=94.85  Aligned_cols=65  Identities=17%  Similarity=0.180  Sum_probs=56.1

Q ss_pred             CCCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCccccee
Q psy4086          57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQM  129 (305)
Q Consensus        57 ~~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~  129 (305)
                      +.+.|+|++||++++++.| ++|++||+|.++++.      +.+|||||+|.++++|++|++ +||+.|.++.
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~   67 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESI   67 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTE
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcE
Confidence            4678999999999997655 579999999999864      456899999999999999996 9999887764

>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=99.38  E-value=4e-13  Score=97.64  Aligned_cols=80  Identities=23%  Similarity=0.308  Sum_probs=68.1

Q ss_pred             CCCceEEecC--CCCCC--------HHHHHHHHhhCCCeEEEEEeeCCC---CCcccEEEEEecCHHHHHHHHHHhCCCC
Q psy4086         136 DPTNLYIANL--PLNFK--------ECDLESLLAKYVTVVSTRILRDNN---NTSKGVGFARLESKDKCDQMIQLFNGST  202 (305)
Q Consensus       136 ~~~~l~V~nl--p~~~t--------e~~l~~~F~~~g~v~~v~i~~~~~---g~~~g~afV~f~~~~~A~~Ai~~l~g~~  202 (305)
                      +++.|.|.||  +..+.        .++|++.|++||.|++|.|.++..   ....|++||+|.+.++|.+|+..|||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4677899999  55443        357999999999999999988763   2456899999999999999999999999


Q ss_pred             CCCCCccEEEEeccC
Q psy4086         203 LPGSKEPLLVKFADS  217 (305)
Q Consensus       203 ~~g~~~~l~v~~a~~  217 (305)
                      ++|  |+|.+.|++.
T Consensus        83 f~g--R~v~v~f~~~   95 (104)
T d1o0pa_          83 FAN--RVVVTKYCDP   95 (104)
T ss_dssp             SSS--SCCEEEEECH
T ss_pred             ECC--eEEEEEEcCH
Confidence            999  7799999864

>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=99.31  E-value=2e-12  Score=92.99  Aligned_cols=78  Identities=19%  Similarity=0.205  Sum_probs=64.1

Q ss_pred             CCCCeEEEcCC--CCCCc---------HHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCc
Q psy4086          56 LSKTNLYIRGL--TQDTT---------DKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKG  124 (305)
Q Consensus        56 ~~~~~l~V~~L--p~~~t---------~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~  124 (305)
                      ...++|+|.||  |.++.         ++||++.|++||.|..|++..+    ..+|+|||+|.+.++|.+|+..|||+.
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            34577999999  55432         3678999999999999998755    357999999999999999999999999


Q ss_pred             ccceecccccCCC
Q psy4086         125 IHAQMARQQEQDP  137 (305)
Q Consensus       125 i~~~~~~~~~~~~  137 (305)
                      +.++.++..-.++
T Consensus        82 ~~gr~i~v~~~~g   94 (99)
T d2dita1          82 FGGRQITAQAWDG   94 (99)
T ss_dssp             ETTEECEEEECCS
T ss_pred             ECCEEEEEEEeCC
Confidence            9999887554433

>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=8.3e-12  Score=90.51  Aligned_cols=74  Identities=19%  Similarity=0.218  Sum_probs=62.0

Q ss_pred             CCeEEEcCC--CCCC--------cHHHHHHHHhccCCeeEEEEeeCCCCC--CccceEEEEecchhhHHHHHHHhccCcc
Q psy4086          58 KTNLYIRGL--TQDT--------TDKDLINMCSQYGPIISTKAILDKTTN--KCRGYGFVDFESGGYALAAVKALQDKGI  125 (305)
Q Consensus        58 ~~~l~V~~L--p~~~--------t~~~L~~~f~~~G~i~~~~i~~~~~~g--~~~G~afV~f~~~~~A~~a~~~l~g~~i  125 (305)
                      ++.|.|.||  +.++        ..+||++.|++||.|++|+|.++..+.  ...|++||+|.+.++|.+|++.|||+.+
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            466999999  5443        235789999999999999998876543  4568999999999999999999999999


Q ss_pred             cceecc
Q psy4086         126 HAQMAR  131 (305)
Q Consensus       126 ~~~~~~  131 (305)
                      .++.+.
T Consensus        84 ~gR~v~   89 (104)
T d1o0pa_          84 ANRVVV   89 (104)
T ss_dssp             SSSCCE
T ss_pred             CCeEEE
Confidence            988764

>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=97.88  E-value=3.2e-05  Score=52.82  Aligned_cols=69  Identities=10%  Similarity=0.050  Sum_probs=58.1

Q ss_pred             CeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCC--ccceEEEEecchhhHHHHHHHhccCcccc
Q psy4086          59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNK--CRGYGFVDFESGGYALAAVKALQDKGIHA  127 (305)
Q Consensus        59 ~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~--~~G~afV~f~~~~~A~~a~~~l~g~~i~~  127 (305)
                      |+|.|+.||+++||+++.+.+...|++........+.+-+  .-.-|+|.|.+.+++....+.++|+.+..
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            5799999999999999999999999998888777664432  22459999999999999999999987654

>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=97.68  E-value=0.00012  Score=49.86  Aligned_cols=80  Identities=14%  Similarity=0.220  Sum_probs=63.4

Q ss_pred             CceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCC-CC-C-cccEEEEEecCHHHHHHHHHHhCCCCCCCC---CccEE
Q psy4086         138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NN-T-SKGVGFARLESKDKCDQMIQLFNGSTLPGS---KEPLL  211 (305)
Q Consensus       138 ~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~-~g-~-~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~---~~~l~  211 (305)
                      ++|.|++||+.+||+++.+.+...+++........+ +. . .-.-|+|.|.+.++...-.+.++|+.+.+.   ..+-.
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            578999999999999999999999998888777765 22 1 224599999999999999999999987442   23456


Q ss_pred             EEeccC
Q psy4086         212 VKFADS  217 (305)
Q Consensus       212 v~~a~~  217 (305)
                      |+||--
T Consensus        82 VE~AP~   87 (91)
T d1uw4a_          82 VEFAPF   87 (91)
T ss_dssp             EEECSS
T ss_pred             EEEcCc
Confidence            777654

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.58  E-value=0.00018  Score=45.87  Aligned_cols=62  Identities=13%  Similarity=0.138  Sum_probs=53.6

Q ss_pred             HHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEeccC
Q psy4086         152 CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS  217 (305)
Q Consensus       152 ~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a~~  217 (305)
                      +.|.+.|.+++.|.++.|....++..  .|-|...+..+|.-|+..|+-..|+.  +.|.|.++..
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~--KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGS--KKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETT--EEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCC--eEEEEEEecC
Confidence            45677889999999999987766554  59999999999999999999999999  7799999753

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.15  E-value=0.00032  Score=47.00  Aligned_cols=54  Identities=17%  Similarity=0.264  Sum_probs=47.6

Q ss_pred             HHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhCCCCCCCCCccEEEEec
Q psy4086         152 CDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA  215 (305)
Q Consensus       152 ~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~v~~a  215 (305)
                      .+|.+.|..||+|.-+++..+       -..|+|.+-+.|.+|+. |+|.++.|  +.|+|...
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d-------~mwVTF~dG~SAL~al~-l~g~~v~G--~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLD-VDGMKVKG--RAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHH-GGGSEETT--EEEEEECC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC-------eEEEEECCcHHHHHHhc-cCCeEEcc--eEEEEecC
Confidence            478889999999999999866       58999999999999996 89999999  77888763

>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=96.71  E-value=0.001  Score=44.46  Aligned_cols=50  Identities=16%  Similarity=0.345  Sum_probs=42.9

Q ss_pred             HHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceecc
Q psy4086          73 KDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMAR  131 (305)
Q Consensus        73 ~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~~  131 (305)
                      .+|.+.|..||+|.-++++.+.        ..|+|.+-+.|.+|++ ++|.++.++.++
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d~--------mwVTF~dG~SAL~al~-l~g~~v~G~~l~   88 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVKGRAVK   88 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEETTEEEE
T ss_pred             HHHHHHHhhCCeEEEEEEeCCe--------EEEEECCcHHHHHHhc-cCCeEEcceEEE
Confidence            3577788999999999988764        7999999999999998 899988887664

>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=96.55  E-value=0.0079  Score=40.77  Aligned_cols=56  Identities=20%  Similarity=0.250  Sum_probs=46.4

Q ss_pred             CCeEEEcCCCCCCcHHHHHHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhc
Q psy4086          58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ  121 (305)
Q Consensus        58 ~~~l~V~~Lp~~~t~~~L~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~  121 (305)
                      +..||.-..|......||.++|+.||.|. |..+-|-       .|||...+.++|..++..++
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            34599999999999999999999999875 4444443       69999999999999887654

>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=96.34  E-value=0.0083  Score=37.96  Aligned_cols=59  Identities=19%  Similarity=0.157  Sum_probs=46.0

Q ss_pred             CCcHHHH----HHHHhccCCeeEEEEeeCCCCCCccceEEEEecchhhHHHHHHHhccCcccceec
Q psy4086          69 DTTDKDL----INMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHAQMA  130 (305)
Q Consensus        69 ~~t~~~L----~~~f~~~G~i~~~~i~~~~~~g~~~G~afV~f~~~~~A~~a~~~l~g~~i~~~~~  130 (305)
                      .+.+++|    .+.|.+++.|..+.|.... .+.  -.|-|...+.++|..|+..|+.++|..+.+
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~-dg~--~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI   65 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHT-DYQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKI   65 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCC-STT--CCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEecc-CCc--EEEEEEcCCHHHHHHHHHHHHHHhcCCeEE
Confidence            4455554    5678999999999987543 233  369999999999999999999888876654

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.51  E-value=0.075  Score=35.81  Aligned_cols=56  Identities=14%  Similarity=0.297  Sum_probs=46.0

Q ss_pred             CCceEEecCCCCCCHHHHHHHHhhCCCeEEEEEeeCCCCCcccEEEEEecCHHHHHHHHHHhC
Q psy4086         137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN  199 (305)
Q Consensus       137 ~~~l~V~nlp~~~te~~l~~~F~~~g~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~  199 (305)
                      ...+|.-..|..+...||.++|+.||.|.- ..+.|.      -|||...+.++|..++..++
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~V-swIddT------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQI-SWIDDT------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCCC-EEEETT------EEEEECSCHHHHHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceEE-EEecCc------eEEEEecCHHHHHHHHHHhc
Confidence            456888899999999999999999997753 334332      69999999999999987655